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j땀Ebxxvqm%kX+p1`a3;z¶͚&Κj u?&r~\ctJ=@I`[xOnܼ/a,g _2r _ٌ&ZU0^ ߲*:YGٞ+Ū͛7dfPޔnN}/- 'kwR2d5[)aNC'I?$I ?t:N/-IeI?tҟ.NC'SIeI?t:NC't:o 7OO+@Qփ%Ω^CK1Z4E%>ִ/$&.q%~ҧGh'h9-q%ST'Q~a!zf3)~D P[(?R_J)K*1Su|(ӗ>IaaS$K-w˟8ڹ9x)  ,1CxŔSOI7z&/1K/q}K0\8p[/P3RDJ_9K0/Qej0|E~zQp@5S(Cm\%~鄪/PPCmo[j?P8CYъx/6(Ȋx/PéSۉ@ad++xe +_SX!G;r̊xT?:OM+үPӡ~/\vփe$jz/QA-'<+Ǐڊp+K-' ?T ƣ~"Z)TŰzS٢gЙ?E3_Q_|! |Cg(Cg|Q t :E|Ag3_3_Й/t拚"t :$|AgL3_Й/tt6U7\ 0 q#.ͯ<g8"ƒ#ͬ)~`_XX[h,-WPwPw0c>^>BHE1*XNE!h"~w 6C}o +?uuuE|Ñ^pVKKBdB# iA?ePD_̈́+x]vc⮲9Fj75'3Ai4v L#9liMZg>3uD{r̼""AMMl7Q:\o9& EP}4PhB"ߴP,o[VjMR5((7>klr7OP^VXSZ8uVÁb(YB>Malb_b}pHj_siVt[:Yƙ8~@^ /~ Aoe-D;iU=V(rD1~13q- :ρ x Vsʫ jsJl2EjB [{ y6O(r0;zyh]-EƘqX[Xi$-H>n>1ywkܺ{pnlOA%Dևcg[—i?>t*g c"K٨u~ o١_uڽ}ƕɼ葐8,ySY],luNʛ1sZLs*U\TiKIS b2ftCUT]oy}[PzjhÙ+c9@Z0 gӿ@qkb%]c:oI]]iu8U>$0W;TU%([  \y~_&vQ K_j7>Ubccu|?O2G~EÞ SWI󜂕?Wc.ScUs}C-GAڸBޱ _RWIQPyۦ _%$LdaRs$2"Ѯ`ȫ|.Dd/~,I'W}eMVFM}G}Y6+hRkw[Pْ>nAPáwԊ˴!TÉ]evAyD^K{!diP@t[i8DwY6iM+{ms\0nvV$yFw.XS< 9ubNONb.ia;OC1,!ZrX;:cG9ɫ*l_b,iWlN˸V~KGae#JDp2E>,93pr+W}eMVqu3svmr-3)+-t g |#9zQxg!sIXۈ|I}Zgm.\|Wa:Gbeb(W#2*i)_ٳ2oy%$&p+҈.ɝ;:)EM]!ۯ7U"mdm@{*nٴkfV^|z]B (HP~κoR37tn,. ͻ8_֥xUI`Dž;v*QK~a5 1zwHLr0>˥O~"мt`X"dE@ENǡ{ngn!PRՈ}~0 Ӿ'IB,P;l 6?EVZ LmÊUo&)a! ^R];wIȬː3ڶ#!_U'p,vQ;YWvT ^dIÉ+g!Z?vjAY{l Ϟ mS)Q*+gr$ WRrk*DnuBE?x嗴b O^ˉhW };%fso96?lsqô5}؅ZpZ@Td䖖Ш^H-⾾$]} >)"Z[1P5'J(R1Ƈy2rK۝W';proEGdta=>i)ZyY TU!뮱(we^%)ON{zdVbyF7Oo<פՠev3 ^P't7b UXSԈ$my>%2f_4L1bJmD(m+_Mdt]9^Ql !RHҾҬ4!VHFػj!Z68Fޥzzzn>`.?svEF-flԱ Ԉ AmetaMix/inst/extdata/dat1/blastOut2.tab0000644000176200001440000005157213403500106017467 0ustar liggesusersNODE_1597_length_349_cov_49.601719 gi|38018023|ref|NP_937947.1| 99.25 133 1 0 399 1 4175 4307 4e-83 274 NODE_1597_length_349_cov_49.601719 gi|253756606|ref|YP_003038519.1| 98.50 133 2 0 399 1 4175 4307 1e-82 272 NODE_1597_length_349_cov_49.601719 gi|253756607|ref|YP_003038518.1| 98.50 133 2 0 399 1 4175 4307 2e-82 272 NODE_1597_length_349_cov_49.601719 gi|253756581|ref|YP_003038496.1| 97.74 133 3 0 399 1 4175 4307 3e-82 271 NODE_1597_length_349_cov_49.601719 gi|15081555|ref|NP_150074.1| 97.74 133 3 0 399 1 4175 4307 3e-82 271 NODE_1597_length_349_cov_49.601719 gi|253756594|ref|YP_003038508.1| 97.74 133 3 0 399 1 4175 4307 3e-82 271 NODE_1597_length_349_cov_49.601719 gi|253756595|ref|YP_003038507.1| 97.74 133 3 0 399 1 4175 4307 4e-82 271 NODE_1597_length_349_cov_49.601719 gi|253756582|ref|YP_003038495.1| 97.74 133 3 0 399 1 4175 4307 4e-82 271 NODE_1597_length_349_cov_49.601719 gi|26008080|ref|NP_150073.2| 97.74 133 3 0 399 1 4175 4307 4e-82 271 NODE_1597_length_349_cov_49.601719 gi|167600355|ref|YP_001671997.1| 96.99 133 4 0 399 1 4221 4353 6e-82 270 NODE_1607_length_290_cov_156.668961 gi|38018025|ref|NP_937949.1| 94.69 113 5 1 338 3 99 211 7e-68 217 NODE_1607_length_290_cov_156.668961 gi|253756597|ref|YP_003038510.1| 90.27 113 10 1 338 3 99 211 2e-63 205 NODE_1607_length_290_cov_156.668961 gi|253756584|ref|YP_003038498.1| 89.38 113 11 1 338 3 99 211 7e-63 204 NODE_1607_length_290_cov_156.668961 gi|253756609|ref|YP_003038521.1| 89.38 113 11 1 338 3 99 211 1e-62 203 NODE_1607_length_290_cov_156.668961 gi|15081546|ref|NP_150076.1| 89.38 113 11 1 338 3 99 211 1e-62 203 NODE_1607_length_290_cov_156.668961 gi|394935453|ref|YP_005454244.1| 87.61 113 13 1 338 3 99 211 7e-61 199 NODE_1607_length_290_cov_156.668961 gi|85718617|ref|YP_459951.1| 83.19 113 18 1 338 3 99 211 4e-58 192 NODE_1607_length_290_cov_156.668961 gi|167600357|ref|YP_001671999.1| 58.41 113 46 1 338 3 98 210 1e-36 134 NODE_1607_length_290_cov_156.668961 gi|60115394|ref|YP_209232.1| 56.76 111 47 1 338 9 104 214 4e-36 133 NODE_1607_length_290_cov_156.668961 gi|253750534|ref|YP_003029847.1| 56.76 111 47 1 338 9 104 214 2e-34 129 NODE_1713_length_191_cov_280.675385 gi|38018026|ref|NP_937950.1| 95.00 80 4 0 1 240 159 238 4e-47 167 NODE_1713_length_191_cov_280.675385 gi|253756610|ref|YP_003038522.1| 88.75 80 9 0 1 240 153 232 5e-43 155 NODE_1713_length_191_cov_280.675385 gi|253756598|ref|YP_003038511.1| 87.50 80 10 0 1 240 153 232 3e-42 153 NODE_1713_length_191_cov_280.675385 gi|15081547|ref|NP_150077.1| 86.25 80 11 0 1 240 153 232 1e-41 151 NODE_1713_length_191_cov_280.675385 gi|253756585|ref|YP_003038499.1| 86.25 80 11 0 1 240 153 232 2e-41 150 NODE_1713_length_191_cov_280.675385 gi|394935454|ref|YP_005454245.1| 85.00 80 12 0 1 240 152 231 1e-40 148 NODE_1713_length_191_cov_280.675385 gi|85718618|ref|YP_459952.1| 83.75 80 13 0 1 240 153 232 3e-40 147 NODE_1713_length_191_cov_280.675385 gi|167600358|ref|YP_001672000.1| 65.00 80 28 0 1 240 153 232 5e-33 126 NODE_1713_length_191_cov_280.675385 gi|56807326|ref|YP_173238.1| 57.50 80 33 1 1 240 144 222 2e-24 102 NODE_1713_length_191_cov_280.675385 gi|253750535|ref|YP_003029848.1| 49.38 81 40 1 1 240 146 226 1e-20 90.9 NODE_1715_length_142_cov_213.845078 gi|38018026|ref|NP_937950.1| 92.06 63 5 0 191 3 244 306 2e-32 124 NODE_1715_length_142_cov_213.845078 gi|253756598|ref|YP_003038511.1| 80.95 63 8 1 191 3 238 296 1e-26 107 NODE_1715_length_142_cov_213.845078 gi|15081547|ref|NP_150077.1| 80.95 63 8 1 191 3 238 296 1e-26 107 NODE_1715_length_142_cov_213.845078 gi|253756585|ref|YP_003038499.1| 80.95 63 8 1 191 3 238 296 1e-26 107 NODE_1715_length_142_cov_213.845078 gi|253756610|ref|YP_003038522.1| 79.37 63 9 1 191 3 238 296 4e-26 106 NODE_1715_length_142_cov_213.845078 gi|394935454|ref|YP_005454245.1| 80.95 63 8 1 191 3 237 295 4e-26 106 NODE_1715_length_142_cov_213.845078 gi|167600358|ref|YP_001672000.1| 69.84 63 15 1 191 3 238 296 4e-23 97.8 NODE_1715_length_142_cov_213.845078 gi|85718618|ref|YP_459952.1| 69.84 63 15 1 191 3 238 296 2e-22 95.5 NODE_1715_length_142_cov_213.845078 gi|56807326|ref|YP_173238.1| 63.08 65 22 1 191 3 228 292 1e-18 84.7 NODE_1715_length_142_cov_213.845078 gi|9629814|ref|NP_045300.1| 52.38 63 30 0 191 3 232 294 5e-15 73.9 NODE_1766_length_314_cov_463.656036 gi|394935454|ref|YP_005454245.1| 96.67 120 4 0 3 362 908 1027 3e-71 237 NODE_1766_length_314_cov_463.656036 gi|85718618|ref|YP_459952.1| 95.00 120 6 0 3 362 895 1014 2e-70 234 NODE_1766_length_314_cov_463.656036 gi|38018026|ref|NP_937950.1| 97.50 120 3 0 3 362 907 1026 5e-70 234 NODE_1766_length_314_cov_463.656036 gi|253756598|ref|YP_003038511.1| 94.17 120 7 0 3 362 909 1028 9e-69 230 NODE_1766_length_314_cov_463.656036 gi|15081547|ref|NP_150077.1| 94.17 120 7 0 3 362 909 1028 9e-69 230 NODE_1766_length_314_cov_463.656036 gi|253756585|ref|YP_003038499.1| 94.17 120 7 0 3 362 909 1028 1e-68 230 NODE_1766_length_314_cov_463.656036 gi|253756610|ref|YP_003038522.1| 92.50 120 9 0 3 362 909 1028 5e-68 228 NODE_1766_length_314_cov_463.656036 gi|167600358|ref|YP_001672000.1| 90.68 118 11 0 9 362 911 1028 1e-66 224 NODE_1766_length_314_cov_463.656036 gi|56807326|ref|YP_173238.1| 81.51 119 22 0 6 362 901 1019 7e-60 205 NODE_1766_length_314_cov_463.656036 gi|9629814|ref|NP_045300.1| 81.90 116 21 0 15 362 869 984 6e-59 202 NODE_2060_length_233_cov_764.030029 gi|38018026|ref|NP_937950.1| 95.70 93 4 0 3 281 1178 1270 1e-54 189 NODE_2060_length_233_cov_764.030029 gi|394935454|ref|YP_005454245.1| 92.47 93 7 0 3 281 1179 1271 2e-52 182 NODE_2060_length_233_cov_764.030029 gi|253756610|ref|YP_003038522.1| 92.47 93 7 0 3 281 1180 1272 6e-52 181 NODE_2060_length_233_cov_764.030029 gi|253756598|ref|YP_003038511.1| 91.40 93 8 0 3 281 1180 1272 2e-51 180 NODE_2060_length_233_cov_764.030029 gi|253756585|ref|YP_003038499.1| 91.30 92 8 0 6 281 1181 1272 1e-50 177 NODE_2060_length_233_cov_764.030029 gi|15081547|ref|NP_150077.1| 91.40 93 8 0 3 281 1180 1272 1e-50 177 NODE_2060_length_233_cov_764.030029 gi|167600358|ref|YP_001672000.1| 89.25 93 10 0 3 281 1180 1272 3e-50 176 NODE_2060_length_233_cov_764.030029 gi|85718618|ref|YP_459952.1| 84.95 93 14 0 3 281 1166 1258 3e-48 171 NODE_2060_length_233_cov_764.030029 gi|9629814|ref|NP_045300.1| 71.58 95 25 1 3 281 1136 1230 8e-40 146 NODE_2060_length_233_cov_764.030029 gi|60115395|ref|YP_209233.1| 71.58 95 25 1 3 281 1188 1282 2e-39 145 NODE_2345_length_1115_cov_56.699551 gi|26008090|ref|NP_742138.1| 98.97 388 4 0 2 1165 433 820 0.0 803 NODE_2345_length_1115_cov_56.699551 gi|85719076|ref|YP_459941.1| 94.59 388 21 0 2 1165 433 820 0.0 769 NODE_2345_length_1115_cov_56.699551 gi|25121569|ref|NP_740616.1| 93.56 388 25 0 2 1165 433 820 0.0 769 NODE_2345_length_1115_cov_56.699551 gi|60145599|ref|NP_001012452.1| 92.53 388 29 0 2 1165 433 820 0.0 762 NODE_2345_length_1115_cov_56.699551 gi|38018023|ref|NP_937947.1| 100.00 388 0 0 2 1165 4802 5189 0.0 815 NODE_2345_length_1115_cov_56.699551 gi|253756595|ref|YP_003038507.1| 98.97 388 4 0 2 1165 4802 5189 0.0 806 NODE_2345_length_1115_cov_56.699551 gi|26008080|ref|NP_150073.2| 98.97 388 4 0 2 1165 4802 5189 0.0 806 NODE_2345_length_1115_cov_56.699551 gi|253756582|ref|YP_003038495.1| 98.97 388 4 0 2 1165 4802 5189 0.0 806 NODE_2345_length_1115_cov_56.699551 gi|253756607|ref|YP_003038518.1| 98.97 388 4 0 2 1165 4802 5189 0.0 806 NODE_2345_length_1115_cov_56.699551 gi|167600354|ref|YP_001671996.1| 98.97 388 4 0 2 1165 4848 5235 0.0 806 NODE_2652_length_118_cov_2.500000 gi|314953946|ref|YP_004063986.1| 40.91 44 25 1 134 3 903 945 7.9 28.9 NODE_2652_length_118_cov_2.500000 gi|9632197|ref|NP_048906.1| 38.71 31 18 1 7 96 81 111 9.8 27.7 NODE_2838_length_139_cov_133.841721 gi|38018025|ref|NP_937949.1| 96.77 62 2 0 187 2 38 99 5e-35 127 NODE_2838_length_139_cov_133.841721 gi|253756609|ref|YP_003038521.1| 93.55 62 4 0 187 2 38 99 1e-33 124 NODE_2838_length_139_cov_133.841721 gi|85718617|ref|YP_459951.1| 93.55 62 4 0 187 2 38 99 1e-33 124 NODE_2838_length_139_cov_133.841721 gi|394935453|ref|YP_005454244.1| 91.94 62 5 0 187 2 38 99 3e-33 123 NODE_2838_length_139_cov_133.841721 gi|253756597|ref|YP_003038510.1| 90.32 62 6 0 187 2 38 99 5e-32 119 NODE_2838_length_139_cov_133.841721 gi|15081546|ref|NP_150076.1| 90.32 62 6 0 187 2 38 99 5e-32 119 NODE_2838_length_139_cov_133.841721 gi|253756584|ref|YP_003038498.1| 88.71 62 7 0 187 2 38 99 8e-32 119 NODE_2838_length_139_cov_133.841721 gi|167600357|ref|YP_001671999.1| 88.71 62 7 0 187 2 37 98 5e-31 117 NODE_2838_length_139_cov_133.841721 gi|56807325|ref|YP_173237.1| 69.35 62 19 0 187 2 32 93 1e-22 93.2 NODE_2838_length_139_cov_133.841721 gi|60115394|ref|YP_209232.1| 64.52 62 22 0 187 2 43 104 5e-21 89.4 NODE_2854_length_149_cov_752.966431 gi|167600358|ref|YP_001672000.1| 96.97 66 2 0 2 199 1274 1339 1e-37 139 NODE_2854_length_149_cov_752.966431 gi|253756598|ref|YP_003038511.1| 96.97 66 2 0 2 199 1274 1339 2e-37 139 NODE_2854_length_149_cov_752.966431 gi|15081547|ref|NP_150077.1| 96.97 66 2 0 2 199 1274 1339 2e-37 138 NODE_2854_length_149_cov_752.966431 gi|253756585|ref|YP_003038499.1| 96.97 66 2 0 2 199 1274 1339 2e-37 138 NODE_2854_length_149_cov_752.966431 gi|394935454|ref|YP_005454245.1| 96.97 66 2 0 2 199 1273 1338 2e-37 138 NODE_2854_length_149_cov_752.966431 gi|85718618|ref|YP_459952.1| 96.97 66 2 0 2 199 1260 1325 3e-37 138 NODE_2854_length_149_cov_752.966431 gi|38018026|ref|NP_937950.1| 98.48 66 1 0 2 199 1272 1337 3e-37 138 NODE_2854_length_149_cov_752.966431 gi|56807326|ref|YP_173238.1| 76.56 64 15 0 8 199 1269 1332 9e-29 114 NODE_2854_length_149_cov_752.966431 gi|253756610|ref|YP_003038522.1| 94.55 55 3 0 2 166 1274 1328 1e-27 110 NODE_2854_length_149_cov_752.966431 gi|9629814|ref|NP_045300.1| 83.02 53 9 0 8 166 1234 1286 8e-24 99.8 NODE_2962_length_126_cov_1.563492 gi|116686122|ref|NP_036442.3| 87.93 58 7 0 1 174 42 99 2e-30 118 NODE_2962_length_126_cov_1.563492 gi|162287089|ref|NP_032472.2| 87.93 58 7 0 1 174 42 99 3e-30 117 NODE_2962_length_126_cov_1.563492 gi|150010604|ref|NP_001092763.1| 86.21 58 8 0 1 174 42 99 4e-29 114 NODE_2962_length_126_cov_1.563492 gi|355390331|ref|NP_001239032.1| 65.52 58 20 0 1 174 41 98 2e-20 89.7 NODE_2962_length_126_cov_1.563492 gi|355390328|ref|NP_001239031.1| 65.52 58 20 0 1 174 41 98 2e-20 89.7 NODE_2962_length_126_cov_1.563492 gi|86990454|ref|NP_001034561.1| 65.52 58 20 0 1 174 41 98 2e-20 89.7 NODE_2962_length_126_cov_1.563492 gi|83716024|ref|NP_060066.2| 65.52 58 20 0 1 174 41 98 2e-20 89.7 NODE_2962_length_126_cov_1.563492 gi|355390323|ref|NP_001239029.1| 65.52 58 20 0 1 174 41 98 2e-20 89.7 NODE_2962_length_126_cov_1.563492 gi|157823795|ref|NP_001102512.1| 61.40 57 22 0 4 174 43 99 7e-19 85.1 NODE_2962_length_126_cov_1.563492 gi|157823695|ref|NP_057914.2| 61.40 57 22 0 4 174 43 99 7e-19 85.1 NODE_2981_length_212_cov_275.750000 gi|38018026|ref|NP_937950.1| 96.55 87 3 0 2 262 392 478 5e-51 178 NODE_2981_length_212_cov_275.750000 gi|15081547|ref|NP_150077.1| 96.55 87 3 0 2 262 382 468 6e-51 178 NODE_2981_length_212_cov_275.750000 gi|253756585|ref|YP_003038499.1| 96.55 87 3 0 2 262 382 468 7e-51 178 NODE_2981_length_212_cov_275.750000 gi|253756610|ref|YP_003038522.1| 95.40 87 4 0 2 262 382 468 3e-50 176 NODE_2981_length_212_cov_275.750000 gi|253756598|ref|YP_003038511.1| 94.25 87 5 0 2 262 382 468 9e-50 174 NODE_2981_length_212_cov_275.750000 gi|394935454|ref|YP_005454245.1| 93.10 87 6 0 2 262 381 467 2e-49 174 NODE_2981_length_212_cov_275.750000 gi|167600358|ref|YP_001672000.1| 78.16 87 18 1 2 262 382 467 9e-40 146 NODE_2981_length_212_cov_275.750000 gi|85718618|ref|YP_459952.1| 76.71 73 17 0 2 220 382 454 3e-33 127 NODE_2981_length_212_cov_275.750000 gi|60115395|ref|YP_209233.1| 60.76 79 31 0 2 238 380 458 1e-29 117 NODE_2981_length_212_cov_275.750000 gi|56807326|ref|YP_173238.1| 67.12 73 24 0 2 220 378 450 1e-28 114 NODE_3045_length_866_cov_8.483833 gi|34538598|ref|NP_904328.1| 69.07 291 90 0 914 42 26 316 5e-92 283 NODE_3045_length_866_cov_8.483833 gi|251831107|ref|YP_003024026.1| 67.01 291 96 0 914 42 26 316 5e-83 260 NODE_3045_length_866_cov_8.483833 gi|494060707|ref|WP_007002790.1| 44.13 281 150 2 914 93 39 319 3e-52 181 NODE_3045_length_866_cov_8.483833 gi|496406861|ref|WP_009115725.1| 40.61 293 157 4 914 84 44 335 5e-42 155 NODE_3045_length_866_cov_8.483833 gi|496410681|ref|WP_009119545.1| 40.61 293 157 4 914 84 43 334 5e-42 154 NODE_3045_length_866_cov_8.483833 gi|489880086|ref|WP_003783554.1| 41.46 287 152 3 914 102 52 338 1e-41 154 NODE_3045_length_866_cov_8.483833 gi|489884532|ref|WP_003787982.1| 40.96 293 156 4 914 84 52 343 2e-41 153 NODE_3045_length_866_cov_8.483833 gi|491919997|ref|WP_005672482.1| 41.61 298 153 4 914 84 48 345 3e-41 153 NODE_3045_length_866_cov_8.483833 gi|489919582|ref|WP_003822943.1| 41.46 287 152 3 914 102 51 337 4e-41 152 NODE_3045_length_866_cov_8.483833 gi|488718793|ref|WP_002642669.1| 40.20 296 143 4 914 102 52 338 5e-40 149 NODE_3126_length_177_cov_47.276836 gi|26008095|ref|NP_742170.1| 98.67 75 1 0 2 226 247 321 5e-24 99.0 NODE_3126_length_177_cov_47.276836 gi|253756606|ref|YP_003038519.1| 100.00 75 0 0 2 226 2997 3071 2e-23 99.4 NODE_3126_length_177_cov_47.276836 gi|38018023|ref|NP_937947.1| 100.00 75 0 0 2 226 2997 3071 2e-23 99.4 NODE_3126_length_177_cov_47.276836 gi|253756607|ref|YP_003038518.1| 100.00 75 0 0 2 226 2997 3071 3e-23 99.0 NODE_3126_length_177_cov_47.276836 gi|15081555|ref|NP_150074.1| 98.67 75 1 0 2 226 2997 3071 3e-23 99.0 NODE_3126_length_177_cov_47.276836 gi|253756594|ref|YP_003038508.1| 98.67 75 1 0 2 226 2997 3071 3e-23 99.0 NODE_3126_length_177_cov_47.276836 gi|253756581|ref|YP_003038496.1| 98.67 75 1 0 2 226 2997 3071 3e-23 99.0 NODE_3126_length_177_cov_47.276836 gi|253756595|ref|YP_003038507.1| 98.67 75 1 0 2 226 2997 3071 4e-23 98.6 NODE_3126_length_177_cov_47.276836 gi|253756582|ref|YP_003038495.1| 98.67 75 1 0 2 226 2997 3071 4e-23 98.6 NODE_3126_length_177_cov_47.276836 gi|26008080|ref|NP_150073.2| 98.67 75 1 0 2 226 2997 3071 4e-23 98.6 NODE_3187_length_311_cov_218.842438 gi|38018026|ref|NP_937950.1| 87.07 116 13 1 351 4 1 114 1e-56 196 NODE_3187_length_311_cov_218.842438 gi|253756598|ref|YP_003038511.1| 87.93 116 10 1 351 4 1 112 6e-56 194 NODE_3187_length_311_cov_218.842438 gi|15081547|ref|NP_150077.1| 87.93 116 10 1 351 4 1 112 7e-56 194 NODE_3187_length_311_cov_218.842438 gi|253756585|ref|YP_003038499.1| 87.93 116 10 1 351 4 1 112 9e-56 193 NODE_3187_length_311_cov_218.842438 gi|394935454|ref|YP_005454245.1| 86.21 116 12 1 351 4 1 112 5e-55 191 NODE_3187_length_311_cov_218.842438 gi|253756610|ref|YP_003038522.1| 86.21 116 12 1 351 4 1 112 2e-54 189 NODE_3187_length_311_cov_218.842438 gi|85718618|ref|YP_459952.1| 76.07 117 24 1 351 1 1 113 3e-50 177 NODE_3187_length_311_cov_218.842438 gi|167600358|ref|YP_001672000.1| 70.69 116 30 1 351 4 1 112 3e-45 163 NODE_3187_length_311_cov_218.842438 gi|60115395|ref|YP_209233.1| 57.39 115 46 1 351 7 1 112 7e-35 134 NODE_3187_length_311_cov_218.842438 gi|56807326|ref|YP_173238.1| 56.41 117 46 2 351 1 1 112 2e-34 132 NODE_3192_length_109_cov_357.678894 gi|38018023|ref|NP_937947.1| 98.08 52 1 0 2 157 1462 1513 1e-26 107 NODE_3192_length_109_cov_357.678894 gi|253756607|ref|YP_003038518.1| 96.15 52 2 0 2 157 1462 1513 9e-26 105 NODE_3192_length_109_cov_357.678894 gi|253756582|ref|YP_003038495.1| 96.15 52 2 0 2 157 1462 1513 9e-26 105 NODE_3192_length_109_cov_357.678894 gi|26008080|ref|NP_150073.2| 96.15 52 2 0 2 157 1462 1513 9e-26 105 NODE_3192_length_109_cov_357.678894 gi|253756595|ref|YP_003038507.1| 96.15 52 2 0 2 157 1462 1513 9e-26 105 NODE_3192_length_109_cov_357.678894 gi|253756606|ref|YP_003038519.1| 96.15 52 2 0 2 157 1462 1513 1e-25 104 NODE_3192_length_109_cov_357.678894 gi|253756581|ref|YP_003038496.1| 96.15 52 2 0 2 157 1462 1513 1e-25 104 NODE_3192_length_109_cov_357.678894 gi|15081555|ref|NP_150074.1| 96.15 52 2 0 2 157 1462 1513 1e-25 104 NODE_3192_length_109_cov_357.678894 gi|253756594|ref|YP_003038508.1| 96.15 52 2 0 2 157 1462 1513 1e-25 104 NODE_3192_length_109_cov_357.678894 gi|26008083|ref|NP_742169.1| 96.15 52 2 0 2 157 611 662 6e-25 102 NODE_3220_length_578_cov_94.439445 gi|26008094|ref|NP_742142.1| 98.97 195 2 0 1 585 105 299 4e-139 399 NODE_3220_length_578_cov_94.439445 gi|38018023|ref|NP_937947.1| 100.00 195 0 0 1 585 6901 7095 2e-128 408 NODE_3220_length_578_cov_94.439445 gi|253756595|ref|YP_003038507.1| 98.97 195 2 0 1 585 6900 7094 1e-126 403 NODE_3220_length_578_cov_94.439445 gi|253756582|ref|YP_003038495.1| 98.97 195 2 0 1 585 6900 7094 1e-126 403 NODE_3220_length_578_cov_94.439445 gi|26008080|ref|NP_150073.2| 98.97 195 2 0 1 585 6900 7094 1e-126 403 NODE_3220_length_578_cov_94.439445 gi|85718615|ref|YP_459949.1| 98.46 195 3 0 1 585 6901 7095 4e-125 398 NODE_3220_length_578_cov_94.439445 gi|253756607|ref|YP_003038518.1| 97.95 195 4 0 1 585 6900 7094 1e-124 397 NODE_3220_length_578_cov_94.439445 gi|394935459|ref|YP_005454239.1| 97.44 195 5 0 1 585 6957 7151 1e-124 397 NODE_3220_length_578_cov_94.439445 gi|167600354|ref|YP_001671996.1| 96.41 195 7 0 1 585 6934 7128 2e-122 390 NODE_3220_length_578_cov_94.439445 gi|25121573|ref|NP_740620.1| 85.05 194 29 0 1 582 105 298 1e-121 354 NODE_3221_length_169_cov_100.307693 gi|38018024|ref|NP_937948.1| 98.48 66 1 0 20 217 1 66 1e-39 138 NODE_3221_length_169_cov_100.307693 gi|253756596|ref|YP_003038509.1| 95.45 66 3 0 20 217 1 66 5e-39 136 NODE_3221_length_169_cov_100.307693 gi|253756583|ref|YP_003038497.1| 95.45 66 3 0 20 217 1 66 5e-39 136 NODE_3221_length_169_cov_100.307693 gi|15081545|ref|NP_150075.1| 95.45 66 3 0 20 217 1 66 5e-39 136 NODE_3221_length_169_cov_100.307693 gi|253756608|ref|YP_003038520.1| 92.42 66 5 0 20 217 1 66 1e-37 132 NODE_3221_length_169_cov_100.307693 gi|85718616|ref|YP_459950.1| 89.39 66 7 0 20 217 1 66 3e-35 124 NODE_3221_length_169_cov_100.307693 gi|167600356|ref|YP_001671998.1| 64.62 65 23 0 20 214 1 65 6e-25 99.4 NODE_3221_length_169_cov_100.307693 gi|11192310|ref|NP_068669.1| 58.73 63 26 0 26 214 13 75 4e-21 88.6 NODE_3221_length_169_cov_100.307693 gi|253750533|ref|YP_003029846.1| 56.72 67 29 0 14 214 1 67 5e-21 88.6 NODE_3221_length_169_cov_100.307693 gi|394935449|ref|YP_005454240.1| 88.37 43 5 0 20 148 1 43 2e-20 82.4 NODE_3229_length_202_cov_723.222778 gi|85718618|ref|YP_459952.1| 98.80 83 1 0 251 3 1062 1144 6e-48 169 NODE_3229_length_202_cov_723.222778 gi|38018026|ref|NP_937950.1| 100.00 83 0 0 251 3 1074 1156 6e-48 169 NODE_3229_length_202_cov_723.222778 gi|253756585|ref|YP_003038499.1| 98.80 83 1 0 251 3 1076 1158 1e-47 169 NODE_3229_length_202_cov_723.222778 gi|15081547|ref|NP_150077.1| 98.80 83 1 0 251 3 1076 1158 1e-47 168 NODE_3229_length_202_cov_723.222778 gi|253756610|ref|YP_003038522.1| 98.80 83 1 0 251 3 1076 1158 2e-47 168 NODE_3229_length_202_cov_723.222778 gi|253756598|ref|YP_003038511.1| 98.80 83 1 0 251 3 1076 1158 2e-47 168 NODE_3229_length_202_cov_723.222778 gi|394935454|ref|YP_005454245.1| 98.80 83 1 0 251 3 1075 1157 3e-47 167 NODE_3229_length_202_cov_723.222778 gi|167600358|ref|YP_001672000.1| 92.77 83 6 0 251 3 1076 1158 6e-45 160 NODE_3229_length_202_cov_723.222778 gi|253750535|ref|YP_003029848.1| 89.16 83 9 0 251 3 1068 1150 2e-43 156 NODE_3229_length_202_cov_723.222778 gi|60115395|ref|YP_209233.1| 86.75 83 11 0 251 3 1084 1166 4e-43 155 NODE_3236_length_163_cov_391.503082 gi|38018026|ref|NP_937950.1| 90.41 73 4 2 213 1 494 565 1e-34 130 NODE_3236_length_163_cov_391.503082 gi|253756610|ref|YP_003038522.1| 74.70 83 8 3 210 1 485 567 7e-30 117 NODE_3236_length_163_cov_391.503082 gi|253756585|ref|YP_003038499.1| 73.49 83 9 3 210 1 485 567 3e-29 115 NODE_3236_length_163_cov_391.503082 gi|15081547|ref|NP_150077.1| 73.49 83 9 3 210 1 485 567 3e-29 115 NODE_3236_length_163_cov_391.503082 gi|253756598|ref|YP_003038511.1| 74.70 83 8 3 210 1 485 567 4e-29 115 NODE_3236_length_163_cov_391.503082 gi|394935454|ref|YP_005454245.1| 68.29 82 13 3 207 1 485 566 1e-25 105 NODE_3236_length_163_cov_391.503082 gi|167600358|ref|YP_001672000.1| 50.60 83 27 3 207 1 485 567 5e-15 74.3 NODE_3236_length_163_cov_391.503082 gi|56807326|ref|YP_173238.1| 42.17 83 30 3 207 1 473 551 1e-07 53.1 NODE_3236_length_163_cov_391.503082 gi|85718618|ref|YP_459952.1| 35.80 81 33 4 207 1 480 553 8e-05 44.7 NODE_3236_length_163_cov_391.503082 gi|253750535|ref|YP_003029848.1| 33.73 83 37 4 210 1 477 554 4e-04 42.4 NODE_3407_length_174_cov_2.557471 gi|489240182|ref|WP_003148409.1| 40.48 42 18 1 219 115 30 71 5.7 29.6 NODE_3407_length_174_cov_2.557471 gi|495171955|ref|WP_007896750.1| 40.54 37 22 0 83 193 349 385 7.4 29.3 NODE_3407_length_174_cov_2.557471 gi|269797424|ref|YP_003311324.1| 30.77 52 33 1 64 210 217 268 7.4 29.3 NODE_3407_length_174_cov_2.557471 gi|491530222|ref|WP_005387845.1| 30.77 52 33 1 64 210 217 268 9.5 28.9 NODE_3501_length_336_cov_52.416668 gi|26008090|ref|NP_742138.1| 98.44 128 2 0 386 3 77 204 1e-82 267 NODE_3501_length_336_cov_52.416668 gi|38018023|ref|NP_937947.1| 100.00 128 0 0 386 3 4446 4573 4e-82 271 NODE_3501_length_336_cov_52.416668 gi|167600354|ref|YP_001671996.1| 99.22 128 1 0 386 3 4492 4619 1e-81 269 NODE_3501_length_336_cov_52.416668 gi|253756607|ref|YP_003038518.1| 98.44 128 2 0 386 3 4446 4573 2e-81 268 metaMix/inst/extdata/dat1/read_lengths.tab0000644000176200001440000001652513403500106020246 0ustar liggesusersNODE_1597_length_349_cov_49.601719 399 NODE_1607_length_290_cov_156.668961 340 NODE_1713_length_191_cov_280.675385 241 NODE_1715_length_142_cov_213.845078 192 NODE_1766_length_314_cov_463.656036 364 NODE_2060_length_233_cov_764.030029 283 NODE_2345_length_1115_cov_56.699551 1165 NODE_2652_length_118_cov_2.500000 168 NODE_2838_length_139_cov_133.841721 189 NODE_2854_length_149_cov_752.966431 199 NODE_2962_length_126_cov_1.563492 176 NODE_2981_length_212_cov_275.750000 262 NODE_3045_length_866_cov_8.483833 916 NODE_3126_length_177_cov_47.276836 227 NODE_3187_length_311_cov_218.842438 361 NODE_3192_length_109_cov_357.678894 159 NODE_3220_length_578_cov_94.439445 628 NODE_3221_length_169_cov_100.307693 219 NODE_3229_length_202_cov_723.222778 252 NODE_3236_length_163_cov_391.503082 213 NODE_3407_length_174_cov_2.557471 224 NODE_3501_length_336_cov_52.416668 386 NODE_3502_length_463_cov_51.583153 513 NODE_3503_length_114_cov_48.929825 164 NODE_3600_length_758_cov_23.003958 808 NODE_3624_length_129_cov_271.782959 179 NODE_3652_length_317_cov_20.873817 367 NODE_3737_length_1036_cov_70.698845 1086 NODE_3753_length_114_cov_1.421053 164 NODE_3758_length_116_cov_364.594818 166 NODE_3792_length_227_cov_68.550659 277 NODE_3818_length_247_cov_68.971657 297 NODE_3849_length_112_cov_551.357117 162 NODE_3862_length_193_cov_173.751297 243 NODE_3883_length_163_cov_166.533737 213 NODE_3903_length_1067_cov_9.381443 1117 NODE_3927_length_241_cov_381.448120 291 NODE_3950_length_493_cov_447.586212 543 NODE_3954_length_225_cov_85.515556 275 NODE_3974_length_370_cov_90.656754 420 NODE_4055_length_206_cov_71.718445 256 NODE_4128_length_290_cov_40.872414 340 NODE_4155_length_358_cov_5.120112 408 NODE_4157_length_1497_cov_6.110220 1547 NODE_4164_length_250_cov_71.987999 300 NODE_4191_length_210_cov_2.200000 260 NODE_4225_length_322_cov_158.403732 372 NODE_4240_length_404_cov_133.896042 454 NODE_4243_length_386_cov_71.272018 436 NODE_4282_length_145_cov_155.027588 195 NODE_4313_length_149_cov_2.637584 199 NODE_4345_length_248_cov_2.576613 298 NODE_4487_length_453_cov_43.684326 503 NODE_4518_length_558_cov_97.378136 608 NODE_4564_length_261_cov_64.168579 311 NODE_4565_length_451_cov_47.064301 501 NODE_4615_length_136_cov_46.544117 186 NODE_4640_length_153_cov_1.307190 203 NODE_4642_length_542_cov_46.265682 592 NODE_4735_length_230_cov_1.847826 280 NODE_4736_length_116_cov_134.034485 166 NODE_4737_length_160_cov_116.581253 210 NODE_4840_length_172_cov_1.162791 222 NODE_4924_length_160_cov_76.568748 210 NODE_4938_length_190_cov_99.073685 240 NODE_4998_length_189_cov_4.666667 239 NODE_5030_length_103_cov_1.533981 153 NODE_5062_length_348_cov_3.704023 398 NODE_5082_length_104_cov_2.009615 154 NODE_5204_length_218_cov_56.509174 268 NODE_5271_length_115_cov_154.026093 165 NODE_5279_length_232_cov_2.056035 282 NODE_5284_length_651_cov_60.287251 701 NODE_5379_length_132_cov_1.787879 182 NODE_5384_length_295_cov_2.932203 345 NODE_5438_length_290_cov_2.817241 340 NODE_5444_length_181_cov_43.127071 231 NODE_5489_length_365_cov_3.586301 415 NODE_5512_length_108_cov_3.342592 158 NODE_5632_length_736_cov_58.180706 786 NODE_5653_length_165_cov_60.066666 215 NODE_5774_length_149_cov_3.919463 199 NODE_5858_length_103_cov_1.650485 153 NODE_5932_length_129_cov_51.511627 179 NODE_6058_length_104_cov_1.442308 154 NODE_6107_length_107_cov_3.514019 157 NODE_6157_length_218_cov_7.431193 268 NODE_6253_length_265_cov_3.554717 315 NODE_6273_length_225_cov_71.737778 275 NODE_6288_length_109_cov_1.256881 159 NODE_6358_length_763_cov_14.992136 813 NODE_6404_length_262_cov_12.572519 312 NODE_6423_length_125_cov_2.112000 175 NODE_6435_length_241_cov_2.738589 291 NODE_6509_length_200_cov_4.640000 250 NODE_6510_length_132_cov_3.143939 182 NODE_6511_length_223_cov_2.488789 273 NODE_6528_length_178_cov_46.578651 228 NODE_6553_length_103_cov_3.165049 153 NODE_6635_length_151_cov_2.609272 201 NODE_6746_length_271_cov_5.416974 321 NODE_6764_length_107_cov_6.046729 157 NODE_6778_length_138_cov_2.217391 188 NODE_6853_length_169_cov_1.946746 219 NODE_6868_length_118_cov_1.271186 168 NODE_6891_length_386_cov_3.411917 436 NODE_6989_length_106_cov_3.801887 156 NODE_6992_length_686_cov_12.574344 736 NODE_7001_length_124_cov_1.500000 174 NODE_7012_length_166_cov_2.144578 216 NODE_7022_length_111_cov_1.495495 161 NODE_7036_length_103_cov_1.446602 153 NODE_7046_length_139_cov_37.697842 189 NODE_7050_length_193_cov_1.590674 243 NODE_7128_length_123_cov_2.634146 173 NODE_7145_length_161_cov_3.006211 211 NODE_7166_length_197_cov_5.685279 247 NODE_7293_length_267_cov_9.621723 317 NODE_7371_length_145_cov_1.724138 195 NODE_7392_length_282_cov_3.269504 332 NODE_7464_length_104_cov_1.855769 154 NODE_7482_length_126_cov_2.198413 176 NODE_7494_length_149_cov_2.013423 199 NODE_7495_length_113_cov_1.407080 163 NODE_7505_length_132_cov_2.924242 182 NODE_7517_length_154_cov_2.525974 204 NODE_7519_length_130_cov_1.538462 180 NODE_7548_length_125_cov_5.696000 175 NODE_7591_length_136_cov_1.654412 186 NODE_7606_length_123_cov_1.276423 173 NODE_7627_length_225_cov_2.133333 275 NODE_7652_length_129_cov_1.798450 179 NODE_7683_length_195_cov_2.876923 245 NODE_7758_length_125_cov_2.624000 175 NODE_7822_length_119_cov_2.504202 169 NODE_7842_length_107_cov_1.401869 157 NODE_7843_length_420_cov_3.121428 470 NODE_7864_length_229_cov_2.410480 279 NODE_7869_length_118_cov_2.050848 168 NODE_7896_length_117_cov_1.709402 167 NODE_7912_length_187_cov_2.770053 237 NODE_7913_length_149_cov_2.288591 199 NODE_7936_length_112_cov_1.339286 162 NODE_7948_length_125_cov_2.304000 175 NODE_7956_length_500_cov_4.390000 550 NODE_8004_length_261_cov_2.026820 311 NODE_8086_length_177_cov_1.694915 227 NODE_8093_length_115_cov_1.582609 165 NODE_8166_length_106_cov_3.820755 156 NODE_8170_length_107_cov_1.467290 157 NODE_8191_length_149_cov_2.436242 199 NODE_8196_length_109_cov_1.825688 159 NODE_8227_length_113_cov_3.070796 163 NODE_8308_length_195_cov_2.666667 245 NODE_8312_length_134_cov_2.686567 184 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NODE_9004_length_129_cov_2.860465 9 NODE_9018_length_131_cov_1.786260 7 NODE_9050_length_309_cov_9.757281 67 NODE_9075_length_257_cov_2.883269 17 NODE_9116_length_132_cov_3.045455 10 NODE_9133_length_153_cov_1.150327 4 NODE_9165_length_116_cov_1.715517 4 NODE_9187_length_137_cov_2.737226 9 NODE_9198_length_510_cov_4.376471 48 NODE_9328_length_226_cov_3.637168 20 NODE_9356_length_159_cov_1.257862 4 NODE_9391_length_274_cov_3.521898 29 NODE_9428_length_103_cov_1.194175 3 NODE_9481_length_126_cov_1.912698 5 NODE_9523_length_160_cov_2.100000 7 NODE_9533_length_115_cov_1.739130 4 NODE_9571_length_191_cov_2.418848 13 metaMix/inst/extdata/dat1/blastOut_old.tab0000644000176200001440000061576013403500106020250 0ustar liggesusersNODE_1597_length_349_cov_49.601719 gi|38018023|ref|NP_937947.1| 99.25 133 1 0 399 1 4175 4307 4e-83 274 NODE_1597_length_349_cov_49.601719 gi|253756606|ref|YP_003038519.1| 98.50 133 2 0 399 1 4175 4307 1e-82 272 NODE_1597_length_349_cov_49.601719 gi|253756607|ref|YP_003038518.1| 98.50 133 2 0 399 1 4175 4307 2e-82 272 NODE_1597_length_349_cov_49.601719 gi|253756581|ref|YP_003038496.1| 97.74 133 3 0 399 1 4175 4307 3e-82 271 NODE_1597_length_349_cov_49.601719 gi|15081555|ref|NP_150074.1| 97.74 133 3 0 399 1 4175 4307 3e-82 271 NODE_1597_length_349_cov_49.601719 gi|253756594|ref|YP_003038508.1| 97.74 133 3 0 399 1 4175 4307 3e-82 271 NODE_1597_length_349_cov_49.601719 gi|253756595|ref|YP_003038507.1| 97.74 133 3 0 399 1 4175 4307 4e-82 271 NODE_1597_length_349_cov_49.601719 gi|253756582|ref|YP_003038495.1| 97.74 133 3 0 399 1 4175 4307 4e-82 271 NODE_1597_length_349_cov_49.601719 gi|26008080|ref|NP_150073.2| 97.74 133 3 0 399 1 4175 4307 4e-82 271 NODE_1597_length_349_cov_49.601719 gi|167600355|ref|YP_001671997.1| 96.99 133 4 0 399 1 4221 4353 6e-82 270 NODE_1607_length_290_cov_156.668961 gi|38018025|ref|NP_937949.1| 94.69 113 5 1 338 3 99 211 7e-68 217 NODE_1607_length_290_cov_156.668961 gi|253756597|ref|YP_003038510.1| 90.27 113 10 1 338 3 99 211 2e-63 205 NODE_1607_length_290_cov_156.668961 gi|253756584|ref|YP_003038498.1| 89.38 113 11 1 338 3 99 211 7e-63 204 NODE_1607_length_290_cov_156.668961 gi|253756609|ref|YP_003038521.1| 89.38 113 11 1 338 3 99 211 1e-62 203 NODE_1607_length_290_cov_156.668961 gi|15081546|ref|NP_150076.1| 89.38 113 11 1 338 3 99 211 1e-62 203 NODE_1607_length_290_cov_156.668961 gi|394935453|ref|YP_005454244.1| 87.61 113 13 1 338 3 99 211 7e-61 199 NODE_1607_length_290_cov_156.668961 gi|85718617|ref|YP_459951.1| 83.19 113 18 1 338 3 99 211 4e-58 192 NODE_1607_length_290_cov_156.668961 gi|167600357|ref|YP_001671999.1| 58.41 113 46 1 338 3 98 210 1e-36 134 NODE_1607_length_290_cov_156.668961 gi|60115394|ref|YP_209232.1| 56.76 111 47 1 338 9 104 214 4e-36 133 NODE_1607_length_290_cov_156.668961 gi|253750534|ref|YP_003029847.1| 56.76 111 47 1 338 9 104 214 2e-34 129 NODE_1713_length_191_cov_280.675385 gi|38018026|ref|NP_937950.1| 95.00 80 4 0 1 240 159 238 4e-47 167 NODE_1713_length_191_cov_280.675385 gi|253756610|ref|YP_003038522.1| 88.75 80 9 0 1 240 153 232 5e-43 155 NODE_1713_length_191_cov_280.675385 gi|253756598|ref|YP_003038511.1| 87.50 80 10 0 1 240 153 232 3e-42 153 NODE_1713_length_191_cov_280.675385 gi|15081547|ref|NP_150077.1| 86.25 80 11 0 1 240 153 232 1e-41 151 NODE_1713_length_191_cov_280.675385 gi|253756585|ref|YP_003038499.1| 86.25 80 11 0 1 240 153 232 2e-41 150 NODE_1713_length_191_cov_280.675385 gi|394935454|ref|YP_005454245.1| 85.00 80 12 0 1 240 152 231 1e-40 148 NODE_1713_length_191_cov_280.675385 gi|85718618|ref|YP_459952.1| 83.75 80 13 0 1 240 153 232 3e-40 147 NODE_1713_length_191_cov_280.675385 gi|167600358|ref|YP_001672000.1| 65.00 80 28 0 1 240 153 232 5e-33 126 NODE_1713_length_191_cov_280.675385 gi|56807326|ref|YP_173238.1| 57.50 80 33 1 1 240 144 222 2e-24 102 NODE_1713_length_191_cov_280.675385 gi|253750535|ref|YP_003029848.1| 49.38 81 40 1 1 240 146 226 1e-20 90.9 NODE_1715_length_142_cov_213.845078 gi|38018026|ref|NP_937950.1| 92.06 63 5 0 191 3 244 306 2e-32 124 NODE_1715_length_142_cov_213.845078 gi|253756598|ref|YP_003038511.1| 80.95 63 8 1 191 3 238 296 1e-26 107 NODE_1715_length_142_cov_213.845078 gi|15081547|ref|NP_150077.1| 80.95 63 8 1 191 3 238 296 1e-26 107 NODE_1715_length_142_cov_213.845078 gi|253756585|ref|YP_003038499.1| 80.95 63 8 1 191 3 238 296 1e-26 107 NODE_1715_length_142_cov_213.845078 gi|253756610|ref|YP_003038522.1| 79.37 63 9 1 191 3 238 296 4e-26 106 NODE_1715_length_142_cov_213.845078 gi|394935454|ref|YP_005454245.1| 80.95 63 8 1 191 3 237 295 4e-26 106 NODE_1715_length_142_cov_213.845078 gi|167600358|ref|YP_001672000.1| 69.84 63 15 1 191 3 238 296 4e-23 97.8 NODE_1715_length_142_cov_213.845078 gi|85718618|ref|YP_459952.1| 69.84 63 15 1 191 3 238 296 2e-22 95.5 NODE_1715_length_142_cov_213.845078 gi|56807326|ref|YP_173238.1| 63.08 65 22 1 191 3 228 292 1e-18 84.7 NODE_1715_length_142_cov_213.845078 gi|9629814|ref|NP_045300.1| 52.38 63 30 0 191 3 232 294 5e-15 73.9 NODE_1766_length_314_cov_463.656036 gi|394935454|ref|YP_005454245.1| 96.67 120 4 0 3 362 908 1027 3e-71 237 NODE_1766_length_314_cov_463.656036 gi|85718618|ref|YP_459952.1| 95.00 120 6 0 3 362 895 1014 2e-70 234 NODE_1766_length_314_cov_463.656036 gi|38018026|ref|NP_937950.1| 97.50 120 3 0 3 362 907 1026 5e-70 234 NODE_1766_length_314_cov_463.656036 gi|253756598|ref|YP_003038511.1| 94.17 120 7 0 3 362 909 1028 9e-69 230 NODE_1766_length_314_cov_463.656036 gi|15081547|ref|NP_150077.1| 94.17 120 7 0 3 362 909 1028 9e-69 230 NODE_1766_length_314_cov_463.656036 gi|253756585|ref|YP_003038499.1| 94.17 120 7 0 3 362 909 1028 1e-68 230 NODE_1766_length_314_cov_463.656036 gi|253756610|ref|YP_003038522.1| 92.50 120 9 0 3 362 909 1028 5e-68 228 NODE_1766_length_314_cov_463.656036 gi|167600358|ref|YP_001672000.1| 90.68 118 11 0 9 362 911 1028 1e-66 224 NODE_1766_length_314_cov_463.656036 gi|56807326|ref|YP_173238.1| 81.51 119 22 0 6 362 901 1019 7e-60 205 NODE_1766_length_314_cov_463.656036 gi|9629814|ref|NP_045300.1| 81.90 116 21 0 15 362 869 984 6e-59 202 NODE_2060_length_233_cov_764.030029 gi|38018026|ref|NP_937950.1| 95.70 93 4 0 3 281 1178 1270 1e-54 189 NODE_2060_length_233_cov_764.030029 gi|394935454|ref|YP_005454245.1| 92.47 93 7 0 3 281 1179 1271 2e-52 182 NODE_2060_length_233_cov_764.030029 gi|253756610|ref|YP_003038522.1| 92.47 93 7 0 3 281 1180 1272 6e-52 181 NODE_2060_length_233_cov_764.030029 gi|253756598|ref|YP_003038511.1| 91.40 93 8 0 3 281 1180 1272 2e-51 180 NODE_2060_length_233_cov_764.030029 gi|253756585|ref|YP_003038499.1| 91.30 92 8 0 6 281 1181 1272 1e-50 177 NODE_2060_length_233_cov_764.030029 gi|15081547|ref|NP_150077.1| 91.40 93 8 0 3 281 1180 1272 1e-50 177 NODE_2060_length_233_cov_764.030029 gi|167600358|ref|YP_001672000.1| 89.25 93 10 0 3 281 1180 1272 3e-50 176 NODE_2060_length_233_cov_764.030029 gi|85718618|ref|YP_459952.1| 84.95 93 14 0 3 281 1166 1258 3e-48 171 NODE_2060_length_233_cov_764.030029 gi|9629814|ref|NP_045300.1| 71.58 95 25 1 3 281 1136 1230 8e-40 146 NODE_2060_length_233_cov_764.030029 gi|60115395|ref|YP_209233.1| 71.58 95 25 1 3 281 1188 1282 2e-39 145 NODE_2345_length_1115_cov_56.699551 gi|26008090|ref|NP_742138.1| 98.97 388 4 0 2 1165 433 820 0.0 803 NODE_2345_length_1115_cov_56.699551 gi|85719076|ref|YP_459941.1| 94.59 388 21 0 2 1165 433 820 0.0 769 NODE_2345_length_1115_cov_56.699551 gi|25121569|ref|NP_740616.1| 93.56 388 25 0 2 1165 433 820 0.0 769 NODE_2345_length_1115_cov_56.699551 gi|60145599|ref|NP_001012452.1| 92.53 388 29 0 2 1165 433 820 0.0 762 NODE_2345_length_1115_cov_56.699551 gi|38018023|ref|NP_937947.1| 100.00 388 0 0 2 1165 4802 5189 0.0 815 NODE_2345_length_1115_cov_56.699551 gi|253756595|ref|YP_003038507.1| 98.97 388 4 0 2 1165 4802 5189 0.0 806 NODE_2345_length_1115_cov_56.699551 gi|26008080|ref|NP_150073.2| 98.97 388 4 0 2 1165 4802 5189 0.0 806 NODE_2345_length_1115_cov_56.699551 gi|253756582|ref|YP_003038495.1| 98.97 388 4 0 2 1165 4802 5189 0.0 806 NODE_2345_length_1115_cov_56.699551 gi|253756607|ref|YP_003038518.1| 98.97 388 4 0 2 1165 4802 5189 0.0 806 NODE_2345_length_1115_cov_56.699551 gi|167600354|ref|YP_001671996.1| 98.97 388 4 0 2 1165 4848 5235 0.0 806 NODE_2652_length_118_cov_2.500000 gi|314953946|ref|YP_004063986.1| 40.91 44 25 1 134 3 903 945 7.9 28.9 NODE_2652_length_118_cov_2.500000 gi|9632197|ref|NP_048906.1| 38.71 31 18 1 7 96 81 111 9.8 27.7 NODE_2838_length_139_cov_133.841721 gi|38018025|ref|NP_937949.1| 96.77 62 2 0 187 2 38 99 5e-35 127 NODE_2838_length_139_cov_133.841721 gi|253756609|ref|YP_003038521.1| 93.55 62 4 0 187 2 38 99 1e-33 124 NODE_2838_length_139_cov_133.841721 gi|85718617|ref|YP_459951.1| 93.55 62 4 0 187 2 38 99 1e-33 124 NODE_2838_length_139_cov_133.841721 gi|394935453|ref|YP_005454244.1| 91.94 62 5 0 187 2 38 99 3e-33 123 NODE_2838_length_139_cov_133.841721 gi|253756597|ref|YP_003038510.1| 90.32 62 6 0 187 2 38 99 5e-32 119 NODE_2838_length_139_cov_133.841721 gi|15081546|ref|NP_150076.1| 90.32 62 6 0 187 2 38 99 5e-32 119 NODE_2838_length_139_cov_133.841721 gi|253756584|ref|YP_003038498.1| 88.71 62 7 0 187 2 38 99 8e-32 119 NODE_2838_length_139_cov_133.841721 gi|167600357|ref|YP_001671999.1| 88.71 62 7 0 187 2 37 98 5e-31 117 NODE_2838_length_139_cov_133.841721 gi|56807325|ref|YP_173237.1| 69.35 62 19 0 187 2 32 93 1e-22 93.2 NODE_2838_length_139_cov_133.841721 gi|60115394|ref|YP_209232.1| 64.52 62 22 0 187 2 43 104 5e-21 89.4 NODE_2854_length_149_cov_752.966431 gi|167600358|ref|YP_001672000.1| 96.97 66 2 0 2 199 1274 1339 1e-37 139 NODE_2854_length_149_cov_752.966431 gi|253756598|ref|YP_003038511.1| 96.97 66 2 0 2 199 1274 1339 2e-37 139 NODE_2854_length_149_cov_752.966431 gi|15081547|ref|NP_150077.1| 96.97 66 2 0 2 199 1274 1339 2e-37 138 NODE_2854_length_149_cov_752.966431 gi|253756585|ref|YP_003038499.1| 96.97 66 2 0 2 199 1274 1339 2e-37 138 NODE_2854_length_149_cov_752.966431 gi|394935454|ref|YP_005454245.1| 96.97 66 2 0 2 199 1273 1338 2e-37 138 NODE_2854_length_149_cov_752.966431 gi|85718618|ref|YP_459952.1| 96.97 66 2 0 2 199 1260 1325 3e-37 138 NODE_2854_length_149_cov_752.966431 gi|38018026|ref|NP_937950.1| 98.48 66 1 0 2 199 1272 1337 3e-37 138 NODE_2854_length_149_cov_752.966431 gi|56807326|ref|YP_173238.1| 76.56 64 15 0 8 199 1269 1332 9e-29 114 NODE_2854_length_149_cov_752.966431 gi|253756610|ref|YP_003038522.1| 94.55 55 3 0 2 166 1274 1328 1e-27 110 NODE_2854_length_149_cov_752.966431 gi|9629814|ref|NP_045300.1| 83.02 53 9 0 8 166 1234 1286 8e-24 99.8 NODE_2962_length_126_cov_1.563492 gi|116686122|ref|NP_036442.3| 87.93 58 7 0 1 174 42 99 2e-30 118 NODE_2962_length_126_cov_1.563492 gi|162287089|ref|NP_032472.2| 87.93 58 7 0 1 174 42 99 3e-30 117 NODE_2962_length_126_cov_1.563492 gi|150010604|ref|NP_001092763.1| 86.21 58 8 0 1 174 42 99 4e-29 114 NODE_2962_length_126_cov_1.563492 gi|355390331|ref|NP_001239032.1| 65.52 58 20 0 1 174 41 98 2e-20 89.7 NODE_2962_length_126_cov_1.563492 gi|355390328|ref|NP_001239031.1| 65.52 58 20 0 1 174 41 98 2e-20 89.7 NODE_2962_length_126_cov_1.563492 gi|86990454|ref|NP_001034561.1| 65.52 58 20 0 1 174 41 98 2e-20 89.7 NODE_2962_length_126_cov_1.563492 gi|83716024|ref|NP_060066.2| 65.52 58 20 0 1 174 41 98 2e-20 89.7 NODE_2962_length_126_cov_1.563492 gi|355390323|ref|NP_001239029.1| 65.52 58 20 0 1 174 41 98 2e-20 89.7 NODE_2962_length_126_cov_1.563492 gi|157823795|ref|NP_001102512.1| 61.40 57 22 0 4 174 43 99 7e-19 85.1 NODE_2962_length_126_cov_1.563492 gi|157823695|ref|NP_057914.2| 61.40 57 22 0 4 174 43 99 7e-19 85.1 NODE_2981_length_212_cov_275.750000 gi|38018026|ref|NP_937950.1| 96.55 87 3 0 2 262 392 478 5e-51 178 NODE_2981_length_212_cov_275.750000 gi|15081547|ref|NP_150077.1| 96.55 87 3 0 2 262 382 468 6e-51 178 NODE_2981_length_212_cov_275.750000 gi|253756585|ref|YP_003038499.1| 96.55 87 3 0 2 262 382 468 7e-51 178 NODE_2981_length_212_cov_275.750000 gi|253756610|ref|YP_003038522.1| 95.40 87 4 0 2 262 382 468 3e-50 176 NODE_2981_length_212_cov_275.750000 gi|253756598|ref|YP_003038511.1| 94.25 87 5 0 2 262 382 468 9e-50 174 NODE_2981_length_212_cov_275.750000 gi|394935454|ref|YP_005454245.1| 93.10 87 6 0 2 262 381 467 2e-49 174 NODE_2981_length_212_cov_275.750000 gi|167600358|ref|YP_001672000.1| 78.16 87 18 1 2 262 382 467 9e-40 146 NODE_2981_length_212_cov_275.750000 gi|85718618|ref|YP_459952.1| 76.71 73 17 0 2 220 382 454 3e-33 127 NODE_2981_length_212_cov_275.750000 gi|60115395|ref|YP_209233.1| 60.76 79 31 0 2 238 380 458 1e-29 117 NODE_2981_length_212_cov_275.750000 gi|56807326|ref|YP_173238.1| 67.12 73 24 0 2 220 378 450 1e-28 114 NODE_3045_length_866_cov_8.483833 gi|34538598|ref|NP_904328.1| 69.07 291 90 0 914 42 26 316 5e-92 283 NODE_3045_length_866_cov_8.483833 gi|251831107|ref|YP_003024026.1| 67.01 291 96 0 914 42 26 316 5e-83 260 NODE_3045_length_866_cov_8.483833 gi|494060707|ref|WP_007002790.1| 44.13 281 150 2 914 93 39 319 3e-52 181 NODE_3045_length_866_cov_8.483833 gi|496406861|ref|WP_009115725.1| 40.61 293 157 4 914 84 44 335 5e-42 155 NODE_3045_length_866_cov_8.483833 gi|496410681|ref|WP_009119545.1| 40.61 293 157 4 914 84 43 334 5e-42 154 NODE_3045_length_866_cov_8.483833 gi|489880086|ref|WP_003783554.1| 41.46 287 152 3 914 102 52 338 1e-41 154 NODE_3045_length_866_cov_8.483833 gi|489884532|ref|WP_003787982.1| 40.96 293 156 4 914 84 52 343 2e-41 153 NODE_3045_length_866_cov_8.483833 gi|491919997|ref|WP_005672482.1| 41.61 298 153 4 914 84 48 345 3e-41 153 NODE_3045_length_866_cov_8.483833 gi|489919582|ref|WP_003822943.1| 41.46 287 152 3 914 102 51 337 4e-41 152 NODE_3045_length_866_cov_8.483833 gi|488718793|ref|WP_002642669.1| 40.20 296 143 4 914 102 52 338 5e-40 149 NODE_3126_length_177_cov_47.276836 gi|26008095|ref|NP_742170.1| 98.67 75 1 0 2 226 247 321 5e-24 99.0 NODE_3126_length_177_cov_47.276836 gi|253756606|ref|YP_003038519.1| 100.00 75 0 0 2 226 2997 3071 2e-23 99.4 NODE_3126_length_177_cov_47.276836 gi|38018023|ref|NP_937947.1| 100.00 75 0 0 2 226 2997 3071 2e-23 99.4 NODE_3126_length_177_cov_47.276836 gi|253756607|ref|YP_003038518.1| 100.00 75 0 0 2 226 2997 3071 3e-23 99.0 NODE_3126_length_177_cov_47.276836 gi|15081555|ref|NP_150074.1| 98.67 75 1 0 2 226 2997 3071 3e-23 99.0 NODE_3126_length_177_cov_47.276836 gi|253756594|ref|YP_003038508.1| 98.67 75 1 0 2 226 2997 3071 3e-23 99.0 NODE_3126_length_177_cov_47.276836 gi|253756581|ref|YP_003038496.1| 98.67 75 1 0 2 226 2997 3071 3e-23 99.0 NODE_3126_length_177_cov_47.276836 gi|253756595|ref|YP_003038507.1| 98.67 75 1 0 2 226 2997 3071 4e-23 98.6 NODE_3126_length_177_cov_47.276836 gi|253756582|ref|YP_003038495.1| 98.67 75 1 0 2 226 2997 3071 4e-23 98.6 NODE_3126_length_177_cov_47.276836 gi|26008080|ref|NP_150073.2| 98.67 75 1 0 2 226 2997 3071 4e-23 98.6 NODE_3187_length_311_cov_218.842438 gi|38018026|ref|NP_937950.1| 87.07 116 13 1 351 4 1 114 1e-56 196 NODE_3187_length_311_cov_218.842438 gi|253756598|ref|YP_003038511.1| 87.93 116 10 1 351 4 1 112 6e-56 194 NODE_3187_length_311_cov_218.842438 gi|15081547|ref|NP_150077.1| 87.93 116 10 1 351 4 1 112 7e-56 194 NODE_3187_length_311_cov_218.842438 gi|253756585|ref|YP_003038499.1| 87.93 116 10 1 351 4 1 112 9e-56 193 NODE_3187_length_311_cov_218.842438 gi|394935454|ref|YP_005454245.1| 86.21 116 12 1 351 4 1 112 5e-55 191 NODE_3187_length_311_cov_218.842438 gi|253756610|ref|YP_003038522.1| 86.21 116 12 1 351 4 1 112 2e-54 189 NODE_3187_length_311_cov_218.842438 gi|85718618|ref|YP_459952.1| 76.07 117 24 1 351 1 1 113 3e-50 177 NODE_3187_length_311_cov_218.842438 gi|167600358|ref|YP_001672000.1| 70.69 116 30 1 351 4 1 112 3e-45 163 NODE_3187_length_311_cov_218.842438 gi|60115395|ref|YP_209233.1| 57.39 115 46 1 351 7 1 112 7e-35 134 NODE_3187_length_311_cov_218.842438 gi|56807326|ref|YP_173238.1| 56.41 117 46 2 351 1 1 112 2e-34 132 NODE_3192_length_109_cov_357.678894 gi|38018023|ref|NP_937947.1| 98.08 52 1 0 2 157 1462 1513 1e-26 107 NODE_3192_length_109_cov_357.678894 gi|253756607|ref|YP_003038518.1| 96.15 52 2 0 2 157 1462 1513 9e-26 105 NODE_3192_length_109_cov_357.678894 gi|253756582|ref|YP_003038495.1| 96.15 52 2 0 2 157 1462 1513 9e-26 105 NODE_3192_length_109_cov_357.678894 gi|26008080|ref|NP_150073.2| 96.15 52 2 0 2 157 1462 1513 9e-26 105 NODE_3192_length_109_cov_357.678894 gi|253756595|ref|YP_003038507.1| 96.15 52 2 0 2 157 1462 1513 9e-26 105 NODE_3192_length_109_cov_357.678894 gi|253756606|ref|YP_003038519.1| 96.15 52 2 0 2 157 1462 1513 1e-25 104 NODE_3192_length_109_cov_357.678894 gi|253756581|ref|YP_003038496.1| 96.15 52 2 0 2 157 1462 1513 1e-25 104 NODE_3192_length_109_cov_357.678894 gi|15081555|ref|NP_150074.1| 96.15 52 2 0 2 157 1462 1513 1e-25 104 NODE_3192_length_109_cov_357.678894 gi|253756594|ref|YP_003038508.1| 96.15 52 2 0 2 157 1462 1513 1e-25 104 NODE_3192_length_109_cov_357.678894 gi|26008083|ref|NP_742169.1| 96.15 52 2 0 2 157 611 662 6e-25 102 NODE_3220_length_578_cov_94.439445 gi|26008094|ref|NP_742142.1| 98.97 195 2 0 1 585 105 299 4e-139 399 NODE_3220_length_578_cov_94.439445 gi|38018023|ref|NP_937947.1| 100.00 195 0 0 1 585 6901 7095 2e-128 408 NODE_3220_length_578_cov_94.439445 gi|253756595|ref|YP_003038507.1| 98.97 195 2 0 1 585 6900 7094 1e-126 403 NODE_3220_length_578_cov_94.439445 gi|253756582|ref|YP_003038495.1| 98.97 195 2 0 1 585 6900 7094 1e-126 403 NODE_3220_length_578_cov_94.439445 gi|26008080|ref|NP_150073.2| 98.97 195 2 0 1 585 6900 7094 1e-126 403 NODE_3220_length_578_cov_94.439445 gi|85718615|ref|YP_459949.1| 98.46 195 3 0 1 585 6901 7095 4e-125 398 NODE_3220_length_578_cov_94.439445 gi|253756607|ref|YP_003038518.1| 97.95 195 4 0 1 585 6900 7094 1e-124 397 NODE_3220_length_578_cov_94.439445 gi|394935459|ref|YP_005454239.1| 97.44 195 5 0 1 585 6957 7151 1e-124 397 NODE_3220_length_578_cov_94.439445 gi|167600354|ref|YP_001671996.1| 96.41 195 7 0 1 585 6934 7128 2e-122 390 NODE_3220_length_578_cov_94.439445 gi|25121573|ref|NP_740620.1| 85.05 194 29 0 1 582 105 298 1e-121 354 NODE_3221_length_169_cov_100.307693 gi|38018024|ref|NP_937948.1| 98.48 66 1 0 20 217 1 66 1e-39 138 NODE_3221_length_169_cov_100.307693 gi|253756596|ref|YP_003038509.1| 95.45 66 3 0 20 217 1 66 5e-39 136 NODE_3221_length_169_cov_100.307693 gi|253756583|ref|YP_003038497.1| 95.45 66 3 0 20 217 1 66 5e-39 136 NODE_3221_length_169_cov_100.307693 gi|15081545|ref|NP_150075.1| 95.45 66 3 0 20 217 1 66 5e-39 136 NODE_3221_length_169_cov_100.307693 gi|253756608|ref|YP_003038520.1| 92.42 66 5 0 20 217 1 66 1e-37 132 NODE_3221_length_169_cov_100.307693 gi|85718616|ref|YP_459950.1| 89.39 66 7 0 20 217 1 66 3e-35 124 NODE_3221_length_169_cov_100.307693 gi|167600356|ref|YP_001671998.1| 64.62 65 23 0 20 214 1 65 6e-25 99.4 NODE_3221_length_169_cov_100.307693 gi|11192310|ref|NP_068669.1| 58.73 63 26 0 26 214 13 75 4e-21 88.6 NODE_3221_length_169_cov_100.307693 gi|253750533|ref|YP_003029846.1| 56.72 67 29 0 14 214 1 67 5e-21 88.6 NODE_3221_length_169_cov_100.307693 gi|394935449|ref|YP_005454240.1| 88.37 43 5 0 20 148 1 43 2e-20 82.4 NODE_3229_length_202_cov_723.222778 gi|85718618|ref|YP_459952.1| 98.80 83 1 0 251 3 1062 1144 6e-48 169 NODE_3229_length_202_cov_723.222778 gi|38018026|ref|NP_937950.1| 100.00 83 0 0 251 3 1074 1156 6e-48 169 NODE_3229_length_202_cov_723.222778 gi|253756585|ref|YP_003038499.1| 98.80 83 1 0 251 3 1076 1158 1e-47 169 NODE_3229_length_202_cov_723.222778 gi|15081547|ref|NP_150077.1| 98.80 83 1 0 251 3 1076 1158 1e-47 168 NODE_3229_length_202_cov_723.222778 gi|253756610|ref|YP_003038522.1| 98.80 83 1 0 251 3 1076 1158 2e-47 168 NODE_3229_length_202_cov_723.222778 gi|253756598|ref|YP_003038511.1| 98.80 83 1 0 251 3 1076 1158 2e-47 168 NODE_3229_length_202_cov_723.222778 gi|394935454|ref|YP_005454245.1| 98.80 83 1 0 251 3 1075 1157 3e-47 167 NODE_3229_length_202_cov_723.222778 gi|167600358|ref|YP_001672000.1| 92.77 83 6 0 251 3 1076 1158 6e-45 160 NODE_3229_length_202_cov_723.222778 gi|253750535|ref|YP_003029848.1| 89.16 83 9 0 251 3 1068 1150 2e-43 156 NODE_3229_length_202_cov_723.222778 gi|60115395|ref|YP_209233.1| 86.75 83 11 0 251 3 1084 1166 4e-43 155 NODE_3236_length_163_cov_391.503082 gi|38018026|ref|NP_937950.1| 90.41 73 4 2 213 1 494 565 1e-34 130 NODE_3236_length_163_cov_391.503082 gi|253756610|ref|YP_003038522.1| 74.70 83 8 3 210 1 485 567 7e-30 117 NODE_3236_length_163_cov_391.503082 gi|253756585|ref|YP_003038499.1| 73.49 83 9 3 210 1 485 567 3e-29 115 NODE_3236_length_163_cov_391.503082 gi|15081547|ref|NP_150077.1| 73.49 83 9 3 210 1 485 567 3e-29 115 NODE_3236_length_163_cov_391.503082 gi|253756598|ref|YP_003038511.1| 74.70 83 8 3 210 1 485 567 4e-29 115 NODE_3236_length_163_cov_391.503082 gi|394935454|ref|YP_005454245.1| 68.29 82 13 3 207 1 485 566 1e-25 105 NODE_3236_length_163_cov_391.503082 gi|167600358|ref|YP_001672000.1| 50.60 83 27 3 207 1 485 567 5e-15 74.3 NODE_3236_length_163_cov_391.503082 gi|56807326|ref|YP_173238.1| 42.17 83 30 3 207 1 473 551 1e-07 53.1 NODE_3236_length_163_cov_391.503082 gi|85718618|ref|YP_459952.1| 35.80 81 33 4 207 1 480 553 8e-05 44.7 NODE_3236_length_163_cov_391.503082 gi|253750535|ref|YP_003029848.1| 33.73 83 37 4 210 1 477 554 4e-04 42.4 NODE_3407_length_174_cov_2.557471 gi|489240182|ref|WP_003148409.1| 40.48 42 18 1 219 115 30 71 5.7 29.6 NODE_3407_length_174_cov_2.557471 gi|495171955|ref|WP_007896750.1| 40.54 37 22 0 83 193 349 385 7.4 29.3 NODE_3407_length_174_cov_2.557471 gi|269797424|ref|YP_003311324.1| 30.77 52 33 1 64 210 217 268 7.4 29.3 NODE_3407_length_174_cov_2.557471 gi|491530222|ref|WP_005387845.1| 30.77 52 33 1 64 210 217 268 9.5 28.9 NODE_3501_length_336_cov_52.416668 gi|26008090|ref|NP_742138.1| 98.44 128 2 0 386 3 77 204 1e-82 267 NODE_3501_length_336_cov_52.416668 gi|38018023|ref|NP_937947.1| 100.00 128 0 0 386 3 4446 4573 4e-82 271 NODE_3501_length_336_cov_52.416668 gi|167600354|ref|YP_001671996.1| 99.22 128 1 0 386 3 4492 4619 1e-81 269 NODE_3501_length_336_cov_52.416668 gi|253756607|ref|YP_003038518.1| 98.44 128 2 0 386 3 4446 4573 2e-81 268 NODE_3501_length_336_cov_52.416668 gi|253756595|ref|YP_003038507.1| 98.44 128 2 0 386 3 4446 4573 2e-81 268 NODE_3501_length_336_cov_52.416668 gi|26008080|ref|NP_150073.2| 98.44 128 2 0 386 3 4446 4573 2e-81 268 NODE_3501_length_336_cov_52.416668 gi|253756582|ref|YP_003038495.1| 98.44 128 2 0 386 3 4446 4573 2e-81 268 NODE_3501_length_336_cov_52.416668 gi|85718615|ref|YP_459949.1| 97.66 128 3 0 386 3 4446 4573 2e-80 266 NODE_3501_length_336_cov_52.416668 gi|394935459|ref|YP_005454239.1| 88.28 128 15 0 386 3 4506 4633 1e-72 244 NODE_3501_length_336_cov_52.416668 gi|25121569|ref|NP_740616.1| 77.34 128 29 0 386 3 77 204 2e-63 213 NODE_3502_length_463_cov_51.583153 gi|38018023|ref|NP_937947.1| 98.85 87 1 0 263 3 4375 4461 2e-92 181 NODE_3502_length_463_cov_51.583153 gi|38018023|ref|NP_937947.1| 98.82 85 1 0 511 257 4292 4376 2e-92 179 NODE_3502_length_463_cov_51.583153 gi|253756607|ref|YP_003038518.1| 98.84 86 1 0 511 254 4292 4377 3e-90 182 NODE_3502_length_463_cov_51.583153 gi|253756607|ref|YP_003038518.1| 94.25 87 5 0 263 3 4375 4461 3e-90 172 NODE_3502_length_463_cov_51.583153 gi|85718615|ref|YP_459949.1| 97.67 86 2 0 511 254 4292 4377 5e-90 181 NODE_3502_length_463_cov_51.583153 gi|85718615|ref|YP_459949.1| 94.25 87 5 0 263 3 4375 4461 5e-90 172 NODE_3502_length_463_cov_51.583153 gi|26008080|ref|NP_150073.2| 97.67 86 2 0 511 254 4292 4377 5e-90 181 NODE_3502_length_463_cov_51.583153 gi|26008080|ref|NP_150073.2| 94.25 87 5 0 263 3 4375 4461 5e-90 172 NODE_3502_length_463_cov_51.583153 gi|253756582|ref|YP_003038495.1| 97.67 86 2 0 511 254 4292 4377 6e-90 181 NODE_3502_length_463_cov_51.583153 gi|253756582|ref|YP_003038495.1| 94.25 87 5 0 263 3 4375 4461 6e-90 172 NODE_3502_length_463_cov_51.583153 gi|253756595|ref|YP_003038507.1| 97.67 86 2 0 511 254 4292 4377 6e-90 181 NODE_3502_length_463_cov_51.583153 gi|253756595|ref|YP_003038507.1| 94.25 87 5 0 263 3 4375 4461 6e-90 172 NODE_3502_length_463_cov_51.583153 gi|167600354|ref|YP_001671996.1| 96.51 86 3 0 511 254 4338 4423 2e-89 179 NODE_3502_length_463_cov_51.583153 gi|167600354|ref|YP_001671996.1| 94.25 87 5 0 263 3 4421 4507 2e-89 171 NODE_3502_length_463_cov_51.583153 gi|394935459|ref|YP_005454239.1| 91.86 86 7 0 511 254 4352 4437 1e-83 173 NODE_3502_length_463_cov_51.583153 gi|394935459|ref|YP_005454239.1| 86.05 86 12 0 263 6 4435 4520 1e-83 158 NODE_3502_length_463_cov_51.583153 gi|26007546|ref|NP_068668.2| 88.37 86 10 0 511 254 4379 4464 3e-76 167 NODE_3502_length_463_cov_51.583153 gi|26007546|ref|NP_068668.2| 74.71 87 22 0 263 3 4462 4548 3e-76 139 NODE_3502_length_463_cov_51.583153 gi|253750532|ref|YP_003029844.1| 87.21 86 11 0 511 254 4373 4458 1e-75 165 NODE_3502_length_463_cov_51.583153 gi|253750532|ref|YP_003029844.1| 74.71 87 22 0 263 3 4456 4542 1e-75 139 NODE_3503_length_114_cov_48.929825 gi|13128860|ref|NP_004955.2| 100.00 54 0 0 164 3 429 482 6e-04 41.2 NODE_3503_length_114_cov_48.929825 gi|6680193|ref|NP_032254.1| 100.00 54 0 0 164 3 429 482 6e-04 40.8 NODE_3600_length_758_cov_23.003958 gi|34538600|ref|NP_904330.1| 74.50 251 64 0 3 755 264 514 9e-122 365 NODE_3600_length_758_cov_23.003958 gi|251831109|ref|YP_003024028.1| 72.69 249 68 0 3 749 264 512 1e-114 347 NODE_3600_length_758_cov_23.003958 gi|488801869|ref|WP_002714275.1| 53.78 251 114 1 3 749 251 501 5e-75 244 NODE_3600_length_758_cov_23.003958 gi|492887319|ref|WP_006022898.1| 54.18 251 113 1 3 749 288 538 3e-74 243 NODE_3600_length_758_cov_23.003958 gi|488804983|ref|WP_002717389.1| 53.88 245 111 1 3 731 291 535 1e-73 242 NODE_3600_length_758_cov_23.003958 gi|490319116|ref|WP_004208609.1| 52.65 245 114 1 3 731 309 553 2e-72 239 NODE_3600_length_758_cov_23.003958 gi|494060889|ref|WP_007002972.1| 52.03 246 116 1 3 734 286 531 2e-70 233 NODE_3600_length_758_cov_23.003958 gi|488806148|ref|WP_002718554.1| 52.03 246 116 2 3 734 289 534 8e-68 226 NODE_3600_length_758_cov_23.003958 gi|493432515|ref|WP_006388093.1| 44.22 251 138 1 3 749 285 535 1e-55 194 NODE_3600_length_758_cov_23.003958 gi|493248467|ref|WP_006216867.1| 43.82 251 139 1 3 749 285 535 6e-55 192 NODE_3624_length_129_cov_271.782959 gi|38018023|ref|NP_937947.1| 100.00 59 0 0 179 3 1630 1688 2e-32 124 NODE_3624_length_129_cov_271.782959 gi|85718615|ref|YP_459949.1| 94.92 59 3 0 179 3 1630 1688 4e-29 115 NODE_3624_length_129_cov_271.782959 gi|26008083|ref|NP_742169.1| 93.22 59 4 0 179 3 779 837 7e-29 114 NODE_3624_length_129_cov_271.782959 gi|253756594|ref|YP_003038508.1| 93.22 59 4 0 179 3 1630 1688 1e-28 114 NODE_3624_length_129_cov_271.782959 gi|15081555|ref|NP_150074.1| 93.22 59 4 0 179 3 1630 1688 1e-28 114 NODE_3624_length_129_cov_271.782959 gi|253756581|ref|YP_003038496.1| 93.22 59 4 0 179 3 1630 1688 1e-28 114 NODE_3624_length_129_cov_271.782959 gi|253756595|ref|YP_003038507.1| 93.22 59 4 0 179 3 1630 1688 1e-28 114 NODE_3624_length_129_cov_271.782959 gi|26008080|ref|NP_150073.2| 93.22 59 4 0 179 3 1630 1688 1e-28 114 NODE_3624_length_129_cov_271.782959 gi|253756606|ref|YP_003038519.1| 93.22 59 4 0 179 3 1630 1688 1e-28 114 NODE_3624_length_129_cov_271.782959 gi|253756582|ref|YP_003038495.1| 93.22 59 4 0 179 3 1630 1688 1e-28 114 NODE_3652_length_317_cov_20.873817 gi|34538600|ref|NP_904330.1| 92.45 106 8 0 50 367 114 219 2e-43 154 NODE_3652_length_317_cov_20.873817 gi|251831109|ref|YP_003024028.1| 90.20 102 10 0 62 367 118 219 4e-40 145 NODE_3652_length_317_cov_20.873817 gi|488806148|ref|WP_002718554.1| 64.36 101 35 1 65 367 146 245 1e-21 94.4 NODE_3652_length_317_cov_20.873817 gi|494060889|ref|WP_007002972.1| 56.73 104 45 0 56 367 139 242 3e-21 93.6 NODE_3652_length_317_cov_20.873817 gi|488804983|ref|WP_002717389.1| 64.65 99 34 1 71 367 150 247 4e-21 93.2 NODE_3652_length_317_cov_20.873817 gi|488801869|ref|WP_002714275.1| 62.63 99 36 1 71 367 110 207 2e-20 90.9 NODE_3652_length_317_cov_20.873817 gi|492887319|ref|WP_006022898.1| 62.63 99 36 1 71 367 147 244 2e-20 90.9 NODE_3652_length_317_cov_20.873817 gi|490319116|ref|WP_004208609.1| 65.22 92 31 1 92 367 175 265 4e-16 79.0 NODE_3652_length_317_cov_20.873817 gi|493248467|ref|WP_006216867.1| 51.40 107 48 2 50 367 138 241 3e-14 73.9 NODE_3652_length_317_cov_20.873817 gi|493432515|ref|WP_006388093.1| 49.53 107 50 2 50 367 138 241 4e-14 73.2 NODE_3737_length_1036_cov_70.698845 gi|38018023|ref|NP_937947.1| 99.45 362 2 0 1 1086 6266 6627 0.0 728 NODE_3737_length_1036_cov_70.698845 gi|253756595|ref|YP_003038507.1| 98.34 361 6 0 1 1083 6266 6626 0.0 719 NODE_3737_length_1036_cov_70.698845 gi|253756582|ref|YP_003038495.1| 98.34 361 6 0 1 1083 6266 6626 0.0 719 NODE_3737_length_1036_cov_70.698845 gi|26008080|ref|NP_150073.2| 98.34 361 6 0 1 1083 6266 6626 0.0 719 NODE_3737_length_1036_cov_70.698845 gi|253756607|ref|YP_003038518.1| 97.78 361 8 0 1 1083 6266 6626 0.0 715 NODE_3737_length_1036_cov_70.698845 gi|85718615|ref|YP_459949.1| 97.24 362 10 0 1 1086 6266 6627 0.0 714 NODE_3737_length_1036_cov_70.698845 gi|167600354|ref|YP_001671996.1| 91.69 361 26 1 1 1083 6308 6664 0.0 669 NODE_3737_length_1036_cov_70.698845 gi|394935459|ref|YP_005454239.1| 90.70 355 33 0 1 1065 6322 6676 0.0 655 NODE_3737_length_1036_cov_70.698845 gi|26007546|ref|NP_068668.2| 81.16 361 68 0 1 1083 6350 6710 0.0 602 NODE_3737_length_1036_cov_70.698845 gi|253750532|ref|YP_003029844.1| 80.95 357 68 0 1 1071 6344 6700 0.0 595 NODE_3753_length_114_cov_1.421053 gi|388556516|ref|NP_001253974.1| 88.68 53 6 0 2 160 50 102 4e-26 101 NODE_3753_length_114_cov_1.421053 gi|30410794|ref|NP_005780.2| 88.68 53 6 0 2 160 39 91 4e-26 101 NODE_3753_length_114_cov_1.421053 gi|6755214|ref|NP_035322.1| 88.68 53 6 0 2 160 39 91 4e-26 101 NODE_3753_length_114_cov_1.421053 gi|30410796|ref|NP_789839.1| 88.68 53 6 0 2 160 39 91 9e-26 100 NODE_3753_length_114_cov_1.421053 gi|30581141|ref|NP_788955.1| 51.61 31 15 0 5 97 39 69 0.002 38.9 NODE_3753_length_114_cov_1.421053 gi|5453990|ref|NP_006254.1| 51.61 31 15 0 5 97 39 69 0.002 38.9 NODE_3753_length_114_cov_1.421053 gi|6755212|ref|NP_035319.1| 51.61 31 15 0 5 97 39 69 0.002 38.9 NODE_3753_length_114_cov_1.421053 gi|269846918|ref|NP_689575.2| 37.50 32 20 0 159 64 152 183 0.56 31.6 NODE_3753_length_114_cov_1.421053 gi|269846912|ref|NP_001161414.1| 37.50 32 20 0 159 64 152 183 0.56 31.6 NODE_3753_length_114_cov_1.421053 gi|491790517|ref|WP_005601312.1| 40.62 32 19 0 62 157 310 341 3.4 29.6 NODE_3758_length_116_cov_364.594818 gi|38018026|ref|NP_937950.1| 96.36 55 2 0 165 1 313 367 7e-30 116 NODE_3758_length_116_cov_364.594818 gi|394935454|ref|YP_005454245.1| 92.73 55 4 0 165 1 302 356 9e-29 113 NODE_3758_length_116_cov_364.594818 gi|15081547|ref|NP_150077.1| 92.73 55 4 0 165 1 303 357 1e-28 113 NODE_3758_length_116_cov_364.594818 gi|253756598|ref|YP_003038511.1| 92.73 55 4 0 165 1 303 357 1e-28 113 NODE_3758_length_116_cov_364.594818 gi|253756610|ref|YP_003038522.1| 92.73 55 4 0 165 1 303 357 1e-28 113 NODE_3758_length_116_cov_364.594818 gi|253756585|ref|YP_003038499.1| 92.73 55 4 0 165 1 303 357 1e-28 112 NODE_3758_length_116_cov_364.594818 gi|85718618|ref|YP_459952.1| 85.45 55 8 0 165 1 303 357 2e-26 106 NODE_3758_length_116_cov_364.594818 gi|167600358|ref|YP_001672000.1| 74.55 55 14 0 165 1 303 357 5e-22 94.0 NODE_3758_length_116_cov_364.594818 gi|9629814|ref|NP_045300.1| 74.55 55 14 0 165 1 301 355 1e-21 93.2 NODE_3758_length_116_cov_364.594818 gi|60115395|ref|YP_209233.1| 72.73 55 15 0 165 1 301 355 2e-21 92.4 NODE_3792_length_227_cov_68.550659 gi|38018023|ref|NP_937947.1| 98.91 92 1 0 2 277 4084 4175 6e-54 188 NODE_3792_length_227_cov_68.550659 gi|15081555|ref|NP_150074.1| 97.83 92 2 0 2 277 4084 4175 3e-53 186 NODE_3792_length_227_cov_68.550659 gi|253756581|ref|YP_003038496.1| 97.83 92 2 0 2 277 4084 4175 4e-53 186 NODE_3792_length_227_cov_68.550659 gi|253756606|ref|YP_003038519.1| 97.83 92 2 0 2 277 4084 4175 4e-53 186 NODE_3792_length_227_cov_68.550659 gi|253756594|ref|YP_003038508.1| 97.83 92 2 0 2 277 4084 4175 4e-53 186 NODE_3792_length_227_cov_68.550659 gi|167600355|ref|YP_001671997.1| 97.83 92 2 0 2 277 4130 4221 4e-53 186 NODE_3792_length_227_cov_68.550659 gi|167600354|ref|YP_001671996.1| 97.83 92 2 0 2 277 4130 4221 4e-53 186 NODE_3792_length_227_cov_68.550659 gi|253756582|ref|YP_003038495.1| 97.83 92 2 0 2 277 4084 4175 5e-53 185 NODE_3792_length_227_cov_68.550659 gi|253756607|ref|YP_003038518.1| 97.83 92 2 0 2 277 4084 4175 5e-53 185 NODE_3792_length_227_cov_68.550659 gi|253756595|ref|YP_003038507.1| 97.83 92 2 0 2 277 4084 4175 5e-53 185 NODE_3818_length_247_cov_68.971657 gi|26008085|ref|NP_742133.1| 94.95 99 5 0 297 1 50 148 4e-59 190 NODE_3818_length_247_cov_68.971657 gi|38018023|ref|NP_937947.1| 98.99 99 1 0 297 1 3599 3697 1e-57 199 NODE_3818_length_247_cov_68.971657 gi|253756594|ref|YP_003038508.1| 94.95 99 5 0 297 1 3599 3697 2e-55 192 NODE_3818_length_247_cov_68.971657 gi|15081555|ref|NP_150074.1| 94.95 99 5 0 297 1 3599 3697 2e-55 192 NODE_3818_length_247_cov_68.971657 gi|253756581|ref|YP_003038496.1| 94.95 99 5 0 297 1 3599 3697 2e-55 192 NODE_3818_length_247_cov_68.971657 gi|253756606|ref|YP_003038519.1| 94.95 99 5 0 297 1 3599 3697 2e-55 192 NODE_3818_length_247_cov_68.971657 gi|253756582|ref|YP_003038495.1| 94.95 99 5 0 297 1 3599 3697 3e-55 192 NODE_3818_length_247_cov_68.971657 gi|253756595|ref|YP_003038507.1| 94.95 99 5 0 297 1 3599 3697 3e-55 192 NODE_3818_length_247_cov_68.971657 gi|26008080|ref|NP_150073.2| 94.95 99 5 0 297 1 3599 3697 3e-55 192 NODE_3818_length_247_cov_68.971657 gi|253756607|ref|YP_003038518.1| 94.95 99 5 0 297 1 3599 3697 3e-55 192 NODE_3849_length_112_cov_551.357117 gi|38018023|ref|NP_937947.1| 98.15 54 1 0 1 162 1289 1342 4e-18 83.2 NODE_3849_length_112_cov_551.357117 gi|26008083|ref|NP_742169.1| 96.30 54 2 0 1 162 438 491 3e-17 80.5 NODE_3849_length_112_cov_551.357117 gi|253756594|ref|YP_003038508.1| 96.30 54 2 0 1 162 1289 1342 3e-17 80.9 NODE_3849_length_112_cov_551.357117 gi|253756581|ref|YP_003038496.1| 96.30 54 2 0 1 162 1289 1342 3e-17 80.5 NODE_3849_length_112_cov_551.357117 gi|15081555|ref|NP_150074.1| 96.30 54 2 0 1 162 1289 1342 3e-17 80.5 NODE_3849_length_112_cov_551.357117 gi|253756606|ref|YP_003038519.1| 96.30 54 2 0 1 162 1289 1342 3e-17 80.5 NODE_3849_length_112_cov_551.357117 gi|85718615|ref|YP_459949.1| 96.30 54 2 0 1 162 1289 1342 3e-17 80.5 NODE_3849_length_112_cov_551.357117 gi|253756595|ref|YP_003038507.1| 96.30 54 2 0 1 162 1289 1342 3e-17 80.5 NODE_3849_length_112_cov_551.357117 gi|253756582|ref|YP_003038495.1| 96.30 54 2 0 1 162 1289 1342 3e-17 80.5 NODE_3849_length_112_cov_551.357117 gi|26008080|ref|NP_150073.2| 96.30 54 2 0 1 162 1289 1342 3e-17 80.5 NODE_3862_length_193_cov_173.751297 gi|38018023|ref|NP_937947.1| 98.75 80 1 0 3 242 2060 2139 4e-44 159 NODE_3862_length_193_cov_173.751297 gi|26008083|ref|NP_742169.1| 92.50 80 6 0 3 242 1209 1288 4e-41 150 NODE_3862_length_193_cov_173.751297 gi|15081555|ref|NP_150074.1| 92.50 80 6 0 3 242 2060 2139 6e-41 150 NODE_3862_length_193_cov_173.751297 gi|26008080|ref|NP_150073.2| 92.50 80 6 0 3 242 2060 2139 8e-41 149 NODE_3862_length_193_cov_173.751297 gi|253756594|ref|YP_003038508.1| 91.25 80 7 0 3 242 2060 2139 1e-40 149 NODE_3862_length_193_cov_173.751297 gi|253756595|ref|YP_003038507.1| 91.25 80 7 0 3 242 2060 2139 2e-40 148 NODE_3862_length_193_cov_173.751297 gi|253756581|ref|YP_003038496.1| 91.25 80 7 0 3 242 2060 2139 4e-40 147 NODE_3862_length_193_cov_173.751297 gi|253756582|ref|YP_003038495.1| 91.25 80 7 0 3 242 2060 2139 5e-40 147 NODE_3862_length_193_cov_173.751297 gi|253756606|ref|YP_003038519.1| 90.00 80 8 0 3 242 2060 2139 2e-39 145 NODE_3862_length_193_cov_173.751297 gi|253756607|ref|YP_003038518.1| 90.00 80 8 0 3 242 2060 2139 2e-39 145 NODE_3883_length_163_cov_166.533737 gi|38018023|ref|NP_937947.1| 98.57 70 1 0 211 2 2230 2299 2e-40 148 NODE_3883_length_163_cov_166.533737 gi|26008083|ref|NP_742169.1| 98.57 70 1 0 211 2 1379 1448 2e-40 147 NODE_3883_length_163_cov_166.533737 gi|253756594|ref|YP_003038508.1| 98.57 70 1 0 211 2 2230 2299 3e-40 147 NODE_3883_length_163_cov_166.533737 gi|253756581|ref|YP_003038496.1| 98.57 70 1 0 211 2 2230 2299 3e-40 147 NODE_3883_length_163_cov_166.533737 gi|15081555|ref|NP_150074.1| 98.57 70 1 0 211 2 2230 2299 3e-40 147 NODE_3883_length_163_cov_166.533737 gi|253756595|ref|YP_003038507.1| 98.57 70 1 0 211 2 2230 2299 4e-40 147 NODE_3883_length_163_cov_166.533737 gi|253756582|ref|YP_003038495.1| 98.57 70 1 0 211 2 2230 2299 4e-40 147 NODE_3883_length_163_cov_166.533737 gi|26008080|ref|NP_150073.2| 98.57 70 1 0 211 2 2230 2299 4e-40 147 NODE_3883_length_163_cov_166.533737 gi|167600355|ref|YP_001671997.1| 97.14 70 2 0 211 2 2276 2345 9e-40 146 NODE_3883_length_163_cov_166.533737 gi|167600354|ref|YP_001671996.1| 97.14 70 2 0 211 2 2276 2345 1e-39 145 NODE_3903_length_1067_cov_9.381443 gi|34538610|ref|NP_904340.1| 71.77 372 105 0 1116 1 3 374 2e-174 499 NODE_3903_length_1067_cov_9.381443 gi|251831119|ref|YP_003024038.1| 69.81 371 112 0 1113 1 4 374 7e-156 451 NODE_3903_length_1067_cov_9.381443 gi|494061236|ref|WP_007003318.1| 49.07 375 187 2 1113 1 18 392 2e-106 327 NODE_3903_length_1067_cov_9.381443 gi|488802282|ref|WP_002714688.1| 47.75 377 189 3 1113 1 17 391 8e-102 323 NODE_3903_length_1067_cov_9.381443 gi|492875618|ref|WP_006018984.1| 46.68 377 193 3 1113 1 17 391 8e-102 323 NODE_3903_length_1067_cov_9.381443 gi|488804222|ref|WP_002716628.1| 47.59 374 192 2 1113 4 17 390 4e-99 316 NODE_3903_length_1067_cov_9.381443 gi|490318665|ref|WP_004208160.1| 46.21 383 194 4 1113 1 19 401 1e-91 289 NODE_3903_length_1067_cov_9.381443 gi|489840120|ref|WP_003743825.1| 40.58 382 200 7 1098 34 21 402 9e-69 230 NODE_3903_length_1067_cov_9.381443 gi|489879342|ref|WP_003782815.1| 42.23 341 171 6 1113 169 16 356 4e-68 228 NODE_3903_length_1067_cov_9.381443 gi|488717304|ref|WP_002641180.1| 42.36 347 173 8 1113 154 17 363 7e-67 225 NODE_3927_length_241_cov_381.448120 gi|38018026|ref|NP_937950.1| 94.79 96 5 0 2 289 562 657 2e-55 191 NODE_3927_length_241_cov_381.448120 gi|394935454|ref|YP_005454245.1| 92.71 96 7 0 2 289 563 658 4e-55 191 NODE_3927_length_241_cov_381.448120 gi|253756585|ref|YP_003038499.1| 90.62 96 9 0 2 289 564 659 7e-55 189 NODE_3927_length_241_cov_381.448120 gi|15081547|ref|NP_150077.1| 90.62 96 9 0 2 289 564 659 8e-55 189 NODE_3927_length_241_cov_381.448120 gi|253756598|ref|YP_003038511.1| 90.62 96 9 0 2 289 564 659 1e-54 189 NODE_3927_length_241_cov_381.448120 gi|253756610|ref|YP_003038522.1| 88.54 96 11 0 2 289 564 659 3e-53 185 NODE_3927_length_241_cov_381.448120 gi|167600358|ref|YP_001672000.1| 71.88 96 27 0 2 289 564 659 9e-43 155 NODE_3927_length_241_cov_381.448120 gi|85718618|ref|YP_459952.1| 72.92 96 26 0 2 289 550 645 1e-42 155 NODE_3927_length_241_cov_381.448120 gi|253750535|ref|YP_003029848.1| 62.89 97 35 1 2 289 551 647 3e-34 130 NODE_3927_length_241_cov_381.448120 gi|60115395|ref|YP_209233.1| 59.00 100 37 2 2 289 561 660 4e-31 122 NODE_3950_length_493_cov_447.586212 gi|38018026|ref|NP_937950.1| 98.33 180 3 0 541 2 726 905 5e-114 360 NODE_3950_length_493_cov_447.586212 gi|253756610|ref|YP_003038522.1| 95.00 180 9 0 541 2 728 907 7e-110 348 NODE_3950_length_493_cov_447.586212 gi|253756585|ref|YP_003038499.1| 94.44 180 10 0 541 2 728 907 8e-110 348 NODE_3950_length_493_cov_447.586212 gi|15081547|ref|NP_150077.1| 94.44 180 10 0 541 2 728 907 2e-109 347 NODE_3950_length_493_cov_447.586212 gi|253756598|ref|YP_003038511.1| 94.44 180 10 0 541 2 728 907 2e-109 347 NODE_3950_length_493_cov_447.586212 gi|394935454|ref|YP_005454245.1| 93.89 180 11 0 541 2 727 906 6e-109 345 NODE_3950_length_493_cov_447.586212 gi|85718618|ref|YP_459952.1| 87.22 180 23 0 541 2 714 893 8e-103 328 NODE_3950_length_493_cov_447.586212 gi|167600358|ref|YP_001672000.1| 82.78 180 31 0 541 2 728 907 2e-96 310 NODE_3950_length_493_cov_447.586212 gi|253750535|ref|YP_003029848.1| 68.33 180 57 0 541 2 716 895 2e-79 263 NODE_3950_length_493_cov_447.586212 gi|60115395|ref|YP_209233.1| 67.22 180 59 0 541 2 729 908 7e-79 261 NODE_3954_length_225_cov_85.515556 gi|26008094|ref|NP_742142.1| 100.00 91 0 0 1 273 12 102 2e-59 190 NODE_3954_length_225_cov_85.515556 gi|38018023|ref|NP_937947.1| 100.00 91 0 0 1 273 6808 6898 1e-58 201 NODE_3954_length_225_cov_85.515556 gi|253756607|ref|YP_003038518.1| 100.00 91 0 0 1 273 6807 6897 1e-58 201 NODE_3954_length_225_cov_85.515556 gi|253756582|ref|YP_003038495.1| 100.00 91 0 0 1 273 6807 6897 1e-58 201 NODE_3954_length_225_cov_85.515556 gi|26008080|ref|NP_150073.2| 100.00 91 0 0 1 273 6807 6897 1e-58 201 NODE_3954_length_225_cov_85.515556 gi|253756595|ref|YP_003038507.1| 100.00 91 0 0 1 273 6807 6897 1e-58 201 NODE_3954_length_225_cov_85.515556 gi|85718615|ref|YP_459949.1| 100.00 91 0 0 1 273 6808 6898 1e-58 201 NODE_3954_length_225_cov_85.515556 gi|167600354|ref|YP_001671996.1| 97.80 91 2 0 1 273 6841 6931 1e-57 198 NODE_3954_length_225_cov_85.515556 gi|394935459|ref|YP_005454239.1| 95.60 91 4 0 1 273 6864 6954 8e-57 196 NODE_3954_length_225_cov_85.515556 gi|60115406|ref|YP_209243.1| 89.01 91 10 0 1 273 12 102 2e-53 175 NODE_3974_length_370_cov_90.656754 gi|26008091|ref|NP_742139.1| 99.29 140 1 0 420 1 22 161 3e-97 299 NODE_3974_length_370_cov_90.656754 gi|38018023|ref|NP_937947.1| 100.00 140 0 0 420 1 5319 5458 1e-91 298 NODE_3974_length_370_cov_90.656754 gi|26008080|ref|NP_150073.2| 99.29 140 1 0 420 1 5319 5458 2e-91 298 NODE_3974_length_370_cov_90.656754 gi|253756582|ref|YP_003038495.1| 99.29 140 1 0 420 1 5319 5458 3e-91 298 NODE_3974_length_370_cov_90.656754 gi|253756595|ref|YP_003038507.1| 99.29 140 1 0 420 1 5319 5458 3e-91 298 NODE_3974_length_370_cov_90.656754 gi|253756607|ref|YP_003038518.1| 99.29 140 1 0 420 1 5319 5458 3e-91 298 NODE_3974_length_370_cov_90.656754 gi|167600354|ref|YP_001671996.1| 99.29 140 1 0 420 1 5365 5504 3e-91 298 NODE_3974_length_370_cov_90.656754 gi|85718615|ref|YP_459949.1| 98.57 140 2 0 420 1 5319 5458 5e-91 297 NODE_3974_length_370_cov_90.656754 gi|25121570|ref|NP_740617.1| 92.14 140 11 0 420 1 22 161 9e-91 282 NODE_3974_length_370_cov_90.656754 gi|394935459|ref|YP_005454239.1| 97.86 140 3 0 420 1 5379 5518 2e-90 295 NODE_4055_length_206_cov_71.718445 gi|38018023|ref|NP_937947.1| 100.00 85 0 0 1 255 3477 3561 2e-50 177 NODE_4055_length_206_cov_71.718445 gi|85718615|ref|YP_459949.1| 97.65 85 2 0 1 255 3477 3561 5e-49 173 NODE_4055_length_206_cov_71.718445 gi|253756607|ref|YP_003038518.1| 97.65 85 2 0 1 255 3477 3561 1e-48 172 NODE_4055_length_206_cov_71.718445 gi|253756582|ref|YP_003038495.1| 97.65 85 2 0 1 255 3477 3561 1e-48 172 NODE_4055_length_206_cov_71.718445 gi|26008080|ref|NP_150073.2| 97.65 85 2 0 1 255 3477 3561 1e-48 172 NODE_4055_length_206_cov_71.718445 gi|167600354|ref|YP_001671996.1| 97.65 85 2 0 1 255 3523 3607 1e-48 172 NODE_4055_length_206_cov_71.718445 gi|253756595|ref|YP_003038507.1| 96.47 85 3 0 1 255 3477 3561 2e-48 172 NODE_4055_length_206_cov_71.718445 gi|253756606|ref|YP_003038519.1| 97.65 85 2 0 1 255 3477 3561 2e-48 171 NODE_4055_length_206_cov_71.718445 gi|253756581|ref|YP_003038496.1| 97.65 85 2 0 1 255 3477 3561 2e-48 171 NODE_4055_length_206_cov_71.718445 gi|15081555|ref|NP_150074.1| 97.65 85 2 0 1 255 3477 3561 8e-48 170 NODE_4128_length_290_cov_40.872414 gi|26008087|ref|NP_742135.1| 98.21 112 2 0 338 3 58 169 7e-74 225 NODE_4128_length_290_cov_40.872414 gi|38018023|ref|NP_937947.1| 100.00 112 0 0 338 3 3983 4094 2e-67 228 NODE_4128_length_290_cov_40.872414 gi|25121566|ref|NP_740613.1| 90.18 112 11 0 338 3 55 166 2e-67 209 NODE_4128_length_290_cov_40.872414 gi|85719069|ref|YP_460020.1| 87.50 112 14 0 338 3 55 166 2e-67 208 NODE_4128_length_290_cov_40.872414 gi|15081555|ref|NP_150074.1| 98.21 112 2 0 338 3 3983 4094 1e-66 225 NODE_4128_length_290_cov_40.872414 gi|253756581|ref|YP_003038496.1| 98.21 112 2 0 338 3 3983 4094 1e-66 225 NODE_4128_length_290_cov_40.872414 gi|253756594|ref|YP_003038508.1| 98.21 112 2 0 338 3 3983 4094 1e-66 225 NODE_4128_length_290_cov_40.872414 gi|253756606|ref|YP_003038519.1| 98.21 112 2 0 338 3 3983 4094 1e-66 225 NODE_4128_length_290_cov_40.872414 gi|167600355|ref|YP_001671997.1| 98.21 112 2 0 338 3 4029 4140 2e-66 225 NODE_4128_length_290_cov_40.872414 gi|253756607|ref|YP_003038518.1| 98.21 112 2 0 338 3 3983 4094 2e-66 225 NODE_4157_length_1497_cov_6.110220 gi|34538607|ref|NP_904337.1| 57.53 365 155 0 1103 9 59 423 9e-86 280 NODE_4157_length_1497_cov_6.110220 gi|251831116|ref|YP_003024035.1| 60.81 347 136 0 1049 9 77 423 9e-81 266 NODE_4157_length_1497_cov_6.110220 gi|488803228|ref|WP_002715634.1| 35.01 337 208 5 1109 105 83 410 6e-24 109 NODE_4157_length_1497_cov_6.110220 gi|492880177|ref|WP_006020755.1| 35.01 337 208 5 1109 105 83 410 7e-24 109 NODE_4157_length_1497_cov_6.110220 gi|488799188|ref|WP_002711594.1| 35.31 337 207 5 1109 105 86 413 8e-24 109 NODE_4157_length_1497_cov_6.110220 gi|494060702|ref|WP_007002785.1| 34.49 345 215 5 1145 117 73 408 2e-23 108 NODE_4157_length_1497_cov_6.110220 gi|490654140|ref|WP_004519131.1| 32.93 334 211 5 1109 126 81 407 8e-21 100 NODE_4157_length_1497_cov_6.110220 gi|489773080|ref|WP_003676981.1| 32.93 334 211 5 1109 126 81 407 2e-20 99.4 NODE_4157_length_1497_cov_6.110220 gi|489844193|ref|WP_003747888.1| 32.63 334 212 5 1109 126 81 407 2e-20 99.4 NODE_4157_length_1497_cov_6.110220 gi|488144434|ref|WP_002215642.1| 32.63 334 212 5 1109 126 81 407 3e-20 98.6 NODE_4164_length_250_cov_71.987999 gi|26008092|ref|NP_742140.1| 98.99 99 1 0 2 298 29 127 7e-63 206 NODE_4164_length_250_cov_71.987999 gi|253756595|ref|YP_003038507.1| 98.99 99 1 0 2 298 5929 6027 7e-60 205 NODE_4164_length_250_cov_71.987999 gi|253756582|ref|YP_003038495.1| 98.99 99 1 0 2 298 5929 6027 7e-60 205 NODE_4164_length_250_cov_71.987999 gi|26008080|ref|NP_150073.2| 98.99 99 1 0 2 298 5929 6027 7e-60 205 NODE_4164_length_250_cov_71.987999 gi|253756607|ref|YP_003038518.1| 98.99 99 1 0 2 298 5929 6027 8e-60 205 NODE_4164_length_250_cov_71.987999 gi|38018023|ref|NP_937947.1| 98.99 99 1 0 2 298 5929 6027 8e-60 205 NODE_4164_length_250_cov_71.987999 gi|85718615|ref|YP_459949.1| 97.98 99 2 0 2 298 5929 6027 5e-59 203 NODE_4164_length_250_cov_71.987999 gi|60115404|ref|YP_209241.1| 86.87 99 13 0 2 298 27 125 2e-56 189 NODE_4164_length_250_cov_71.987999 gi|25121571|ref|NP_740618.1| 86.87 99 13 0 2 298 29 127 7e-56 187 NODE_4164_length_250_cov_71.987999 gi|394935459|ref|YP_005454239.1| 89.90 99 10 0 2 298 5985 6083 2e-55 192 NODE_4191_length_210_cov_2.200000 gi|156071462|ref|NP_001627.2| 96.51 86 3 0 1 258 39 124 2e-55 180 NODE_4191_length_210_cov_2.200000 gi|156071462|ref|NP_001627.2| 38.24 34 21 0 25 126 247 280 1.9 31.2 NODE_4191_length_210_cov_2.200000 gi|22094075|ref|NP_031477.1| 96.51 86 3 0 1 258 39 124 5e-54 176 NODE_4191_length_210_cov_2.200000 gi|22094075|ref|NP_031477.1| 35.29 34 22 0 25 126 247 280 1.3 31.6 NODE_4191_length_210_cov_2.200000 gi|156071459|ref|NP_001143.2| 95.35 86 4 0 1 258 39 124 5e-53 174 NODE_4191_length_210_cov_2.200000 gi|156071459|ref|NP_001143.2| 35.29 34 22 0 25 126 247 280 2.5 30.8 NODE_4191_length_210_cov_2.200000 gi|148747424|ref|NP_031476.3| 93.02 86 6 0 1 258 39 124 2e-52 172 NODE_4191_length_210_cov_2.200000 gi|148747424|ref|NP_031476.3| 41.18 34 20 0 25 126 247 280 0.20 34.3 NODE_4191_length_210_cov_2.200000 gi|55749577|ref|NP_001142.2| 93.02 86 6 0 1 258 39 124 6e-52 171 NODE_4191_length_210_cov_2.200000 gi|55749577|ref|NP_001142.2| 38.46 39 24 0 10 126 242 280 0.11 34.7 NODE_4191_length_210_cov_2.200000 gi|13775208|ref|NP_112581.1| 74.42 86 22 0 1 258 51 136 2e-41 144 NODE_4191_length_210_cov_2.200000 gi|13775208|ref|NP_112581.1| 43.40 53 29 1 25 183 257 308 5e-05 45.1 NODE_4191_length_210_cov_2.200000 gi|13775208|ref|NP_112581.1| 34.62 26 17 0 28 105 163 188 7.0 29.6 NODE_4191_length_210_cov_2.200000 gi|254692892|ref|NP_848473.2| 73.26 86 23 0 1 258 52 137 3e-41 144 NODE_4191_length_210_cov_2.200000 gi|254692892|ref|NP_848473.2| 41.18 51 29 1 25 177 258 307 1e-04 43.9 NODE_4191_length_210_cov_2.200000 gi|27369998|ref|NP_766273.1| 36.67 60 38 0 73 252 241 300 1e-04 44.3 NODE_4191_length_210_cov_2.200000 gi|148491091|ref|NP_037518.3| 36.67 60 38 0 73 252 243 302 1e-04 44.3 NODE_4191_length_210_cov_2.200000 gi|148491091|ref|NP_037518.3| 29.31 58 41 0 34 207 323 380 0.026 37.0 NODE_4191_length_210_cov_2.200000 gi|47458041|ref|NP_998816.1| 36.67 60 38 0 73 252 224 283 1e-04 43.9 NODE_4191_length_210_cov_2.200000 gi|47458041|ref|NP_998816.1| 29.31 58 41 0 34 207 304 361 0.026 37.0 NODE_4225_length_322_cov_158.403732 gi|38018024|ref|NP_937948.1| 99.19 124 1 0 1 372 143 266 1e-87 263 NODE_4225_length_322_cov_158.403732 gi|253756608|ref|YP_003038520.1| 94.35 124 7 0 1 372 143 266 2e-82 250 NODE_4225_length_322_cov_158.403732 gi|253756596|ref|YP_003038509.1| 93.55 124 8 0 1 372 143 266 3e-82 249 NODE_4225_length_322_cov_158.403732 gi|253756583|ref|YP_003038497.1| 93.55 124 8 0 1 372 143 266 3e-82 249 NODE_4225_length_322_cov_158.403732 gi|15081545|ref|NP_150075.1| 91.94 124 10 0 1 372 143 266 3e-81 247 NODE_4225_length_322_cov_158.403732 gi|167600356|ref|YP_001671998.1| 72.13 122 34 0 4 369 144 265 3e-62 198 NODE_4225_length_322_cov_158.403732 gi|253750533|ref|YP_003029846.1| 46.72 122 60 1 19 369 142 263 3e-32 120 NODE_4225_length_322_cov_158.403732 gi|60115393|ref|YP_209231.1| 46.72 122 60 1 19 369 142 263 1e-31 119 NODE_4225_length_322_cov_158.403732 gi|394935452|ref|YP_005454243.1| 87.10 62 5 1 187 372 1 59 3e-31 112 NODE_4225_length_322_cov_158.403732 gi|11192310|ref|NP_068669.1| 46.28 121 60 1 22 369 151 271 3e-30 115 NODE_4240_length_404_cov_133.896042 gi|38018025|ref|NP_937949.1| 96.03 151 6 0 454 2 211 361 3e-99 299 NODE_4240_length_404_cov_133.896042 gi|253756584|ref|YP_003038498.1| 95.36 151 7 0 454 2 211 361 3e-99 299 NODE_4240_length_404_cov_133.896042 gi|15081546|ref|NP_150076.1| 95.36 151 7 0 454 2 211 361 4e-99 299 NODE_4240_length_404_cov_133.896042 gi|253756609|ref|YP_003038521.1| 94.70 151 8 0 454 2 211 361 3e-98 297 NODE_4240_length_404_cov_133.896042 gi|253756597|ref|YP_003038510.1| 94.70 151 8 0 454 2 211 361 4e-98 296 NODE_4240_length_404_cov_133.896042 gi|394935453|ref|YP_005454244.1| 94.04 151 9 0 454 2 211 361 3e-97 294 NODE_4240_length_404_cov_133.896042 gi|85718617|ref|YP_459951.1| 90.73 151 14 0 454 2 211 361 5e-95 288 NODE_4240_length_404_cov_133.896042 gi|167600357|ref|YP_001671999.1| 71.52 151 43 0 454 2 210 360 1e-71 228 NODE_4240_length_404_cov_133.896042 gi|253750534|ref|YP_003029847.1| 61.18 152 53 2 439 2 226 377 2e-55 186 NODE_4240_length_404_cov_133.896042 gi|11192311|ref|NP_068670.1| 57.89 152 58 2 439 2 99 250 7e-54 179 NODE_4243_length_386_cov_71.272018 gi|38018023|ref|NP_937947.1| 100.00 144 0 0 3 434 5191 5334 2e-92 301 NODE_4243_length_386_cov_71.272018 gi|253756595|ref|YP_003038507.1| 98.61 144 2 0 3 434 5191 5334 4e-91 297 NODE_4243_length_386_cov_71.272018 gi|253756582|ref|YP_003038495.1| 98.61 144 2 0 3 434 5191 5334 4e-91 297 NODE_4243_length_386_cov_71.272018 gi|26008080|ref|NP_150073.2| 98.61 144 2 0 3 434 5191 5334 4e-91 297 NODE_4243_length_386_cov_71.272018 gi|253756607|ref|YP_003038518.1| 98.61 144 2 0 3 434 5191 5334 4e-91 297 NODE_4243_length_386_cov_71.272018 gi|394935459|ref|YP_005454239.1| 98.61 144 2 0 3 434 5251 5394 5e-91 297 NODE_4243_length_386_cov_71.272018 gi|167600354|ref|YP_001671996.1| 98.61 144 2 0 3 434 5237 5380 5e-91 297 NODE_4243_length_386_cov_71.272018 gi|85718615|ref|YP_459949.1| 97.92 144 3 0 3 434 5191 5334 2e-90 296 NODE_4243_length_386_cov_71.272018 gi|253750532|ref|YP_003029844.1| 94.44 144 8 0 3 434 5272 5415 7e-87 285 NODE_4243_length_386_cov_71.272018 gi|26007546|ref|NP_068668.2| 93.75 144 9 0 3 434 5278 5421 1e-86 285 NODE_4282_length_145_cov_155.027588 gi|38018024|ref|NP_937948.1| 100.00 28 0 0 193 110 251 278 5e-12 63.2 NODE_4282_length_145_cov_155.027588 gi|38018025|ref|NP_937949.1| 96.77 31 1 0 95 3 1 31 8e-12 63.9 NODE_4282_length_145_cov_155.027588 gi|394935453|ref|YP_005454244.1| 93.55 31 2 0 95 3 1 31 3e-11 62.4 NODE_4282_length_145_cov_155.027588 gi|253756609|ref|YP_003038521.1| 90.32 31 3 0 95 3 1 31 4e-11 62.0 NODE_4282_length_145_cov_155.027588 gi|253756584|ref|YP_003038498.1| 90.32 31 3 0 95 3 1 31 5e-11 62.0 NODE_4282_length_145_cov_155.027588 gi|15081546|ref|NP_150076.1| 90.32 31 3 0 95 3 1 31 5e-11 61.6 NODE_4282_length_145_cov_155.027588 gi|253756597|ref|YP_003038510.1| 90.32 31 3 0 95 3 1 31 6e-11 61.6 NODE_4282_length_145_cov_155.027588 gi|253756608|ref|YP_003038520.1| 88.89 27 3 0 193 113 251 277 2e-08 53.9 NODE_4282_length_145_cov_155.027588 gi|15081545|ref|NP_150075.1| 88.89 27 3 0 193 113 251 277 2e-08 53.9 NODE_4282_length_145_cov_155.027588 gi|253756596|ref|YP_003038509.1| 88.89 27 3 0 193 113 251 277 2e-08 53.9 NODE_4313_length_149_cov_2.637584 gi|375151590|ref|NP_001243506.1| 98.48 66 1 0 2 199 18 83 6e-40 137 NODE_4313_length_149_cov_2.637584 gi|82931053|ref|XP_894815.1| 98.48 66 1 0 2 199 18 83 1e-39 136 NODE_4313_length_149_cov_2.637584 gi|242397462|ref|NP_001156405.1| 98.48 66 1 0 2 199 18 83 2e-39 135 NODE_4313_length_149_cov_2.637584 gi|223890243|ref|NP_006004.2| 98.48 66 1 0 2 199 18 83 2e-39 135 NODE_4313_length_149_cov_2.637584 gi|16418339|ref|NP_443067.1| 98.48 66 1 0 2 199 18 83 2e-39 135 NODE_4313_length_149_cov_2.637584 gi|309266590|ref|XP_003086805.1| 96.97 66 2 0 2 199 18 83 2e-38 133 NODE_4313_length_149_cov_2.637584 gi|18152783|ref|NP_542784.1| 95.45 66 3 0 2 199 18 83 1e-37 131 NODE_4313_length_149_cov_2.637584 gi|375151597|ref|NP_001243509.1| 45.45 66 0 1 2 199 18 47 1e-06 47.4 NODE_4313_length_149_cov_2.637584 gi|490135401|ref|WP_004035761.1| 31.15 61 39 1 14 196 10 67 2e-04 41.6 NODE_4313_length_149_cov_2.637584 gi|148643049|ref|YP_001273562.1| 31.15 61 39 1 14 196 10 67 2e-04 41.2 NODE_4345_length_248_cov_2.576613 gi|47132549|ref|NP_997639.1| 90.91 99 9 0 1 297 741 839 4e-52 182 NODE_4345_length_248_cov_2.576613 gi|47132549|ref|NP_997639.1| 26.97 89 64 1 16 282 1384 1471 3e-05 46.6 NODE_4345_length_248_cov_2.576613 gi|47132549|ref|NP_997639.1| 30.85 94 62 3 19 297 934 1025 0.002 41.2 NODE_4345_length_248_cov_2.576613 gi|47132549|ref|NP_997639.1| 26.80 97 68 1 16 297 1474 1570 0.003 40.4 NODE_4345_length_248_cov_2.576613 gi|47132549|ref|NP_997639.1| 25.51 98 71 2 4 297 1746 1841 0.052 36.6 NODE_4345_length_248_cov_2.576613 gi|47132549|ref|NP_997639.1| 26.88 93 67 1 19 297 1295 1386 0.053 36.6 NODE_4345_length_248_cov_2.576613 gi|47132549|ref|NP_997639.1| 32.84 67 44 1 97 297 1595 1660 0.94 32.7 NODE_4345_length_248_cov_2.576613 gi|47132553|ref|NP_997641.1| 90.91 99 9 0 1 297 741 839 5e-52 182 NODE_4345_length_248_cov_2.576613 gi|47132553|ref|NP_997641.1| 26.97 89 64 1 16 282 1384 1471 3e-05 46.6 NODE_4345_length_248_cov_2.576613 gi|47132553|ref|NP_997641.1| 30.85 94 62 3 19 297 934 1025 0.002 41.6 NODE_4345_length_248_cov_2.576613 gi|47132553|ref|NP_997641.1| 26.80 97 68 1 16 297 1474 1570 0.003 40.4 NODE_4345_length_248_cov_2.576613 gi|47132553|ref|NP_997641.1| 25.51 98 71 2 4 297 1746 1841 0.053 36.6 NODE_4345_length_248_cov_2.576613 gi|47132553|ref|NP_997641.1| 26.88 93 67 1 19 297 1295 1386 0.057 36.6 NODE_4345_length_248_cov_2.576613 gi|47132553|ref|NP_997641.1| 32.84 67 44 1 97 297 1595 1660 0.91 32.7 NODE_4345_length_248_cov_2.576613 gi|47132555|ref|NP_997643.1| 90.91 99 9 0 1 297 741 839 5e-52 182 NODE_4345_length_248_cov_2.576613 gi|47132555|ref|NP_997643.1| 26.97 89 64 1 16 282 1384 1471 3e-05 46.6 NODE_4345_length_248_cov_2.576613 gi|47132555|ref|NP_997643.1| 30.85 94 62 3 19 297 934 1025 0.002 41.6 NODE_4345_length_248_cov_2.576613 gi|47132555|ref|NP_997643.1| 26.80 97 68 1 16 297 1474 1570 0.003 40.4 NODE_4345_length_248_cov_2.576613 gi|47132555|ref|NP_997643.1| 25.51 98 71 2 4 297 1836 1931 0.051 36.6 NODE_4345_length_248_cov_2.576613 gi|47132555|ref|NP_997643.1| 26.88 93 67 1 19 297 1295 1386 0.055 36.6 NODE_4345_length_248_cov_2.576613 gi|47132555|ref|NP_997643.1| 32.84 67 44 1 97 297 1595 1660 0.44 33.9 NODE_4345_length_248_cov_2.576613 gi|47132555|ref|NP_997643.1| 27.96 93 66 1 19 297 1659 1750 0.45 33.5 NODE_4345_length_248_cov_2.576613 gi|16933542|ref|NP_002017.1| 90.91 99 9 0 1 297 741 839 6e-52 182 NODE_4345_length_248_cov_2.576613 gi|16933542|ref|NP_002017.1| 26.97 89 64 1 16 282 1384 1471 4e-05 46.6 NODE_4345_length_248_cov_2.576613 gi|16933542|ref|NP_002017.1| 30.85 94 62 3 19 297 934 1025 0.002 41.2 NODE_4345_length_248_cov_2.576613 gi|16933542|ref|NP_002017.1| 26.80 97 68 1 16 297 1474 1570 0.003 40.4 NODE_4345_length_248_cov_2.576613 gi|16933542|ref|NP_002017.1| 25.51 98 71 2 4 297 1836 1931 0.056 36.6 NODE_4345_length_248_cov_2.576613 gi|16933542|ref|NP_002017.1| 26.88 93 67 1 19 297 1295 1386 0.060 36.2 NODE_4345_length_248_cov_2.576613 gi|16933542|ref|NP_002017.1| 32.84 67 44 1 97 297 1595 1660 0.47 33.5 NODE_4345_length_248_cov_2.576613 gi|16933542|ref|NP_002017.1| 27.96 93 66 1 19 297 1659 1750 0.47 33.5 NODE_4345_length_248_cov_2.576613 gi|46849812|ref|NP_034363.1| 90.91 99 9 0 1 297 740 838 6e-52 182 NODE_4345_length_248_cov_2.576613 gi|46849812|ref|NP_034363.1| 33.33 93 59 3 19 294 933 1023 7e-04 42.4 NODE_4345_length_248_cov_2.576613 gi|46849812|ref|NP_034363.1| 25.51 98 71 2 4 297 1926 2021 0.007 39.3 NODE_4345_length_248_cov_2.576613 gi|46849812|ref|NP_034363.1| 31.08 74 50 1 76 297 1404 1476 0.008 39.3 NODE_4345_length_248_cov_2.576613 gi|46849812|ref|NP_034363.1| 23.71 97 71 1 16 297 1564 1660 0.030 37.4 NODE_4345_length_248_cov_2.576613 gi|46849812|ref|NP_034363.1| 25.00 88 65 1 19 282 1475 1561 0.073 36.2 NODE_4345_length_248_cov_2.576613 gi|46849812|ref|NP_034363.1| 32.84 67 44 1 97 297 1685 1750 0.20 34.7 NODE_4345_length_248_cov_2.576613 gi|47132557|ref|NP_997647.1| 90.91 99 9 0 1 297 741 839 7e-52 182 NODE_4345_length_248_cov_2.576613 gi|47132557|ref|NP_997647.1| 26.97 89 64 1 16 282 1475 1562 3e-05 46.6 NODE_4345_length_248_cov_2.576613 gi|47132557|ref|NP_997647.1| 30.85 94 62 3 19 297 934 1025 0.002 41.2 NODE_4345_length_248_cov_2.576613 gi|47132557|ref|NP_997647.1| 26.80 97 68 1 16 297 1565 1661 0.003 40.4 NODE_4345_length_248_cov_2.576613 gi|47132557|ref|NP_997647.1| 26.88 93 67 1 19 297 1386 1477 0.052 36.6 NODE_4345_length_248_cov_2.576613 gi|47132557|ref|NP_997647.1| 25.51 98 71 2 4 297 1927 2022 0.053 36.6 NODE_4345_length_248_cov_2.576613 gi|47132557|ref|NP_997647.1| 32.84 67 44 1 97 297 1686 1751 0.43 33.9 NODE_4345_length_248_cov_2.576613 gi|47132557|ref|NP_997647.1| 27.96 93 66 1 19 297 1750 1841 0.45 33.9 NODE_4345_length_248_cov_2.576613 gi|20665034|ref|NP_115859.2| 32.22 90 57 3 28 294 215 301 6e-05 45.4 NODE_4345_length_248_cov_2.576613 gi|188528648|ref|NP_061978.6| 32.22 90 57 3 28 294 3784 3870 6e-05 45.8 NODE_4345_length_248_cov_2.576613 gi|188528648|ref|NP_061978.6| 29.90 97 57 3 28 294 3194 3287 0.004 40.0 NODE_4345_length_248_cov_2.576613 gi|188528648|ref|NP_061978.6| 28.87 97 67 2 7 294 772 867 0.011 38.5 NODE_4345_length_248_cov_2.576613 gi|188528648|ref|NP_061978.6| 28.42 95 58 3 28 288 1607 1699 0.11 35.4 NODE_4345_length_248_cov_2.576613 gi|188528648|ref|NP_061978.6| 27.55 98 57 4 28 288 2125 2219 0.12 35.4 NODE_4345_length_248_cov_2.576613 gi|188528648|ref|NP_061978.6| 26.36 110 55 4 28 288 2441 2547 0.91 32.7 NODE_4345_length_248_cov_2.576613 gi|188528648|ref|NP_061978.6| 26.47 102 57 4 28 288 1504 1602 6.8 30.4 NODE_4345_length_248_cov_2.576613 gi|188528648|ref|NP_061978.6| 24.04 104 60 3 28 288 2766 2867 8.6 30.0 NODE_4345_length_248_cov_2.576613 gi|188528648|ref|NP_061978.6| 23.85 109 59 4 28 288 1291 1397 9.5 29.6 NODE_4345_length_248_cov_2.576613 gi|226958549|ref|NP_071707.2| 38.03 71 43 1 82 294 462 531 3e-04 43.5 NODE_4345_length_248_cov_2.576613 gi|226958549|ref|NP_071707.2| 32.39 71 45 2 82 291 732 800 0.31 34.3 NODE_4345_length_248_cov_2.576613 gi|226958549|ref|NP_071707.2| 28.57 70 47 2 85 294 647 713 1.2 32.3 NODE_4345_length_248_cov_2.576613 gi|226958549|ref|NP_071707.2| 30.99 71 48 1 82 294 822 891 1.9 32.0 NODE_4345_length_248_cov_2.576613 gi|54607033|ref|NP_001005731.1| 30.36 112 56 4 19 291 1487 1597 0.001 41.6 NODE_4487_length_453_cov_43.684326 gi|26008090|ref|NP_742138.1| 99.40 167 1 0 501 1 205 371 2e-114 353 NODE_4487_length_453_cov_43.684326 gi|38018023|ref|NP_937947.1| 100.00 167 0 0 501 1 4574 4740 2e-111 357 NODE_4487_length_453_cov_43.684326 gi|253756582|ref|YP_003038495.1| 99.40 167 1 0 501 1 4574 4740 6e-111 355 NODE_4487_length_453_cov_43.684326 gi|26008080|ref|NP_150073.2| 99.40 167 1 0 501 1 4574 4740 6e-111 355 NODE_4487_length_453_cov_43.684326 gi|85718615|ref|YP_459949.1| 99.40 167 1 0 501 1 4574 4740 6e-111 355 NODE_4487_length_453_cov_43.684326 gi|253756595|ref|YP_003038507.1| 99.40 167 1 0 501 1 4574 4740 6e-111 355 NODE_4487_length_453_cov_43.684326 gi|253756607|ref|YP_003038518.1| 99.40 167 1 0 501 1 4574 4740 7e-111 355 NODE_4487_length_453_cov_43.684326 gi|167600354|ref|YP_001671996.1| 96.41 167 6 0 501 1 4620 4786 3e-108 348 NODE_4487_length_453_cov_43.684326 gi|394935459|ref|YP_005454239.1| 94.61 167 9 0 501 1 4634 4800 2e-107 345 NODE_4487_length_453_cov_43.684326 gi|25121569|ref|NP_740616.1| 87.43 167 21 0 501 1 205 371 7e-101 317 NODE_4518_length_558_cov_97.378136 gi|38018023|ref|NP_937947.1| 99.01 202 2 0 606 1 6612 6813 6e-121 386 NODE_4518_length_558_cov_97.378136 gi|85718615|ref|YP_459949.1| 96.53 202 7 0 606 1 6612 6813 2e-117 376 NODE_4518_length_558_cov_97.378136 gi|253756607|ref|YP_003038518.1| 96.52 201 6 1 603 1 6613 6812 4e-116 372 NODE_4518_length_558_cov_97.378136 gi|253756595|ref|YP_003038507.1| 96.52 201 6 1 603 1 6613 6812 5e-116 372 NODE_4518_length_558_cov_97.378136 gi|253756582|ref|YP_003038495.1| 96.02 201 7 1 603 1 6613 6812 1e-115 371 NODE_4518_length_558_cov_97.378136 gi|26008080|ref|NP_150073.2| 96.02 201 7 1 603 1 6613 6812 1e-115 371 NODE_4518_length_558_cov_97.378136 gi|167600354|ref|YP_001671996.1| 95.00 200 5 1 600 1 6652 6846 1e-112 362 NODE_4518_length_558_cov_97.378136 gi|26008093|ref|NP_742141.1| 95.65 184 7 1 603 52 192 374 1e-111 332 NODE_4518_length_558_cov_97.378136 gi|394935459|ref|YP_005454239.1| 88.12 202 24 0 606 1 6668 6869 3e-98 320 NODE_4518_length_558_cov_97.378136 gi|26007546|ref|NP_068668.2| 78.50 200 42 1 600 1 6698 6896 3e-91 300 NODE_4564_length_261_cov_64.168579 gi|26008084|ref|NP_742132.1| 99.03 103 1 0 309 1 1 103 4e-68 213 NODE_4564_length_261_cov_64.168579 gi|167600355|ref|YP_001671997.1| 99.03 103 1 0 309 1 3293 3395 3e-63 215 NODE_4564_length_261_cov_64.168579 gi|15081555|ref|NP_150074.1| 99.03 103 1 0 309 1 3247 3349 4e-63 215 NODE_4564_length_261_cov_64.168579 gi|253756594|ref|YP_003038508.1| 99.03 103 1 0 309 1 3247 3349 4e-63 215 NODE_4564_length_261_cov_64.168579 gi|253756581|ref|YP_003038496.1| 99.03 103 1 0 309 1 3247 3349 4e-63 215 NODE_4564_length_261_cov_64.168579 gi|253756606|ref|YP_003038519.1| 99.03 103 1 0 309 1 3247 3349 4e-63 215 NODE_4564_length_261_cov_64.168579 gi|253756582|ref|YP_003038495.1| 99.03 103 1 0 309 1 3247 3349 5e-63 214 NODE_4564_length_261_cov_64.168579 gi|26008080|ref|NP_150073.2| 99.03 103 1 0 309 1 3247 3349 5e-63 214 NODE_4564_length_261_cov_64.168579 gi|253756595|ref|YP_003038507.1| 99.03 103 1 0 309 1 3247 3349 6e-63 214 NODE_4564_length_261_cov_64.168579 gi|253756607|ref|YP_003038518.1| 99.03 103 1 0 309 1 3247 3349 6e-63 214 NODE_4565_length_451_cov_47.064301 gi|253756606|ref|YP_003038519.1| 98.80 167 2 0 1 501 3096 3262 2e-108 348 NODE_4565_length_451_cov_47.064301 gi|167600355|ref|YP_001671997.1| 98.20 167 3 0 1 501 3142 3308 4e-108 347 NODE_4565_length_451_cov_47.064301 gi|253756581|ref|YP_003038496.1| 98.20 167 3 0 1 501 3096 3262 4e-108 347 NODE_4565_length_451_cov_47.064301 gi|253756594|ref|YP_003038508.1| 98.20 167 3 0 1 501 3096 3262 4e-108 347 NODE_4565_length_451_cov_47.064301 gi|15081555|ref|NP_150074.1| 98.20 167 3 0 1 501 3096 3262 4e-108 347 NODE_4565_length_451_cov_47.064301 gi|253756607|ref|YP_003038518.1| 98.80 167 2 0 1 501 3096 3262 4e-108 347 NODE_4565_length_451_cov_47.064301 gi|38018023|ref|NP_937947.1| 98.80 167 2 0 1 501 3096 3262 4e-108 347 NODE_4565_length_451_cov_47.064301 gi|253756595|ref|YP_003038507.1| 98.20 167 3 0 1 501 3096 3262 8e-108 347 NODE_4565_length_451_cov_47.064301 gi|253756582|ref|YP_003038495.1| 98.20 167 3 0 1 501 3096 3262 8e-108 347 NODE_4565_length_451_cov_47.064301 gi|26008080|ref|NP_150073.2| 98.20 167 3 0 1 501 3096 3262 8e-108 347 NODE_4615_length_136_cov_46.544117 gi|26008091|ref|NP_742139.1| 100.00 61 0 0 185 3 186 246 3e-34 127 NODE_4615_length_136_cov_46.544117 gi|167600354|ref|YP_001671996.1| 100.00 61 0 0 185 3 5529 5589 3e-33 127 NODE_4615_length_136_cov_46.544117 gi|85718615|ref|YP_459949.1| 100.00 61 0 0 185 3 5483 5543 3e-33 127 NODE_4615_length_136_cov_46.544117 gi|253756595|ref|YP_003038507.1| 100.00 61 0 0 185 3 5483 5543 3e-33 127 NODE_4615_length_136_cov_46.544117 gi|253756582|ref|YP_003038495.1| 100.00 61 0 0 185 3 5483 5543 3e-33 127 NODE_4615_length_136_cov_46.544117 gi|26008080|ref|NP_150073.2| 100.00 61 0 0 185 3 5483 5543 3e-33 127 NODE_4615_length_136_cov_46.544117 gi|38018023|ref|NP_937947.1| 100.00 61 0 0 185 3 5483 5543 3e-33 127 NODE_4615_length_136_cov_46.544117 gi|253756607|ref|YP_003038518.1| 100.00 61 0 0 185 3 5483 5543 4e-33 126 NODE_4615_length_136_cov_46.544117 gi|394935459|ref|YP_005454239.1| 98.36 61 1 0 185 3 5543 5603 5e-33 126 NODE_4615_length_136_cov_46.544117 gi|25121570|ref|NP_740617.1| 91.80 61 5 0 185 3 186 246 1e-31 120 NODE_4640_length_153_cov_1.307190 gi|493308571|ref|WP_006266084.1| 37.10 62 39 0 202 17 333 394 0.003 39.3 NODE_4640_length_153_cov_1.307190 gi|493304973|ref|WP_006262529.1| 37.10 62 39 0 202 17 333 394 0.004 39.3 NODE_4640_length_153_cov_1.307190 gi|493300186|ref|WP_006257801.1| 37.10 62 39 0 202 17 333 394 0.004 39.3 NODE_4640_length_153_cov_1.307190 gi|489079252|ref|WP_002989190.1| 35.38 65 42 0 196 2 335 399 0.004 38.9 NODE_4640_length_153_cov_1.307190 gi|489088389|ref|WP_002998290.1| 41.94 62 36 0 202 17 333 394 0.008 38.1 NODE_4640_length_153_cov_1.307190 gi|490516256|ref|WP_004381808.1| 72.73 22 6 0 202 137 276 297 0.023 36.6 NODE_4640_length_153_cov_1.307190 gi|494222853|ref|WP_007135001.1| 42.50 40 23 0 202 83 276 315 0.037 36.2 NODE_4640_length_153_cov_1.307190 gi|489099428|ref|WP_003009297.1| 40.32 62 37 0 202 17 333 394 0.040 36.2 NODE_4640_length_153_cov_1.307190 gi|490512353|ref|WP_004377959.1| 42.50 40 23 0 202 83 276 315 0.079 35.0 NODE_4640_length_153_cov_1.307190 gi|490506982|ref|WP_004373026.1| 42.50 40 23 0 202 83 276 315 0.082 35.0 NODE_4642_length_542_cov_46.265682 gi|38018023|ref|NP_937947.1| 99.49 196 1 0 590 3 3788 3983 2e-125 399 NODE_4642_length_542_cov_46.265682 gi|85718615|ref|YP_459949.1| 97.96 196 4 0 590 3 3788 3983 1e-122 390 NODE_4642_length_542_cov_46.265682 gi|253756594|ref|YP_003038508.1| 97.45 196 5 0 590 3 3788 3983 1e-122 390 NODE_4642_length_542_cov_46.265682 gi|167600355|ref|YP_001671997.1| 97.45 196 5 0 590 3 3834 4029 1e-122 390 NODE_4642_length_542_cov_46.265682 gi|253756606|ref|YP_003038519.1| 97.45 196 5 0 590 3 3788 3983 2e-122 390 NODE_4642_length_542_cov_46.265682 gi|15081555|ref|NP_150074.1| 97.45 196 5 0 590 3 3788 3983 2e-122 390 NODE_4642_length_542_cov_46.265682 gi|253756581|ref|YP_003038496.1| 97.45 196 5 0 590 3 3788 3983 2e-122 390 NODE_4642_length_542_cov_46.265682 gi|253756595|ref|YP_003038507.1| 97.45 196 5 0 590 3 3788 3983 3e-122 389 NODE_4642_length_542_cov_46.265682 gi|26008080|ref|NP_150073.2| 97.45 196 5 0 590 3 3788 3983 3e-122 389 NODE_4642_length_542_cov_46.265682 gi|253756607|ref|YP_003038518.1| 97.45 196 5 0 590 3 3788 3983 3e-122 389 NODE_4735_length_230_cov_1.847826 gi|47132549|ref|NP_997639.1| 82.42 91 16 0 6 278 864 954 1e-43 158 NODE_4735_length_230_cov_1.847826 gi|47132549|ref|NP_997639.1| 36.78 87 47 2 3 263 960 1038 4e-10 61.2 NODE_4735_length_230_cov_1.847826 gi|47132549|ref|NP_997639.1| 36.05 86 48 1 3 260 1595 1673 3e-09 58.9 NODE_4735_length_230_cov_1.847826 gi|47132549|ref|NP_997639.1| 35.56 90 47 2 3 260 1501 1583 6e-09 57.8 NODE_4735_length_230_cov_1.847826 gi|47132549|ref|NP_997639.1| 30.23 86 53 1 6 263 1322 1400 1e-07 53.5 NODE_4735_length_230_cov_1.847826 gi|47132549|ref|NP_997639.1| 27.37 95 52 2 6 260 1777 1864 1e-06 50.8 NODE_4735_length_230_cov_1.847826 gi|47132549|ref|NP_997639.1| 33.73 83 47 3 3 248 1230 1305 1e-06 50.8 NODE_4735_length_230_cov_1.847826 gi|47132549|ref|NP_997639.1| 29.87 77 48 1 3 233 773 843 3e-05 47.0 NODE_4735_length_230_cov_1.847826 gi|47132549|ref|NP_997639.1| 35.53 76 42 3 6 233 1412 1480 2e-04 44.3 NODE_4735_length_230_cov_1.847826 gi|47132549|ref|NP_997639.1| 28.57 84 53 2 3 251 1685 1762 5e-04 42.7 NODE_4735_length_230_cov_1.847826 gi|47132549|ref|NP_997639.1| 27.96 93 57 4 6 278 1137 1221 1.2 32.3 NODE_4735_length_230_cov_1.847826 gi|47132549|ref|NP_997639.1| 31.75 63 37 1 15 203 1053 1109 9.4 29.6 NODE_4735_length_230_cov_1.847826 gi|47132555|ref|NP_997643.1| 82.42 91 16 0 6 278 864 954 1e-43 157 NODE_4735_length_230_cov_1.847826 gi|47132555|ref|NP_997643.1| 36.78 87 47 2 3 263 960 1038 4e-10 61.2 NODE_4735_length_230_cov_1.847826 gi|47132555|ref|NP_997643.1| 35.37 82 46 1 15 260 1689 1763 5e-10 60.8 NODE_4735_length_230_cov_1.847826 gi|47132555|ref|NP_997643.1| 35.56 90 47 2 3 260 1501 1583 7e-09 57.8 NODE_4735_length_230_cov_1.847826 gi|47132555|ref|NP_997643.1| 30.23 86 53 1 6 263 1322 1400 2e-07 53.5 NODE_4735_length_230_cov_1.847826 gi|47132555|ref|NP_997643.1| 33.73 83 47 3 3 248 1230 1305 1e-06 50.8 NODE_4735_length_230_cov_1.847826 gi|47132555|ref|NP_997643.1| 27.37 95 52 2 6 260 1867 1954 1e-06 50.8 NODE_4735_length_230_cov_1.847826 gi|47132555|ref|NP_997643.1| 38.96 77 40 2 3 233 1595 1664 1e-05 48.1 NODE_4735_length_230_cov_1.847826 gi|47132555|ref|NP_997643.1| 29.87 77 48 1 3 233 773 843 2e-05 47.0 NODE_4735_length_230_cov_1.847826 gi|47132555|ref|NP_997643.1| 35.53 76 42 3 6 233 1412 1480 2e-04 44.3 NODE_4735_length_230_cov_1.847826 gi|47132555|ref|NP_997643.1| 28.57 84 53 2 3 251 1775 1852 5e-04 42.7 NODE_4735_length_230_cov_1.847826 gi|47132555|ref|NP_997643.1| 27.96 93 57 4 6 278 1137 1221 1.3 32.0 NODE_4735_length_230_cov_1.847826 gi|47132555|ref|NP_997643.1| 31.75 63 37 1 15 203 1053 1109 9.7 29.6 NODE_4735_length_230_cov_1.847826 gi|16933542|ref|NP_002017.1| 82.42 91 16 0 6 278 864 954 2e-43 157 NODE_4735_length_230_cov_1.847826 gi|16933542|ref|NP_002017.1| 36.78 87 47 2 3 263 960 1038 5e-10 61.2 NODE_4735_length_230_cov_1.847826 gi|16933542|ref|NP_002017.1| 35.37 82 46 1 15 260 1689 1763 5e-10 60.8 NODE_4735_length_230_cov_1.847826 gi|16933542|ref|NP_002017.1| 35.56 90 47 2 3 260 1501 1583 7e-09 57.8 NODE_4735_length_230_cov_1.847826 gi|16933542|ref|NP_002017.1| 30.23 86 53 1 6 263 1322 1400 2e-07 53.5 NODE_4735_length_230_cov_1.847826 gi|16933542|ref|NP_002017.1| 33.73 83 47 3 3 248 1230 1305 1e-06 50.8 NODE_4735_length_230_cov_1.847826 gi|16933542|ref|NP_002017.1| 27.37 95 52 2 6 260 1867 1954 1e-06 50.8 NODE_4735_length_230_cov_1.847826 gi|16933542|ref|NP_002017.1| 38.96 77 40 2 3 233 1595 1664 1e-05 48.1 NODE_4735_length_230_cov_1.847826 gi|16933542|ref|NP_002017.1| 29.87 77 48 1 3 233 773 843 2e-05 47.0 NODE_4735_length_230_cov_1.847826 gi|16933542|ref|NP_002017.1| 35.53 76 42 3 6 233 1412 1480 2e-04 44.3 NODE_4735_length_230_cov_1.847826 gi|16933542|ref|NP_002017.1| 28.57 84 53 2 3 251 1775 1852 5e-04 42.7 NODE_4735_length_230_cov_1.847826 gi|16933542|ref|NP_002017.1| 32.84 67 44 1 3 203 1956 2021 0.006 39.3 NODE_4735_length_230_cov_1.847826 gi|16933542|ref|NP_002017.1| 27.96 93 57 4 6 278 1137 1221 1.3 32.0 NODE_4735_length_230_cov_1.847826 gi|16933542|ref|NP_002017.1| 31.75 63 37 1 15 203 1053 1109 9.6 29.6 NODE_4735_length_230_cov_1.847826 gi|47132553|ref|NP_997641.1| 82.42 91 16 0 6 278 864 954 2e-43 157 NODE_4735_length_230_cov_1.847826 gi|47132553|ref|NP_997641.1| 36.78 87 47 2 3 263 960 1038 5e-10 61.2 NODE_4735_length_230_cov_1.847826 gi|47132553|ref|NP_997641.1| 36.05 86 48 1 3 260 1595 1673 3e-09 58.5 NODE_4735_length_230_cov_1.847826 gi|47132553|ref|NP_997641.1| 35.56 90 47 2 3 260 1501 1583 7e-09 57.8 NODE_4735_length_230_cov_1.847826 gi|47132553|ref|NP_997641.1| 30.23 86 53 1 6 263 1322 1400 2e-07 53.5 NODE_4735_length_230_cov_1.847826 gi|47132553|ref|NP_997641.1| 33.73 83 47 3 3 248 1230 1305 1e-06 50.8 NODE_4735_length_230_cov_1.847826 gi|47132553|ref|NP_997641.1| 27.37 95 52 2 6 260 1777 1864 1e-06 50.4 NODE_4735_length_230_cov_1.847826 gi|47132553|ref|NP_997641.1| 29.87 77 48 1 3 233 773 843 2e-05 47.0 NODE_4735_length_230_cov_1.847826 gi|47132553|ref|NP_997641.1| 35.53 76 42 3 6 233 1412 1480 2e-04 44.3 NODE_4735_length_230_cov_1.847826 gi|47132553|ref|NP_997641.1| 28.57 84 53 2 3 251 1685 1762 6e-04 42.7 NODE_4735_length_230_cov_1.847826 gi|47132553|ref|NP_997641.1| 32.84 67 44 1 3 203 1866 1931 0.006 39.3 NODE_4735_length_230_cov_1.847826 gi|47132553|ref|NP_997641.1| 27.96 93 57 4 6 278 1137 1221 1.3 32.0 NODE_4735_length_230_cov_1.847826 gi|47132553|ref|NP_997641.1| 31.75 63 37 1 15 203 1053 1109 9.2 29.6 NODE_4735_length_230_cov_1.847826 gi|47132557|ref|NP_997647.1| 82.42 91 16 0 6 278 864 954 2e-43 157 NODE_4735_length_230_cov_1.847826 gi|47132557|ref|NP_997647.1| 36.78 87 47 2 3 263 960 1038 5e-10 60.8 NODE_4735_length_230_cov_1.847826 gi|47132557|ref|NP_997647.1| 35.37 82 46 1 15 260 1780 1854 6e-10 60.8 NODE_4735_length_230_cov_1.847826 gi|47132557|ref|NP_997647.1| 37.08 89 42 4 3 248 1230 1311 2e-09 59.3 NODE_4735_length_230_cov_1.847826 gi|47132557|ref|NP_997647.1| 35.56 90 47 2 3 260 1592 1674 7e-09 57.4 NODE_4735_length_230_cov_1.847826 gi|47132557|ref|NP_997647.1| 30.23 86 53 1 6 263 1413 1491 2e-07 53.5 NODE_4735_length_230_cov_1.847826 gi|47132557|ref|NP_997647.1| 27.37 95 52 2 6 260 1958 2045 2e-06 50.4 NODE_4735_length_230_cov_1.847826 gi|47132557|ref|NP_997647.1| 38.96 77 40 2 3 233 1686 1755 1e-05 47.8 NODE_4735_length_230_cov_1.847826 gi|47132557|ref|NP_997647.1| 29.87 77 48 1 3 233 773 843 3e-05 46.6 NODE_4735_length_230_cov_1.847826 gi|47132557|ref|NP_997647.1| 35.53 76 42 3 6 233 1503 1571 2e-04 44.3 NODE_4735_length_230_cov_1.847826 gi|47132557|ref|NP_997647.1| 31.25 80 47 2 12 248 1324 1396 5e-04 42.7 NODE_4735_length_230_cov_1.847826 gi|47132557|ref|NP_997647.1| 28.57 84 53 2 3 251 1866 1943 6e-04 42.7 NODE_4735_length_230_cov_1.847826 gi|47132557|ref|NP_997647.1| 32.84 67 44 1 3 203 2047 2112 0.007 39.3 NODE_4735_length_230_cov_1.847826 gi|47132557|ref|NP_997647.1| 27.96 93 57 4 6 278 1137 1221 1.3 32.0 NODE_4735_length_230_cov_1.847826 gi|46849812|ref|NP_034363.1| 81.32 91 17 0 6 278 863 953 2e-42 154 NODE_4735_length_230_cov_1.847826 gi|46849812|ref|NP_034363.1| 36.78 87 47 2 3 263 959 1037 5e-10 60.8 NODE_4735_length_230_cov_1.847826 gi|46849812|ref|NP_034363.1| 38.20 89 41 4 3 248 1229 1310 1e-09 60.1 NODE_4735_length_230_cov_1.847826 gi|46849812|ref|NP_034363.1| 32.93 82 48 1 15 260 1779 1853 4e-07 52.4 NODE_4735_length_230_cov_1.847826 gi|46849812|ref|NP_034363.1| 32.22 90 50 2 3 260 1591 1673 7e-07 51.6 NODE_4735_length_230_cov_1.847826 gi|46849812|ref|NP_034363.1| 38.96 77 40 2 3 233 1685 1754 3e-06 49.7 NODE_4735_length_230_cov_1.847826 gi|46849812|ref|NP_034363.1| 26.32 95 53 2 6 260 1957 2044 8e-06 48.1 NODE_4735_length_230_cov_1.847826 gi|46849812|ref|NP_034363.1| 35.53 76 42 1 6 233 1502 1570 1e-05 48.1 NODE_4735_length_230_cov_1.847826 gi|46849812|ref|NP_034363.1| 28.57 77 49 1 3 233 772 842 6e-05 45.8 NODE_4735_length_230_cov_1.847826 gi|46849812|ref|NP_034363.1| 29.76 84 52 2 3 251 1865 1942 4e-04 43.1 NODE_4735_length_230_cov_1.847826 gi|46849812|ref|NP_034363.1| 28.38 74 46 1 6 227 1412 1478 6e-04 42.4 NODE_4735_length_230_cov_1.847826 gi|46849812|ref|NP_034363.1| 32.84 67 38 1 12 212 1323 1382 7e-04 42.4 NODE_4735_length_230_cov_1.847826 gi|46849812|ref|NP_034363.1| 32.84 67 44 1 3 203 2046 2111 0.006 39.3 NODE_4735_length_230_cov_1.847826 gi|46849812|ref|NP_034363.1| 27.96 93 57 4 6 278 1136 1220 0.80 32.7 NODE_4735_length_230_cov_1.847826 gi|153946395|ref|NP_002151.2| 36.36 77 42 1 3 233 948 1017 4e-09 58.2 NODE_4735_length_230_cov_1.847826 gi|153946395|ref|NP_002151.2| 30.99 71 42 1 15 227 1854 1917 4e-04 43.1 NODE_4735_length_230_cov_1.847826 gi|153946395|ref|NP_002151.2| 31.34 67 39 1 3 203 675 734 6e-04 42.4 NODE_4735_length_230_cov_1.847826 gi|153946395|ref|NP_002151.2| 23.08 78 53 1 15 248 1677 1747 0.005 39.7 NODE_4735_length_230_cov_1.847826 gi|153946395|ref|NP_002151.2| 29.33 75 46 1 3 227 1762 1829 0.38 33.9 NODE_4735_length_230_cov_1.847826 gi|153946395|ref|NP_002151.2| 25.00 88 55 3 3 254 766 846 0.65 33.1 NODE_4735_length_230_cov_1.847826 gi|126722834|ref|NP_035737.2| 35.06 77 43 1 3 233 948 1017 2e-07 53.1 NODE_4735_length_230_cov_1.847826 gi|126722834|ref|NP_035737.2| 32.84 67 38 1 3 203 675 734 2e-04 44.3 NODE_4735_length_230_cov_1.847826 gi|126722834|ref|NP_035737.2| 24.36 78 52 1 15 248 1495 1565 0.001 41.6 NODE_4735_length_230_cov_1.847826 gi|126722834|ref|NP_035737.2| 30.99 71 42 1 15 227 1672 1735 0.001 41.6 NODE_4735_length_230_cov_1.847826 gi|126722834|ref|NP_035737.2| 30.67 75 45 2 3 227 1580 1647 0.031 37.0 NODE_4735_length_230_cov_1.847826 gi|126722834|ref|NP_035737.2| 23.86 88 56 3 3 254 766 846 5.1 30.4 NODE_4735_length_230_cov_1.847826 gi|157384973|ref|NP_003276.3| 32.10 81 48 1 3 245 649 722 3e-07 52.8 NODE_4735_length_230_cov_1.847826 gi|157384973|ref|NP_003276.3| 31.40 86 52 1 3 260 378 456 9e-07 51.2 NODE_4735_length_230_cov_1.847826 gi|157384973|ref|NP_003276.3| 30.23 86 49 3 15 272 831 905 0.44 33.5 NODE_4735_length_230_cov_1.847826 gi|157384973|ref|NP_003276.3| 27.14 70 44 1 24 233 564 626 1.8 31.6 NODE_4735_length_230_cov_1.847826 gi|157384973|ref|NP_003276.3| 26.39 72 46 1 3 218 467 531 2.5 31.2 NODE_4735_length_230_cov_1.847826 gi|157384973|ref|NP_003276.3| 26.76 71 45 1 15 227 1008 1071 7.1 30.0 NODE_4735_length_230_cov_1.847826 gi|226958549|ref|NP_071707.2| 30.86 81 49 1 3 245 649 722 8e-07 51.2 NODE_4735_length_230_cov_1.847826 gi|226958549|ref|NP_071707.2| 31.40 86 52 1 3 260 378 456 2e-06 50.1 NODE_4735_length_230_cov_1.847826 gi|226958549|ref|NP_071707.2| 35.29 68 37 1 3 206 737 797 0.24 34.3 NODE_4735_length_230_cov_1.847826 gi|226958549|ref|NP_071707.2| 27.78 72 45 1 3 218 467 531 0.51 33.5 NODE_4735_length_230_cov_1.847826 gi|226958549|ref|NP_071707.2| 27.14 70 44 1 24 233 564 626 1.3 32.0 NODE_4735_length_230_cov_1.847826 gi|226958549|ref|NP_071707.2| 24.00 75 50 1 3 227 916 983 4.5 30.4 NODE_4735_length_230_cov_1.847826 gi|226958549|ref|NP_071707.2| 26.76 71 45 1 15 227 1008 1071 5.8 30.0 NODE_4736_length_116_cov_134.034485 gi|38018024|ref|NP_937948.1| 98.18 55 1 0 1 165 51 105 1e-30 114 NODE_4736_length_116_cov_134.034485 gi|253756596|ref|YP_003038509.1| 92.73 55 4 0 1 165 51 105 3e-29 110 NODE_4736_length_116_cov_134.034485 gi|253756583|ref|YP_003038497.1| 92.73 55 4 0 1 165 51 105 3e-29 110 NODE_4736_length_116_cov_134.034485 gi|15081545|ref|NP_150075.1| 92.73 55 4 0 1 165 51 105 3e-29 110 NODE_4736_length_116_cov_134.034485 gi|85718616|ref|YP_459950.1| 90.91 55 5 0 1 165 51 105 8e-29 107 NODE_4736_length_116_cov_134.034485 gi|394935450|ref|YP_005454241.1| 92.45 53 4 0 7 165 1 53 3e-28 102 NODE_4736_length_116_cov_134.034485 gi|253756608|ref|YP_003038520.1| 87.27 55 7 0 1 165 51 105 8e-27 103 NODE_4736_length_116_cov_134.034485 gi|167600356|ref|YP_001671998.1| 61.82 55 21 0 1 165 51 105 8e-15 70.5 NODE_4736_length_116_cov_134.034485 gi|253750533|ref|YP_003029846.1| 60.00 55 21 1 1 165 53 106 9e-15 70.1 NODE_4736_length_116_cov_134.034485 gi|60115393|ref|YP_209231.1| 60.00 55 21 1 1 165 53 106 7e-14 67.8 NODE_4737_length_160_cov_116.581253 gi|85718616|ref|YP_459950.1| 94.20 69 4 0 2 208 90 158 3e-41 139 NODE_4737_length_160_cov_116.581253 gi|253756596|ref|YP_003038509.1| 97.10 69 2 0 2 208 90 158 7e-41 141 NODE_4737_length_160_cov_116.581253 gi|253756583|ref|YP_003038497.1| 97.10 69 2 0 2 208 90 158 7e-41 141 NODE_4737_length_160_cov_116.581253 gi|38018024|ref|NP_937948.1| 97.10 69 2 0 2 208 90 158 9e-41 140 NODE_4737_length_160_cov_116.581253 gi|253756608|ref|YP_003038520.1| 95.65 69 3 0 2 208 90 158 1e-40 140 NODE_4737_length_160_cov_116.581253 gi|15081545|ref|NP_150075.1| 95.65 69 3 0 2 208 90 158 3e-40 139 NODE_4737_length_160_cov_116.581253 gi|167600356|ref|YP_001671998.1| 73.91 69 18 0 2 208 90 158 1e-28 109 NODE_4737_length_160_cov_116.581253 gi|60115393|ref|YP_209231.1| 55.07 69 23 2 2 208 91 151 4e-18 80.1 NODE_4737_length_160_cov_116.581253 gi|253750533|ref|YP_003029846.1| 56.52 69 22 2 2 208 91 151 1e-17 79.0 NODE_4737_length_160_cov_116.581253 gi|11192310|ref|NP_068669.1| 60.42 48 19 0 2 145 99 146 8e-16 73.9 NODE_4840_length_172_cov_1.162791 gi|117938251|ref|NP_001070908.1| 82.19 73 13 0 220 2 372 444 8e-27 108 NODE_4840_length_172_cov_1.162791 gi|7661958|ref|NP_055554.1| 82.19 73 13 0 220 2 374 446 1e-26 107 NODE_4840_length_172_cov_1.162791 gi|70906449|ref|NP_001020564.1| 75.34 73 18 0 220 2 372 444 5e-24 100 NODE_4840_length_172_cov_1.162791 gi|24496776|ref|NP_722482.1| 75.34 73 18 0 220 2 370 442 7e-24 100 NODE_4840_length_172_cov_1.162791 gi|70906447|ref|NP_001020563.1| 75.34 73 18 0 220 2 372 444 7e-24 100 NODE_4840_length_172_cov_1.162791 gi|496134229|ref|WP_008858736.1| 57.89 19 8 0 75 19 281 299 5.3 29.6 NODE_4840_length_172_cov_1.162791 gi|489087405|ref|WP_002997308.1| 42.22 45 25 1 44 175 279 323 6.4 29.3 NODE_4840_length_172_cov_1.162791 gi|493825454|ref|WP_006772910.1| 40.62 32 19 0 50 145 134 165 6.8 29.3 NODE_4924_length_160_cov_76.568748 gi|38018023|ref|NP_937947.1| 100.00 69 0 0 209 3 3546 3614 8e-39 143 NODE_4924_length_160_cov_76.568748 gi|85718615|ref|YP_459949.1| 97.10 69 2 0 209 3 3546 3614 2e-37 139 NODE_4924_length_160_cov_76.568748 gi|253756594|ref|YP_003038508.1| 95.65 69 3 0 209 3 3546 3614 2e-36 136 NODE_4924_length_160_cov_76.568748 gi|253756606|ref|YP_003038519.1| 95.65 69 3 0 209 3 3546 3614 2e-36 136 NODE_4924_length_160_cov_76.568748 gi|167600355|ref|YP_001671997.1| 95.65 69 3 0 209 3 3592 3660 2e-36 136 NODE_4924_length_160_cov_76.568748 gi|15081555|ref|NP_150074.1| 95.65 69 3 0 209 3 3546 3614 2e-36 136 NODE_4924_length_160_cov_76.568748 gi|253756581|ref|YP_003038496.1| 95.65 69 3 0 209 3 3546 3614 2e-36 136 NODE_4924_length_160_cov_76.568748 gi|253756595|ref|YP_003038507.1| 95.65 69 3 0 209 3 3546 3614 2e-36 136 NODE_4924_length_160_cov_76.568748 gi|253756582|ref|YP_003038495.1| 95.65 69 3 0 209 3 3546 3614 2e-36 136 NODE_4924_length_160_cov_76.568748 gi|26008080|ref|NP_150073.2| 95.65 69 3 0 209 3 3546 3614 2e-36 136 NODE_4938_length_190_cov_99.073685 gi|253756606|ref|YP_003038519.1| 100.00 79 0 0 238 2 2505 2583 7e-45 161 NODE_4938_length_190_cov_99.073685 gi|253756607|ref|YP_003038518.1| 100.00 79 0 0 238 2 2505 2583 1e-44 160 NODE_4938_length_190_cov_99.073685 gi|85718615|ref|YP_459949.1| 100.00 79 0 0 238 2 2505 2583 1e-44 160 NODE_4938_length_190_cov_99.073685 gi|38018023|ref|NP_937947.1| 100.00 79 0 0 238 2 2505 2583 1e-44 160 NODE_4938_length_190_cov_99.073685 gi|26008083|ref|NP_742169.1| 98.73 79 1 0 238 2 1654 1732 2e-44 160 NODE_4938_length_190_cov_99.073685 gi|253756594|ref|YP_003038508.1| 98.73 79 1 0 238 2 2505 2583 2e-44 160 NODE_4938_length_190_cov_99.073685 gi|15081555|ref|NP_150074.1| 98.73 79 1 0 238 2 2505 2583 2e-44 160 NODE_4938_length_190_cov_99.073685 gi|167600355|ref|YP_001671997.1| 98.73 79 1 0 238 2 2551 2629 2e-44 160 NODE_4938_length_190_cov_99.073685 gi|253756581|ref|YP_003038496.1| 98.73 79 1 0 238 2 2505 2583 2e-44 159 NODE_4938_length_190_cov_99.073685 gi|253756595|ref|YP_003038507.1| 98.73 79 1 0 238 2 2505 2583 3e-44 159 NODE_4998_length_189_cov_4.666667 gi|6679439|ref|NP_032933.1| 82.93 41 7 0 238 116 124 164 3e-16 74.3 NODE_4998_length_189_cov_4.666667 gi|10863927|ref|NP_066953.1| 80.49 41 8 0 238 116 124 164 1e-15 72.8 NODE_4998_length_189_cov_4.666667 gi|407263453|ref|XP_001002180.3| 78.05 41 9 0 238 116 144 184 7e-14 68.2 NODE_4998_length_189_cov_4.666667 gi|407261558|ref|XP_003086687.2| 78.05 41 9 0 238 116 144 184 7e-14 68.2 NODE_4998_length_189_cov_4.666667 gi|410171187|ref|XP_003960166.1| 73.17 41 11 0 238 116 120 160 7e-13 65.5 NODE_4998_length_189_cov_4.666667 gi|410172829|ref|XP_003960579.1| 75.61 41 9 1 238 116 134 173 3e-12 63.5 NODE_4998_length_189_cov_4.666667 gi|19527310|ref|NP_598845.1| 71.43 42 12 0 238 113 165 206 7e-12 62.8 NODE_4998_length_189_cov_4.666667 gi|410173623|ref|XP_003960830.1| 70.73 41 12 0 238 116 146 186 7e-12 62.8 NODE_4998_length_189_cov_4.666667 gi|113428306|ref|XP_372741.4| 70.73 41 12 0 238 116 146 186 7e-12 62.8 NODE_4998_length_189_cov_4.666667 gi|410169990|ref|XP_001718975.4| 70.73 41 12 0 238 116 157 197 7e-12 62.8 NODE_5030_length_103_cov_1.533981 gi|4506129|ref|NP_002756.1| 100.00 51 0 0 1 153 85 135 5e-28 107 NODE_5030_length_103_cov_1.533981 gi|13386146|ref|NP_080938.1| 100.00 51 0 0 1 153 85 135 5e-28 107 NODE_5030_length_103_cov_1.533981 gi|256418956|ref|NP_001032835.2| 100.00 51 0 0 1 153 85 135 6e-28 107 NODE_5030_length_103_cov_1.533981 gi|10946854|ref|NP_067438.1| 100.00 51 0 0 1 153 85 135 7e-28 107 NODE_5030_length_103_cov_1.533981 gi|4506127|ref|NP_002755.1| 100.00 51 0 0 1 153 85 135 7e-28 107 NODE_5030_length_103_cov_1.533981 gi|30794182|ref|NP_083570.1| 98.04 51 1 0 1 153 85 135 1e-27 106 NODE_5030_length_103_cov_1.533981 gi|28557709|ref|NP_787082.1| 96.08 51 2 0 1 153 85 135 3e-27 105 NODE_5030_length_103_cov_1.533981 gi|84875539|ref|NP_001034180.1| 94.44 54 0 1 1 153 85 138 5e-26 101 NODE_5030_length_103_cov_1.533981 gi|490974162|ref|WP_004835952.1| 66.67 51 17 0 1 153 97 147 5e-18 79.7 NODE_5030_length_103_cov_1.533981 gi|490965715|ref|WP_004827517.1| 66.67 51 17 0 1 153 95 145 6e-18 79.3 NODE_5062_length_348_cov_3.704023 gi|59859885|ref|NP_001012321.1| 99.24 132 1 0 1 396 24 155 2e-91 274 NODE_5062_length_348_cov_3.704023 gi|9845502|ref|NP_002286.2| 99.24 132 1 0 1 396 24 155 2e-91 274 NODE_5062_length_348_cov_3.704023 gi|309264022|ref|XP_003086186.1| 99.24 132 1 0 1 396 24 155 2e-91 274 NODE_5062_length_348_cov_3.704023 gi|224994260|ref|NP_035159.3| 99.24 132 1 0 1 396 24 155 2e-91 274 NODE_5062_length_348_cov_3.704023 gi|82905443|ref|XP_921694.1| 96.97 132 4 0 1 396 24 155 7e-90 270 NODE_5062_length_348_cov_3.704023 gi|148643497|ref|YP_001274010.1| 42.75 131 74 1 1 393 17 146 3e-31 117 NODE_5062_length_348_cov_3.704023 gi|493572382|ref|WP_006525606.1| 25.15 167 77 4 28 387 26 191 2e-06 50.4 NODE_5062_length_348_cov_3.704023 gi|492952066|ref|WP_006060151.1| 25.00 168 78 3 22 384 19 185 4e-06 49.3 NODE_5062_length_348_cov_3.704023 gi|493676882|ref|WP_006627140.1| 24.55 167 78 4 28 387 42 207 3e-04 43.5 NODE_5062_length_348_cov_3.704023 gi|489794612|ref|WP_003698503.1| 24.40 168 77 4 28 387 26 191 7e-04 42.4 NODE_5082_length_104_cov_2.009615 gi|488385012|ref|WP_002454397.1| 37.93 29 18 0 128 42 42 70 0.78 31.2 NODE_5082_length_104_cov_2.009615 gi|488365121|ref|WP_002434506.1| 37.93 29 18 0 128 42 42 70 0.78 31.2 NODE_5082_length_104_cov_2.009615 gi|495814946|ref|WP_008539525.1| 36.73 49 31 0 6 152 353 401 0.86 31.6 NODE_5082_length_104_cov_2.009615 gi|496436491|ref|WP_009145338.1| 36.73 49 31 0 6 152 353 401 1.4 30.8 NODE_5082_length_104_cov_2.009615 gi|110642360|ref|YP_670090.1| 40.54 37 22 0 116 6 182 218 4.5 29.3 NODE_5082_length_104_cov_2.009615 gi|209919609|ref|YP_002293693.1| 40.54 37 22 0 116 6 182 218 4.5 29.3 NODE_5082_length_104_cov_2.009615 gi|488380092|ref|WP_002449477.1| 37.93 29 18 0 128 42 42 70 4.9 28.9 NODE_5082_length_104_cov_2.009615 gi|491529818|ref|WP_005387441.1| 35.42 48 31 0 9 152 354 401 5.6 28.9 NODE_5082_length_104_cov_2.009615 gi|490832202|ref|WP_004694287.1| 35.42 48 31 0 9 152 354 401 5.6 28.9 NODE_5082_length_104_cov_2.009615 gi|493745716|ref|WP_006694755.1| 36.73 49 31 0 6 152 353 401 7.7 28.5 NODE_5204_length_218_cov_56.509174 gi|38018023|ref|NP_937947.1| 98.86 88 1 0 266 3 3682 3769 2e-39 146 NODE_5204_length_218_cov_56.509174 gi|26008085|ref|NP_742133.1| 92.05 88 7 0 266 3 133 220 7e-38 134 NODE_5204_length_218_cov_56.509174 gi|85718615|ref|YP_459949.1| 92.05 88 7 0 266 3 3682 3769 2e-36 137 NODE_5204_length_218_cov_56.509174 gi|253756595|ref|YP_003038507.1| 92.05 88 7 0 266 3 3682 3769 2e-36 137 NODE_5204_length_218_cov_56.509174 gi|253756607|ref|YP_003038518.1| 92.05 88 7 0 266 3 3682 3769 2e-36 137 NODE_5204_length_218_cov_56.509174 gi|253756582|ref|YP_003038495.1| 92.05 88 7 0 266 3 3682 3769 2e-36 137 NODE_5204_length_218_cov_56.509174 gi|26008080|ref|NP_150073.2| 92.05 88 7 0 266 3 3682 3769 2e-36 137 NODE_5204_length_218_cov_56.509174 gi|253756594|ref|YP_003038508.1| 92.05 88 7 0 266 3 3682 3769 4e-36 136 NODE_5204_length_218_cov_56.509174 gi|253756606|ref|YP_003038519.1| 92.05 88 7 0 266 3 3682 3769 5e-36 136 NODE_5204_length_218_cov_56.509174 gi|253756581|ref|YP_003038496.1| 92.05 88 7 0 266 3 3682 3769 5e-36 136 NODE_5271_length_115_cov_154.026093 gi|38018025|ref|NP_937949.1| 94.44 36 2 0 165 58 389 424 0.53 32.3 NODE_5271_length_115_cov_154.026093 gi|494932944|ref|WP_007658978.1| 42.86 28 15 1 163 83 265 292 1.3 31.2 NODE_5271_length_115_cov_154.026093 gi|253756584|ref|YP_003038498.1| 80.00 15 3 0 102 58 410 424 5.2 29.3 NODE_5271_length_115_cov_154.026093 gi|15081546|ref|NP_150076.1| 80.00 15 3 0 102 58 410 424 5.5 29.3 NODE_5271_length_115_cov_154.026093 gi|253756609|ref|YP_003038521.1| 80.00 15 3 0 102 58 410 424 5.6 28.9 NODE_5271_length_115_cov_154.026093 gi|394935453|ref|YP_005454244.1| 80.00 15 3 0 102 58 410 424 6.5 28.9 NODE_5279_length_232_cov_2.056035 gi|291575128|ref|NP_001167568.1| 90.57 53 5 0 6 164 282 334 6e-25 100 NODE_5279_length_232_cov_2.056035 gi|4557032|ref|NP_002291.1| 90.57 53 5 0 6 164 282 334 6e-25 100 NODE_5279_length_232_cov_2.056035 gi|6678674|ref|NP_032518.1| 88.68 53 6 0 6 164 282 334 1e-24 100 NODE_5279_length_232_cov_2.056035 gi|207028494|ref|NP_001128711.1| 54.90 51 23 0 6 158 223 273 2e-12 65.5 NODE_5279_length_232_cov_2.056035 gi|6754524|ref|NP_034829.1| 56.86 51 22 0 6 158 281 331 3e-12 65.9 NODE_5279_length_232_cov_2.056035 gi|257743039|ref|NP_001129541.2| 56.86 51 22 0 6 158 310 360 4e-12 65.9 NODE_5279_length_232_cov_2.056035 gi|5031857|ref|NP_005557.1| 54.90 51 23 0 6 158 281 331 4e-12 65.5 NODE_5279_length_232_cov_2.056035 gi|260099723|ref|NP_001158886.1| 54.90 51 23 0 6 158 310 360 5e-12 65.5 NODE_5279_length_232_cov_2.056035 gi|30425048|ref|NP_780558.1| 54.90 51 23 0 6 158 331 381 1e-11 64.3 NODE_5279_length_232_cov_2.056035 gi|15082234|ref|NP_149972.1| 56.86 51 22 0 6 158 330 380 2e-11 64.3 NODE_5284_length_651_cov_60.287251 gi|26008092|ref|NP_742140.1| 98.28 233 4 0 701 3 132 364 6e-168 481 NODE_5284_length_651_cov_60.287251 gi|38018023|ref|NP_937947.1| 99.57 233 1 0 701 3 6032 6264 4e-158 494 NODE_5284_length_651_cov_60.287251 gi|253756582|ref|YP_003038495.1| 98.28 233 4 0 701 3 6032 6264 3e-156 489 NODE_5284_length_651_cov_60.287251 gi|253756595|ref|YP_003038507.1| 98.28 233 4 0 701 3 6032 6264 3e-156 489 NODE_5284_length_651_cov_60.287251 gi|26008080|ref|NP_150073.2| 98.28 233 4 0 701 3 6032 6264 3e-156 489 NODE_5284_length_651_cov_60.287251 gi|253756607|ref|YP_003038518.1| 97.85 233 5 0 701 3 6032 6264 9e-155 484 NODE_5284_length_651_cov_60.287251 gi|85718615|ref|YP_459949.1| 96.57 233 8 0 701 3 6032 6264 5e-154 483 NODE_5284_length_651_cov_60.287251 gi|167600354|ref|YP_001671996.1| 88.41 233 27 0 701 3 6074 6306 8e-145 456 NODE_5284_length_651_cov_60.287251 gi|394935459|ref|YP_005454239.1| 87.98 233 28 0 701 3 6088 6320 1e-144 456 NODE_5284_length_651_cov_60.287251 gi|25121571|ref|NP_740618.1| 80.26 233 46 0 701 3 132 364 3e-141 414 NODE_5379_length_132_cov_1.787879 gi|71772415|ref|NP_001025180.1| 98.15 54 1 0 18 179 1 54 3e-30 109 NODE_5379_length_132_cov_1.787879 gi|24762230|ref|NP_733769.1| 98.15 54 1 0 18 179 1 54 3e-30 109 NODE_5379_length_132_cov_1.787879 gi|14165469|ref|NP_001010.2| 98.15 54 1 0 18 179 1 54 3e-30 109 NODE_5379_length_132_cov_1.787879 gi|309265366|ref|XP_003086517.1| 92.59 54 4 0 18 179 1 54 8e-28 103 NODE_5379_length_132_cov_1.787879 gi|149254145|ref|XP_001478545.1| 92.59 54 4 0 18 179 1 54 8e-28 103 NODE_5379_length_132_cov_1.787879 gi|148642806|ref|YP_001273319.1| 46.30 54 29 0 18 179 1 54 4e-07 48.1 NODE_5379_length_132_cov_1.787879 gi|493345609|ref|WP_006302392.1| 40.00 50 29 1 30 179 5 53 0.009 36.2 NODE_5379_length_132_cov_1.787879 gi|492539781|ref|WP_005878802.1| 37.50 48 29 1 30 173 5 51 0.15 32.7 NODE_5379_length_132_cov_1.787879 gi|491047694|ref|WP_004909347.1| 32.69 52 34 1 18 173 1 51 0.17 32.7 NODE_5379_length_132_cov_1.787879 gi|490829218|ref|WP_004691308.1| 31.48 54 36 1 18 179 1 53 0.21 32.3 NODE_5384_length_295_cov_2.932203 gi|158966704|ref|NP_038675.2| 99.05 105 1 0 345 31 42 146 3e-68 209 NODE_5384_length_295_cov_2.932203 gi|4506691|ref|NP_001011.1| 99.05 105 1 0 345 31 42 146 3e-68 209 NODE_5384_length_295_cov_2.932203 gi|377837104|ref|XP_003688797.1| 98.10 105 2 0 345 31 61 165 2e-67 207 NODE_5384_length_295_cov_2.932203 gi|309262384|ref|XP_003085801.1| 98.10 105 2 0 345 31 61 165 2e-67 207 NODE_5384_length_295_cov_2.932203 gi|148643491|ref|YP_001274004.1| 49.04 104 45 2 342 31 38 133 3e-22 90.9 NODE_5384_length_295_cov_2.932203 gi|489077853|ref|WP_002987796.1| 37.62 101 50 2 333 31 41 128 2e-10 59.3 NODE_5384_length_295_cov_2.932203 gi|493302138|ref|WP_006259732.1| 36.63 101 51 2 333 31 41 128 2e-10 58.9 NODE_5384_length_295_cov_2.932203 gi|488744542|ref|WP_002667884.1| 41.58 101 46 3 333 31 41 128 2e-09 56.2 NODE_5384_length_295_cov_2.932203 gi|490497809|ref|WP_004363965.1| 41.00 100 46 3 330 31 42 128 7e-09 54.7 NODE_5384_length_295_cov_2.932203 gi|494609343|ref|WP_007367589.1| 39.00 100 48 3 330 31 42 128 8e-09 54.7 NODE_5438_length_290_cov_2.817241 gi|23956082|ref|NP_058676.1| 93.81 113 7 0 2 340 168 280 6e-58 187 NODE_5438_length_290_cov_2.817241 gi|14591909|ref|NP_000960.2| 92.04 113 9 0 2 340 168 280 3e-57 186 NODE_5438_length_290_cov_2.817241 gi|309267832|ref|XP_001004898.3| 91.15 113 10 0 2 340 219 331 5e-56 184 NODE_5438_length_290_cov_2.817241 gi|309264633|ref|XP_003086324.1| 92.04 113 8 1 2 340 219 330 2e-54 180 NODE_5438_length_290_cov_2.817241 gi|490645790|ref|WP_004510785.1| 28.26 46 30 1 65 193 56 101 3.7 30.8 NODE_5438_length_290_cov_2.817241 gi|488756182|ref|WP_002679439.1| 25.97 77 45 2 8 202 402 478 5.0 31.2 NODE_5438_length_290_cov_2.817241 gi|489099214|ref|WP_003009084.1| 25.93 81 45 3 14 250 52 119 5.2 30.8 NODE_5438_length_290_cov_2.817241 gi|497177964|ref|WP_009498024.1| 31.43 70 42 3 20 217 87 154 5.2 30.8 NODE_5438_length_290_cov_2.817241 gi|489088177|ref|WP_002998078.1| 25.93 81 45 3 14 250 52 119 5.3 30.8 NODE_5438_length_290_cov_2.817241 gi|148642802|ref|YP_001273315.1| 31.82 66 29 3 2 199 125 174 9.3 30.0 NODE_5444_length_181_cov_43.127071 gi|26008084|ref|NP_742132.1| 96.10 77 3 0 231 1 140 216 6e-49 163 NODE_5444_length_181_cov_43.127071 gi|253756606|ref|YP_003038519.1| 97.40 77 2 0 231 1 3386 3462 3e-46 165 NODE_5444_length_181_cov_43.127071 gi|85718615|ref|YP_459949.1| 97.40 77 2 0 231 1 3386 3462 4e-46 164 NODE_5444_length_181_cov_43.127071 gi|253756607|ref|YP_003038518.1| 97.40 77 2 0 231 1 3386 3462 4e-46 164 NODE_5444_length_181_cov_43.127071 gi|253756594|ref|YP_003038508.1| 96.10 77 3 0 231 1 3386 3462 7e-46 164 NODE_5444_length_181_cov_43.127071 gi|253756581|ref|YP_003038496.1| 96.10 77 3 0 231 1 3386 3462 7e-46 164 NODE_5444_length_181_cov_43.127071 gi|15081555|ref|NP_150074.1| 96.10 77 3 0 231 1 3386 3462 7e-46 164 NODE_5444_length_181_cov_43.127071 gi|167600355|ref|YP_001671997.1| 96.10 77 3 0 231 1 3432 3508 7e-46 164 NODE_5444_length_181_cov_43.127071 gi|253756595|ref|YP_003038507.1| 96.10 77 3 0 231 1 3386 3462 8e-46 164 NODE_5444_length_181_cov_43.127071 gi|26008080|ref|NP_150073.2| 96.10 77 3 0 231 1 3386 3462 8e-46 164 NODE_5512_length_108_cov_3.342592 gi|493916220|ref|WP_006861438.1| 50.00 22 11 0 92 157 31 52 1.3 30.8 NODE_5512_length_108_cov_3.342592 gi|493595757|ref|WP_006548507.1| 39.29 28 17 0 62 145 286 313 1.4 30.8 NODE_5512_length_108_cov_3.342592 gi|494177392|ref|WP_007115263.1| 47.22 36 16 2 14 121 25 57 3.0 30.0 NODE_5512_length_108_cov_3.342592 gi|489075498|ref|WP_002985447.1| 42.42 33 18 1 35 130 349 381 8.6 28.5 NODE_5632_length_736_cov_58.180706 gi|38018023|ref|NP_937947.1| 100.00 261 0 0 784 2 5684 5944 1e-174 543 NODE_5632_length_736_cov_58.180706 gi|253756595|ref|YP_003038507.1| 99.62 261 1 0 784 2 5684 5944 2e-174 542 NODE_5632_length_736_cov_58.180706 gi|26008080|ref|NP_150073.2| 99.62 261 1 0 784 2 5684 5944 2e-174 542 NODE_5632_length_736_cov_58.180706 gi|253756607|ref|YP_003038518.1| 99.62 261 1 0 784 2 5684 5944 3e-174 542 NODE_5632_length_736_cov_58.180706 gi|253756582|ref|YP_003038495.1| 99.62 261 1 0 784 2 5684 5944 3e-174 542 NODE_5632_length_736_cov_58.180706 gi|85718615|ref|YP_459949.1| 99.23 260 2 0 784 5 5684 5943 2e-172 537 NODE_5632_length_736_cov_58.180706 gi|394935459|ref|YP_005454239.1| 92.34 261 16 1 784 2 5744 6000 3e-161 504 NODE_5632_length_736_cov_58.180706 gi|167600354|ref|YP_001671996.1| 91.95 261 17 1 784 2 5730 5986 8e-161 503 NODE_5632_length_736_cov_58.180706 gi|26008091|ref|NP_742139.1| 99.54 217 1 0 784 134 387 603 2e-153 449 NODE_5632_length_736_cov_58.180706 gi|253750532|ref|YP_003029844.1| 85.82 261 34 1 784 2 5765 6022 3e-150 473 NODE_5653_length_165_cov_60.066666 gi|26008091|ref|NP_742139.1| 97.18 71 2 0 213 1 283 353 2e-41 147 NODE_5653_length_165_cov_60.066666 gi|38018023|ref|NP_937947.1| 98.59 71 1 0 213 1 5580 5650 5e-41 149 NODE_5653_length_165_cov_60.066666 gi|253756595|ref|YP_003038507.1| 97.18 71 2 0 213 1 5580 5650 1e-40 148 NODE_5653_length_165_cov_60.066666 gi|253756582|ref|YP_003038495.1| 97.18 71 2 0 213 1 5580 5650 1e-40 148 NODE_5653_length_165_cov_60.066666 gi|26008080|ref|NP_150073.2| 97.18 71 2 0 213 1 5580 5650 1e-40 148 NODE_5653_length_165_cov_60.066666 gi|253756607|ref|YP_003038518.1| 97.18 71 2 0 213 1 5580 5650 1e-40 148 NODE_5653_length_165_cov_60.066666 gi|85718615|ref|YP_459949.1| 97.18 71 2 0 213 1 5580 5650 2e-40 148 NODE_5653_length_165_cov_60.066666 gi|167600354|ref|YP_001671996.1| 95.77 71 3 0 213 1 5626 5696 5e-40 147 NODE_5653_length_165_cov_60.066666 gi|25121570|ref|NP_740617.1| 92.96 71 5 0 213 1 283 353 5e-40 143 NODE_5653_length_165_cov_60.066666 gi|394935459|ref|YP_005454239.1| 94.37 71 4 0 213 1 5640 5710 1e-39 145 NODE_5774_length_149_cov_3.919463 gi|489885282|ref|WP_003788732.1| 38.30 47 26 1 27 167 845 888 2.0 30.8 NODE_5774_length_149_cov_3.919463 gi|489880355|ref|WP_003783821.1| 30.77 52 36 0 172 17 97 148 2.9 30.0 NODE_5774_length_149_cov_3.919463 gi|491565168|ref|WP_005422754.1| 46.43 28 15 0 54 137 304 331 5.4 29.3 NODE_5858_length_103_cov_1.650485 gi|493930415|ref|WP_006875012.1| 34.15 41 17 2 11 115 403 439 2.7 30.0 NODE_5858_length_103_cov_1.650485 gi|27370244|ref|NP_766418.1| 40.00 35 15 1 141 37 570 598 8.7 28.5 NODE_5932_length_129_cov_51.511627 gi|38018023|ref|NP_937947.1| 100.00 59 0 0 3 179 5537 5595 9e-34 128 NODE_5932_length_129_cov_51.511627 gi|26008091|ref|NP_742139.1| 98.31 59 1 0 3 179 240 298 1e-33 125 NODE_5932_length_129_cov_51.511627 gi|253756607|ref|YP_003038518.1| 98.31 59 1 0 3 179 5537 5595 2e-33 127 NODE_5932_length_129_cov_51.511627 gi|253756595|ref|YP_003038507.1| 98.31 59 1 0 3 179 5537 5595 2e-33 127 NODE_5932_length_129_cov_51.511627 gi|253756582|ref|YP_003038495.1| 98.31 59 1 0 3 179 5537 5595 2e-33 127 NODE_5932_length_129_cov_51.511627 gi|26008080|ref|NP_150073.2| 98.31 59 1 0 3 179 5537 5595 2e-33 127 NODE_5932_length_129_cov_51.511627 gi|85718615|ref|YP_459949.1| 98.31 59 1 0 3 179 5537 5595 3e-33 127 NODE_5932_length_129_cov_51.511627 gi|394935459|ref|YP_005454239.1| 96.61 59 2 0 3 179 5597 5655 2e-32 124 NODE_5932_length_129_cov_51.511627 gi|167600354|ref|YP_001671996.1| 94.92 59 3 0 3 179 5583 5641 1e-31 122 NODE_5932_length_129_cov_51.511627 gi|253750532|ref|YP_003029844.1| 93.22 59 4 0 3 179 5618 5676 2e-31 121 NODE_6058_length_104_cov_1.442308 gi|488501801|ref|WP_002545240.1| 31.58 38 26 0 152 39 3 40 2.5 27.7 NODE_6058_length_104_cov_1.442308 gi|295131614|ref|YP_003582277.1| 31.58 38 26 0 152 39 6 43 2.8 27.7 NODE_6058_length_104_cov_1.442308 gi|488506867|ref|WP_002550306.1| 31.58 38 26 0 152 39 6 43 3.0 27.7 NODE_6058_length_104_cov_1.442308 gi|491671053|ref|WP_005527195.1| 34.15 41 27 0 2 124 735 775 3.3 30.0 NODE_6058_length_104_cov_1.442308 gi|490982950|ref|WP_004844702.1| 45.45 22 12 0 12 77 105 126 3.6 29.3 NODE_6058_length_104_cov_1.442308 gi|448244957|ref|YP_007392677.1| 51.43 35 15 1 29 127 789 823 4.5 29.3 NODE_6058_length_104_cov_1.442308 gi|496138189|ref|WP_008862696.1| 41.67 36 15 2 32 124 72 106 6.2 28.9 NODE_6058_length_104_cov_1.442308 gi|491791853|ref|WP_005602013.1| 36.96 46 25 2 5 142 31 72 7.9 28.5 NODE_6107_length_107_cov_3.514019 gi|6754222|ref|NP_034578.1| 96.15 52 2 0 1 156 129 180 2e-27 105 NODE_6107_length_107_cov_3.514019 gi|55956921|ref|NP_004490.2| 96.15 52 2 0 1 156 124 175 2e-27 105 NODE_6107_length_107_cov_3.514019 gi|146260280|ref|NP_001041526.1| 96.15 52 2 0 1 156 129 180 1e-25 100 NODE_6107_length_107_cov_3.514019 gi|55956919|ref|NP_112556.2| 96.15 52 2 0 1 156 124 175 2e-25 100 NODE_6107_length_107_cov_3.514019 gi|14110414|ref|NP_002129.2| 71.70 53 14 1 1 156 151 203 3e-18 79.7 NODE_6107_length_107_cov_3.514019 gi|14110420|ref|NP_112738.1| 71.70 53 14 1 1 156 151 203 4e-18 80.5 NODE_6107_length_107_cov_3.514019 gi|116256514|ref|NP_031542.2| 71.70 53 14 1 1 156 151 203 4e-18 79.7 NODE_6107_length_107_cov_3.514019 gi|14110417|ref|NP_112737.1| 71.70 53 14 1 1 156 132 184 4e-18 80.1 NODE_6107_length_107_cov_3.514019 gi|116256512|ref|NP_001070733.1| 71.70 53 14 1 1 156 151 203 4e-18 80.1 NODE_6107_length_107_cov_3.514019 gi|116256518|ref|NP_001070734.1| 71.70 53 14 1 1 156 132 184 4e-18 80.1 NODE_6157_length_218_cov_7.431193 gi|34538609|ref|NP_904339.1| 50.00 72 36 0 266 51 12 83 2e-16 75.5 NODE_6157_length_218_cov_7.431193 gi|251831118|ref|YP_003024037.1| 45.07 71 39 0 260 48 14 84 6e-14 68.6 NODE_6157_length_218_cov_7.431193 gi|489073598|ref|WP_002983555.1| 29.69 64 39 1 266 93 7 70 5.3 29.6 NODE_6253_length_265_cov_3.554717 gi|40254577|ref|NP_035425.2| 100.00 105 0 0 315 1 22 126 1e-69 211 NODE_6253_length_265_cov_3.554717 gi|14277700|ref|NP_001007.2| 100.00 105 0 0 315 1 22 126 1e-69 211 NODE_6253_length_265_cov_3.554717 gi|149250091|ref|XP_001480687.1| 99.05 105 1 0 315 1 22 126 7e-69 210 NODE_6253_length_265_cov_3.554717 gi|377836484|ref|XP_003689024.1| 98.10 105 2 0 315 1 22 126 9e-68 207 NODE_6253_length_265_cov_3.554717 gi|94408240|ref|XP_983229.1| 98.10 105 2 0 315 1 22 126 9e-68 207 NODE_6253_length_265_cov_3.554717 gi|94408233|ref|XP_983012.1| 98.10 105 2 0 315 1 22 126 9e-68 207 NODE_6253_length_265_cov_3.554717 gi|94408225|ref|XP_982634.1| 98.10 105 2 0 315 1 22 126 9e-68 207 NODE_6253_length_265_cov_3.554717 gi|94408152|ref|XP_982204.1| 98.10 105 2 0 315 1 22 126 9e-68 207 NODE_6253_length_265_cov_3.554717 gi|51772387|ref|XP_486761.1| 98.10 105 2 0 315 1 22 126 9e-68 207 NODE_6253_length_265_cov_3.554717 gi|149272225|ref|XP_001472087.1| 97.14 105 3 0 315 1 22 126 2e-67 206 NODE_6273_length_225_cov_71.737778 gi|26008095|ref|NP_742170.1| 97.80 91 2 0 275 3 141 231 3e-57 189 NODE_6273_length_225_cov_71.737778 gi|38018023|ref|NP_937947.1| 98.90 91 1 0 275 3 2891 2981 1e-56 196 NODE_6273_length_225_cov_71.737778 gi|253756606|ref|YP_003038519.1| 97.80 91 2 0 275 3 2891 2981 3e-56 194 NODE_6273_length_225_cov_71.737778 gi|253756594|ref|YP_003038508.1| 97.80 91 2 0 275 3 2891 2981 3e-56 194 NODE_6273_length_225_cov_71.737778 gi|253756581|ref|YP_003038496.1| 97.80 91 2 0 275 3 2891 2981 3e-56 194 NODE_6273_length_225_cov_71.737778 gi|15081555|ref|NP_150074.1| 97.80 91 2 0 275 3 2891 2981 3e-56 194 NODE_6273_length_225_cov_71.737778 gi|167600355|ref|YP_001671997.1| 97.80 91 2 0 275 3 2937 3027 3e-56 194 NODE_6273_length_225_cov_71.737778 gi|253756582|ref|YP_003038495.1| 97.80 91 2 0 275 3 2891 2981 6e-56 194 NODE_6273_length_225_cov_71.737778 gi|26008080|ref|NP_150073.2| 97.80 91 2 0 275 3 2891 2981 6e-56 194 NODE_6273_length_225_cov_71.737778 gi|253756595|ref|YP_003038507.1| 97.80 91 2 0 275 3 2891 2981 6e-56 194 NODE_6288_length_109_cov_1.256881 gi|7657655|ref|NP_055109.1| 78.85 52 11 0 3 158 130 181 3e-23 94.4 NODE_6288_length_109_cov_1.256881 gi|30794386|ref|NP_082449.1| 76.92 52 12 0 3 158 130 181 3e-22 91.7 NODE_6288_length_109_cov_1.256881 gi|145580602|ref|NP_689615.2| 70.59 51 15 0 6 158 131 181 3e-20 86.3 NODE_6288_length_109_cov_1.256881 gi|22122669|ref|NP_666252.1| 63.46 52 19 0 3 158 129 180 3e-17 77.8 NODE_6288_length_109_cov_1.256881 gi|6912450|ref|NP_036420.1| 54.00 50 23 0 9 158 127 176 6e-14 69.3 NODE_6288_length_109_cov_1.256881 gi|28916683|ref|NP_803128.1| 48.08 52 27 0 3 158 125 176 7e-12 63.2 NODE_6288_length_109_cov_1.256881 gi|165972325|ref|NP_080334.3| 35.42 48 31 0 3 146 144 191 0.039 35.4 NODE_6288_length_109_cov_1.256881 gi|492917424|ref|WP_006045156.1| 37.21 43 26 1 21 146 82 124 0.53 32.0 NODE_6288_length_109_cov_1.256881 gi|490496568|ref|WP_004362738.1| 34.88 43 27 1 21 146 74 116 1.1 30.8 NODE_6288_length_109_cov_1.256881 gi|488225960|ref|WP_002297168.1| 41.38 29 15 1 42 122 290 318 1.7 30.4 NODE_6358_length_763_cov_14.992136 gi|34538603|ref|NP_904333.1| 56.15 187 82 0 253 813 35 221 3e-25 105 NODE_6358_length_763_cov_14.992136 gi|251831112|ref|YP_003024031.1| 57.84 185 76 2 262 813 38 221 5e-24 102 NODE_6358_length_763_cov_14.992136 gi|494061063|ref|WP_007003145.1| 37.50 136 82 2 415 813 108 243 1e-07 56.6 NODE_6358_length_763_cov_14.992136 gi|490317897|ref|WP_004207393.1| 38.46 78 44 1 592 813 176 253 1e-04 47.0 NODE_6358_length_763_cov_14.992136 gi|298346222|ref|YP_003718909.1| 41.03 78 42 1 592 813 189 266 0.003 43.5 NODE_6358_length_763_cov_14.992136 gi|490108282|ref|WP_004009035.1| 41.03 78 42 1 592 813 189 266 0.003 43.1 NODE_6358_length_763_cov_14.992136 gi|488757798|ref|WP_002681038.1| 38.16 76 41 2 592 813 275 346 0.003 43.5 NODE_6358_length_763_cov_14.992136 gi|492833537|ref|WP_005987491.1| 34.62 78 47 1 592 813 188 265 0.008 42.0 NODE_6358_length_763_cov_14.992136 gi|493338836|ref|WP_006295782.1| 35.06 77 46 1 595 813 184 260 0.009 41.6 NODE_6358_length_763_cov_14.992136 gi|490738495|ref|WP_004600803.1| 36.36 77 46 1 592 813 179 255 0.009 41.6 NODE_6404_length_262_cov_12.572519 gi|34538601|ref|NP_904331.1| 60.00 100 39 1 302 6 6 105 3e-16 76.3 NODE_6404_length_262_cov_12.572519 gi|251831110|ref|YP_003024029.1| 61.39 101 38 1 305 6 5 105 8e-14 69.3 NODE_6423_length_125_cov_2.112000 gi|33859482|ref|NP_031933.1| 97.87 47 1 0 2 142 80 126 1e-22 95.5 NODE_6423_length_125_cov_2.112000 gi|4503483|ref|NP_001952.1| 95.74 47 2 0 2 142 80 126 3e-22 94.7 NODE_6423_length_125_cov_2.112000 gi|94966752|ref|NP_001035700.1| 72.41 29 8 0 56 142 35 63 2e-07 51.6 NODE_6423_length_125_cov_2.112000 gi|94966754|ref|NP_078856.4| 72.41 29 8 0 56 142 86 114 3e-07 51.6 NODE_6423_length_125_cov_2.112000 gi|227908784|ref|NP_001153144.1| 72.41 29 8 0 56 142 86 114 3e-07 51.6 NODE_6423_length_125_cov_2.112000 gi|227908782|ref|NP_780526.2| 72.41 29 8 0 56 142 86 114 3e-07 51.6 NODE_6423_length_125_cov_2.112000 gi|494010912|ref|WP_006953327.1| 66.67 33 11 0 44 142 74 106 5e-07 50.4 NODE_6423_length_125_cov_2.112000 gi|496139065|ref|WP_008863572.1| 58.33 36 15 0 35 142 69 104 1e-06 49.3 NODE_6423_length_125_cov_2.112000 gi|490744686|ref|WP_004606994.1| 52.63 38 18 0 29 142 67 104 1e-06 49.3 NODE_6423_length_125_cov_2.112000 gi|494221915|ref|WP_007134562.1| 63.64 33 12 0 44 142 74 106 2e-06 48.9 NODE_6509_length_200_cov_4.640000 gi|407261716|ref|XP_003946351.1| 100.00 83 0 0 2 250 239 321 4e-52 174 NODE_6509_length_200_cov_4.640000 gi|407261718|ref|XP_003946352.1| 100.00 83 0 0 2 250 227 309 5e-52 174 NODE_6509_length_200_cov_4.640000 gi|407261714|ref|XP_003946350.1| 100.00 83 0 0 2 250 287 369 9e-52 174 NODE_6509_length_200_cov_4.640000 gi|407261712|ref|XP_003946349.1| 100.00 83 0 0 2 250 287 369 9e-52 174 NODE_6509_length_200_cov_4.640000 gi|407261710|ref|XP_003946348.1| 100.00 83 0 0 2 250 287 369 9e-52 174 NODE_6509_length_200_cov_4.640000 gi|407261708|ref|XP_003946347.1| 100.00 83 0 0 2 250 287 369 9e-52 174 NODE_6509_length_200_cov_4.640000 gi|407261706|ref|XP_003946346.1| 100.00 83 0 0 2 250 287 369 9e-52 174 NODE_6509_length_200_cov_4.640000 gi|407261704|ref|XP_003946345.1| 100.00 83 0 0 2 250 287 369 9e-52 174 NODE_6509_length_200_cov_4.640000 gi|407261698|ref|XP_003946342.1| 100.00 83 0 0 2 250 287 369 9e-52 174 NODE_6509_length_200_cov_4.640000 gi|407261696|ref|XP_003946341.1| 100.00 83 0 0 2 250 287 369 9e-52 174 NODE_6510_length_132_cov_3.143939 gi|407261700|ref|XP_003946343.1| 97.62 42 1 0 182 57 344 385 2e-22 92.8 NODE_6510_length_132_cov_3.143939 gi|4503471|ref|NP_001393.1| 97.62 42 1 0 182 57 391 432 4e-22 92.4 NODE_6510_length_132_cov_3.143939 gi|407261714|ref|XP_003946350.1| 97.62 42 1 0 182 57 391 432 5e-22 92.4 NODE_6510_length_132_cov_3.143939 gi|407261712|ref|XP_003946349.1| 97.62 42 1 0 182 57 391 432 5e-22 92.4 NODE_6510_length_132_cov_3.143939 gi|407261710|ref|XP_003946348.1| 97.62 42 1 0 182 57 391 432 5e-22 92.4 NODE_6510_length_132_cov_3.143939 gi|407261708|ref|XP_003946347.1| 97.62 42 1 0 182 57 391 432 5e-22 92.4 NODE_6510_length_132_cov_3.143939 gi|407261706|ref|XP_003946346.1| 97.62 42 1 0 182 57 391 432 5e-22 92.4 NODE_6510_length_132_cov_3.143939 gi|407261704|ref|XP_003946345.1| 97.62 42 1 0 182 57 391 432 5e-22 92.4 NODE_6510_length_132_cov_3.143939 gi|407261698|ref|XP_003946342.1| 97.62 42 1 0 182 57 391 432 5e-22 92.4 NODE_6510_length_132_cov_3.143939 gi|407261696|ref|XP_003946341.1| 97.62 42 1 0 182 57 391 432 5e-22 92.4 NODE_6511_length_223_cov_2.488789 gi|316983124|ref|NP_066357.2| 94.44 90 5 0 2 271 35 124 3e-55 175 NODE_6511_length_223_cov_2.488789 gi|316983130|ref|NP_001186902.1| 94.44 90 5 0 2 271 35 124 8e-55 174 NODE_6511_length_223_cov_2.488789 gi|13385038|ref|NP_079865.1| 96.59 88 3 0 8 271 1 88 8e-55 172 NODE_6511_length_223_cov_2.488789 gi|9845295|ref|NP_063918.1| 96.59 88 3 0 8 271 1 88 8e-55 172 NODE_6511_length_223_cov_2.488789 gi|4506651|ref|NP_000992.1| 95.45 88 4 0 8 271 1 88 2e-54 171 NODE_6511_length_223_cov_2.488789 gi|149249075|ref|XP_914563.3| 89.77 88 9 0 8 271 1 88 5e-49 158 NODE_6511_length_223_cov_2.488789 gi|149248853|ref|XP_355309.5| 89.77 88 9 0 8 271 1 88 5e-49 158 NODE_6511_length_223_cov_2.488789 gi|316983132|ref|NP_001186903.1| 78.21 78 9 1 2 235 35 104 1e-35 124 NODE_6511_length_223_cov_2.488789 gi|316983126|ref|NP_001186901.1| 80.00 70 14 0 2 211 35 104 1e-33 119 NODE_6511_length_223_cov_2.488789 gi|148643195|ref|YP_001273708.1| 41.10 73 42 1 11 229 1 72 5e-07 48.5 NODE_6528_length_178_cov_46.578651 gi|26008090|ref|NP_742138.1| 98.67 75 1 0 226 2 374 448 2e-43 155 NODE_6528_length_178_cov_46.578651 gi|38018023|ref|NP_937947.1| 100.00 75 0 0 226 2 4743 4817 4e-43 155 NODE_6528_length_178_cov_46.578651 gi|167600354|ref|YP_001671996.1| 98.67 75 1 0 226 2 4789 4863 6e-43 155 NODE_6528_length_178_cov_46.578651 gi|253756607|ref|YP_003038518.1| 98.67 75 1 0 226 2 4743 4817 6e-43 155 NODE_6528_length_178_cov_46.578651 gi|253756595|ref|YP_003038507.1| 98.67 75 1 0 226 2 4743 4817 6e-43 155 NODE_6528_length_178_cov_46.578651 gi|253756582|ref|YP_003038495.1| 98.67 75 1 0 226 2 4743 4817 6e-43 155 NODE_6528_length_178_cov_46.578651 gi|26008080|ref|NP_150073.2| 98.67 75 1 0 226 2 4743 4817 6e-43 155 NODE_6528_length_178_cov_46.578651 gi|85718615|ref|YP_459949.1| 97.33 75 2 0 226 2 4743 4817 1e-42 155 NODE_6528_length_178_cov_46.578651 gi|394935459|ref|YP_005454239.1| 96.00 75 3 0 226 2 4803 4877 6e-42 152 NODE_6528_length_178_cov_46.578651 gi|25121569|ref|NP_740616.1| 96.00 75 3 0 226 2 374 448 9e-42 150 NODE_6553_length_103_cov_3.165049 gi|407262653|ref|XP_003946441.1| 100.00 21 0 0 64 2 29 49 3e-07 48.1 NODE_6553_length_103_cov_3.165049 gi|7305443|ref|NP_038749.1| 100.00 21 0 0 64 2 29 49 1e-06 47.8 NODE_6553_length_103_cov_3.165049 gi|4506661|ref|NP_000963.1| 100.00 21 0 0 64 2 29 49 1e-06 47.8 NODE_6553_length_103_cov_3.165049 gi|407262811|ref|XP_003945666.1| 100.00 21 0 0 64 2 24 44 1e-06 47.8 NODE_6553_length_103_cov_3.165049 gi|407260908|ref|XP_003946090.1| 100.00 21 0 0 64 2 24 44 1e-06 47.8 NODE_6553_length_103_cov_3.165049 gi|407263827|ref|XP_003945548.1| 100.00 21 0 0 64 2 29 49 7e-06 45.8 NODE_6553_length_103_cov_3.165049 gi|407264240|ref|XP_003945689.1| 100.00 21 0 0 64 2 266 286 2e-05 45.4 NODE_6553_length_103_cov_3.165049 gi|493930055|ref|WP_006874666.1| 53.85 26 12 0 54 131 2 27 4.1 29.3 NODE_6553_length_103_cov_3.165049 gi|489908574|ref|WP_003811993.1| 46.15 39 18 1 27 134 1 39 4.9 29.3 NODE_6553_length_103_cov_3.165049 gi|492496619|ref|WP_005864999.1| 38.71 31 19 0 33 125 166 196 6.2 28.9 NODE_6635_length_151_cov_2.609272 gi|57013276|ref|NP_006073.2| 100.00 66 0 0 3 200 194 259 3e-40 142 NODE_6635_length_151_cov_2.609272 gi|34740335|ref|NP_035784.1| 100.00 66 0 0 3 200 194 259 3e-40 142 NODE_6635_length_151_cov_2.609272 gi|17921989|ref|NP_005991.1| 100.00 66 0 0 3 200 194 259 4e-40 142 NODE_6635_length_151_cov_2.609272 gi|6678467|ref|NP_033473.1| 100.00 66 0 0 3 200 194 259 4e-40 142 NODE_6635_length_151_cov_2.609272 gi|14389309|ref|NP_116093.1| 100.00 66 0 0 3 200 194 259 4e-40 142 NODE_6635_length_151_cov_2.609272 gi|6678469|ref|NP_033474.1| 100.00 66 0 0 3 200 194 259 5e-40 142 NODE_6635_length_151_cov_2.609272 gi|301171345|ref|NP_001180343.1| 100.00 66 0 0 3 200 128 193 1e-39 140 NODE_6635_length_151_cov_2.609272 gi|156564363|ref|NP_525125.2| 98.48 66 1 0 3 200 194 259 1e-39 140 NODE_6635_length_151_cov_2.609272 gi|46409270|ref|NP_997195.1| 98.48 66 1 0 3 200 194 259 1e-39 140 NODE_6635_length_151_cov_2.609272 gi|17921993|ref|NP_005992.1| 98.48 66 1 0 3 200 194 259 1e-39 140 NODE_6746_length_271_cov_5.416974 gi|251831108|ref|YP_003024027.1| 45.57 79 43 0 321 85 43 121 2e-15 75.1 NODE_6746_length_271_cov_5.416974 gi|34538599|ref|NP_904329.1| 45.12 82 38 3 321 85 44 121 3e-10 60.8 NODE_6746_length_271_cov_5.416974 gi|489079060|ref|WP_002988999.1| 30.68 88 50 1 315 85 134 221 0.001 41.6 NODE_6746_length_271_cov_5.416974 gi|493308629|ref|WP_006266141.1| 31.65 79 43 1 288 85 143 221 0.002 40.8 NODE_6746_length_271_cov_5.416974 gi|493300089|ref|WP_006257704.1| 31.65 79 43 1 288 85 143 221 0.002 40.8 NODE_6746_length_271_cov_5.416974 gi|491911394|ref|WP_005666451.1| 31.82 88 48 2 312 85 162 249 0.003 40.4 NODE_6746_length_271_cov_5.416974 gi|489895417|ref|WP_003798866.1| 30.12 83 46 1 297 85 154 236 0.005 39.7 NODE_6746_length_271_cov_5.416974 gi|493250100|ref|WP_006217972.1| 31.71 82 44 1 294 85 157 238 0.007 39.3 NODE_6746_length_271_cov_5.416974 gi|492507717|ref|WP_005869747.1| 30.43 92 51 2 321 85 143 234 0.012 38.5 NODE_6746_length_271_cov_5.416974 gi|493897383|ref|WP_006843252.1| 28.89 90 51 1 315 85 138 227 0.016 38.1 NODE_6764_length_107_cov_6.046729 gi|31317305|ref|NP_005782.1| 98.04 51 1 0 3 155 340 390 7e-24 98.2 NODE_6764_length_107_cov_6.046729 gi|68303650|ref|NP_080759.2| 87.50 48 6 0 12 155 344 391 1e-18 83.6 NODE_6764_length_107_cov_6.046729 gi|492845185|ref|WP_005999139.1| 35.29 34 22 0 15 116 52 85 1.7 30.4 NODE_6764_length_107_cov_6.046729 gi|25011657|ref|NP_736052.1| 40.91 44 26 0 15 146 11 54 4.6 28.5 NODE_6764_length_107_cov_6.046729 gi|494835807|ref|WP_007561907.1| 27.27 44 32 0 18 149 49 92 4.9 29.3 NODE_6764_length_107_cov_6.046729 gi|158267614|ref|YP_764499.2| 44.44 27 15 0 75 155 138 164 8.5 28.1 NODE_6778_length_138_cov_2.217391 gi|489749629|ref|WP_003653638.1| 35.42 48 22 2 44 175 450 492 5.3 29.3 NODE_6853_length_169_cov_1.946746 gi|489017254|ref|WP_002927770.1| 53.12 32 12 1 74 169 252 280 0.44 33.1 NODE_6853_length_169_cov_1.946746 gi|489083933|ref|WP_002993846.1| 55.17 29 13 0 108 22 39 67 1.1 31.6 NODE_6853_length_169_cov_1.946746 gi|489100940|ref|WP_003010804.1| 55.17 29 13 0 108 22 39 67 1.2 31.6 NODE_6853_length_169_cov_1.946746 gi|94536848|ref|NP_060888.2| 40.00 40 19 1 179 60 335 369 1.7 31.2 NODE_6853_length_169_cov_1.946746 gi|94536850|ref|NP_001035518.1| 40.00 40 19 1 179 60 303 337 1.8 31.2 NODE_6853_length_169_cov_1.946746 gi|490462342|ref|WP_004332902.1| 38.10 42 26 0 48 173 25 66 5.3 29.3 NODE_6853_length_169_cov_1.946746 gi|146231944|ref|NP_780447.4| 38.64 44 23 1 171 52 357 400 5.8 29.6 NODE_6868_length_118_cov_1.271186 gi|31543956|ref|NP_033542.2| 81.82 55 10 0 167 3 436 490 1e-16 78.2 NODE_6868_length_118_cov_1.271186 gi|221307502|ref|NP_001137448.1| 81.82 55 10 0 167 3 223 277 1e-16 77.0 NODE_6868_length_118_cov_1.271186 gi|4507917|ref|NP_003381.1| 81.82 55 10 0 167 3 437 491 2e-16 77.0 NODE_6868_length_118_cov_1.271186 gi|157738687|ref|NP_001099028.1| 71.43 35 10 0 107 3 374 408 6e-11 61.6 NODE_6868_length_118_cov_1.271186 gi|171846235|ref|NP_958758.2| 74.29 35 9 0 107 3 369 403 8e-11 61.2 NODE_6868_length_118_cov_1.271186 gi|491431526|ref|WP_005289321.1| 54.17 24 11 0 20 91 36 59 5.2 27.7 NODE_6891_length_386_cov_3.411917 gi|493572455|ref|WP_006525678.1| 29.63 54 37 1 267 109 426 479 3.2 32.3 NODE_6891_length_386_cov_3.411917 gi|490463747|ref|WP_004334301.1| 35.85 53 31 2 276 118 137 186 8.4 31.2 NODE_6989_length_106_cov_3.801887 gi|393715095|ref|NP_001257329.1| 100.00 51 0 0 2 154 248 298 2e-31 117 NODE_6989_length_106_cov_3.801887 gi|393715091|ref|NP_001257328.1| 100.00 51 0 0 2 154 283 333 6e-31 116 NODE_6989_length_106_cov_3.801887 gi|17986283|ref|NP_006000.2| 100.00 51 0 0 2 154 283 333 6e-31 116 NODE_6989_length_106_cov_3.801887 gi|6755901|ref|NP_035783.1| 100.00 51 0 0 2 154 283 333 6e-31 116 NODE_6989_length_106_cov_3.801887 gi|57013276|ref|NP_006073.2| 100.00 51 0 0 2 154 283 333 7e-31 115 NODE_6989_length_106_cov_3.801887 gi|34740335|ref|NP_035784.1| 100.00 51 0 0 2 154 283 333 7e-31 115 NODE_6989_length_106_cov_3.801887 gi|14389309|ref|NP_116093.1| 98.04 51 1 0 2 154 283 333 2e-30 114 NODE_6989_length_106_cov_3.801887 gi|6678469|ref|NP_033474.1| 98.04 51 1 0 2 154 283 333 2e-30 114 NODE_6989_length_106_cov_3.801887 gi|82930689|ref|XP_909750.1| 96.08 51 2 0 2 154 282 332 6e-30 113 NODE_6989_length_106_cov_3.801887 gi|51765047|ref|XP_486246.1| 96.08 51 2 0 2 154 282 332 6e-30 113 NODE_6992_length_686_cov_12.574344 gi|251831113|ref|YP_003024032.1| 71.02 245 71 0 1 735 4 248 4e-103 307 NODE_6992_length_686_cov_12.574344 gi|34538604|ref|NP_904334.1| 70.61 245 72 0 1 735 4 248 1e-101 304 NODE_6992_length_686_cov_12.574344 gi|488804979|ref|WP_002717385.1| 48.43 254 120 2 7 735 9 262 2e-55 186 NODE_6992_length_686_cov_12.574344 gi|488801873|ref|WP_002714279.1| 44.94 267 123 2 7 735 9 275 6e-53 180 NODE_6992_length_686_cov_12.574344 gi|492887313|ref|WP_006022894.1| 45.32 267 122 2 7 735 9 275 6e-53 180 NODE_6992_length_686_cov_12.574344 gi|494060885|ref|WP_007002968.1| 50.20 249 120 2 1 735 16 264 8e-48 166 NODE_6992_length_686_cov_12.574344 gi|490319112|ref|WP_004208605.1| 46.43 252 127 3 1 735 5 255 7e-44 155 NODE_6992_length_686_cov_12.574344 gi|493432517|ref|WP_006388095.1| 41.78 213 99 5 169 735 69 280 2e-39 145 NODE_6992_length_686_cov_12.574344 gi|493248475|ref|WP_006216870.1| 41.78 213 99 5 169 735 69 280 3e-39 144 NODE_6992_length_686_cov_12.574344 gi|491913845|ref|WP_005668122.1| 39.62 212 104 4 169 735 69 279 7e-33 127 NODE_7001_length_124_cov_1.500000 gi|495429486|ref|WP_008154182.1| 45.45 33 17 1 2 100 87 118 1.7 30.8 NODE_7001_length_124_cov_1.500000 gi|495428155|ref|WP_008152852.1| 45.45 33 17 1 2 100 87 118 1.7 30.8 NODE_7001_length_124_cov_1.500000 gi|495298804|ref|WP_008023556.1| 42.00 50 28 1 24 173 257 305 2.0 30.4 NODE_7001_length_124_cov_1.500000 gi|495036988|ref|WP_007762511.1| 40.00 50 29 1 24 173 257 305 2.5 30.0 NODE_7001_length_124_cov_1.500000 gi|489813103|ref|WP_003716948.1| 52.00 25 12 0 24 98 10 34 3.4 29.6 NODE_7001_length_124_cov_1.500000 gi|490043695|ref|WP_003946057.1| 48.15 27 14 0 30 110 386 412 6.7 28.9 NODE_7001_length_124_cov_1.500000 gi|492341897|ref|WP_005815874.1| 34.21 38 23 1 51 158 30 67 8.5 28.1 NODE_7022_length_111_cov_1.495495 gi|489884805|ref|WP_003788255.1| 30.77 39 27 0 160 44 112 150 1.2 30.8 NODE_7036_length_103_cov_1.446602 gi|491433351|ref|WP_005291144.1| 45.83 24 13 0 35 106 347 370 5.7 28.9 NODE_7036_length_103_cov_1.446602 gi|496424684|ref|WP_009133531.1| 44.00 25 14 0 75 149 53 77 6.9 28.1 NODE_7046_length_139_cov_37.697842 gi|55956788|ref|NP_005372.2| 100.00 21 0 0 126 188 272 292 3e-04 42.4 NODE_7046_length_139_cov_37.697842 gi|84875537|ref|NP_035010.3| 85.71 21 3 0 126 188 274 294 0.031 36.2 NODE_7050_length_193_cov_1.590674 gi|304434531|ref|NP_001182122.1| 84.62 26 4 0 237 160 71 96 1e-05 47.0 NODE_7050_length_193_cov_1.590674 gi|27262628|ref|NP_002473.2| 84.62 26 4 0 237 160 135 160 1e-05 47.0 NODE_7050_length_193_cov_1.590674 gi|125490378|ref|NP_058057.3| 95.24 21 1 0 237 175 135 155 4e-04 42.7 NODE_7128_length_123_cov_2.634146 gi|83376130|ref|NP_001032752.1| 98.21 56 1 0 2 169 170 225 2e-31 114 NODE_7128_length_123_cov_2.634146 gi|31980922|ref|NP_061266.2| 98.21 56 1 0 2 169 170 225 2e-31 114 NODE_7128_length_123_cov_2.634146 gi|11136628|ref|NP_066944.1| 98.21 56 1 0 2 169 170 225 2e-31 114 NODE_7128_length_123_cov_2.634146 gi|4503477|ref|NP_001950.1| 98.21 56 1 0 2 169 170 225 2e-31 114 NODE_7128_length_123_cov_2.634146 gi|194239729|ref|NP_001123528.1| 83.93 56 9 0 2 169 202 257 2e-27 105 NODE_7128_length_123_cov_2.634146 gi|54287684|ref|NP_075729.2| 83.93 56 9 0 2 169 226 281 2e-27 105 NODE_7128_length_123_cov_2.634146 gi|304555583|ref|NP_001123525.2| 83.93 56 9 0 2 169 592 647 8e-27 106 NODE_7128_length_123_cov_2.634146 gi|304555581|ref|NP_115754.3| 83.93 56 9 0 2 169 592 647 8e-27 106 NODE_7128_length_123_cov_2.634146 gi|56699438|ref|NP_083939.1| 83.93 56 9 0 2 169 605 660 9e-27 106 NODE_7128_length_123_cov_2.634146 gi|304555588|ref|NP_001182132.1| 83.93 56 9 0 2 169 207 262 2e-26 102 NODE_7166_length_197_cov_5.685279 gi|34538608|ref|NP_904338.1| 68.29 82 25 1 5 247 197 278 3e-28 111 NODE_7166_length_197_cov_5.685279 gi|251831117|ref|YP_003024036.1| 68.67 83 21 3 11 247 199 280 4e-17 80.5 NODE_7166_length_197_cov_5.685279 gi|490322262|ref|WP_004211747.1| 49.37 79 40 0 8 244 210 288 2e-14 72.8 NODE_7166_length_197_cov_5.685279 gi|490654142|ref|WP_004519133.1| 47.83 69 36 0 41 247 99 167 5e-12 65.9 NODE_7166_length_197_cov_5.685279 gi|489872613|ref|WP_003776145.1| 49.21 63 32 0 59 247 235 297 5e-12 65.9 NODE_7166_length_197_cov_5.685279 gi|489846871|ref|WP_003750561.1| 49.21 63 32 0 59 247 235 297 5e-12 65.9 NODE_7166_length_197_cov_5.685279 gi|489773082|ref|WP_003676983.1| 49.21 63 32 0 59 247 235 297 5e-12 65.9 NODE_7166_length_197_cov_5.685279 gi|489804261|ref|WP_003708139.1| 49.21 63 32 0 59 247 235 297 5e-12 65.9 NODE_7166_length_197_cov_5.685279 gi|489782824|ref|WP_003686715.1| 49.21 63 32 0 59 247 235 297 5e-12 65.9 NODE_7166_length_197_cov_5.685279 gi|488144427|ref|WP_002215635.1| 49.21 63 32 0 59 247 235 297 6e-12 65.9 NODE_7293_length_267_cov_9.621723 gi|34538600|ref|NP_904330.1| 84.00 100 16 0 2 301 3 102 1e-33 126 NODE_7293_length_267_cov_9.621723 gi|251831109|ref|YP_003024028.1| 82.83 99 17 0 5 301 4 102 4e-31 119 NODE_7293_length_267_cov_9.621723 gi|488804983|ref|WP_002717389.1| 62.50 104 38 1 5 313 27 130 6e-20 89.4 NODE_7293_length_267_cov_9.621723 gi|494060889|ref|WP_007002972.1| 58.49 106 43 1 2 316 26 131 1e-18 85.5 NODE_7293_length_267_cov_9.621723 gi|492887319|ref|WP_006022898.1| 60.58 104 40 1 5 313 24 127 2e-18 85.1 NODE_7293_length_267_cov_9.621723 gi|488806148|ref|WP_002718554.1| 57.69 104 43 1 5 313 25 128 7e-18 83.6 NODE_7293_length_267_cov_9.621723 gi|490319116|ref|WP_004208609.1| 51.75 114 39 1 8 301 32 145 2e-13 70.9 NODE_7293_length_267_cov_9.621723 gi|493248467|ref|WP_006216867.1| 46.08 102 54 1 8 313 30 130 5e-12 66.6 NODE_7293_length_267_cov_9.621723 gi|493432515|ref|WP_006388093.1| 46.08 102 54 1 8 313 30 130 5e-12 66.6 NODE_7293_length_267_cov_9.621723 gi|488801869|ref|WP_002714275.1| 60.00 90 35 1 47 313 1 90 3e-11 64.3 NODE_7371_length_145_cov_1.724138 gi|34538605|ref|NP_904335.1| 70.37 27 8 0 1 81 33 59 3e-06 45.8 NODE_7371_length_145_cov_1.724138 gi|251831114|ref|YP_003024033.1| 68.00 25 8 0 7 81 35 59 1e-05 43.9 NODE_7371_length_145_cov_1.724138 gi|491911423|ref|WP_005666469.1| 51.85 27 13 0 1 81 39 65 1e-04 40.8 NODE_7371_length_145_cov_1.724138 gi|492536241|ref|WP_005877727.1| 55.56 27 12 0 1 81 39 65 8e-04 38.9 NODE_7371_length_145_cov_1.724138 gi|493250087|ref|WP_006217959.1| 30.00 50 35 0 1 150 39 88 0.002 37.7 NODE_7371_length_145_cov_1.724138 gi|493300075|ref|WP_006257690.1| 48.00 25 13 0 7 81 43 67 0.002 37.7 NODE_7371_length_145_cov_1.724138 gi|488803215|ref|WP_002715621.1| 48.15 27 14 0 1 81 41 67 0.004 37.0 NODE_7371_length_145_cov_1.724138 gi|492880225|ref|WP_006020769.1| 48.15 27 14 0 1 81 41 67 0.004 37.0 NODE_7371_length_145_cov_1.724138 gi|488799174|ref|WP_002711580.1| 48.15 27 14 0 1 81 41 67 0.005 37.0 NODE_7371_length_145_cov_1.724138 gi|491911353|ref|WP_005666426.1| 48.15 27 14 0 1 81 39 65 0.005 37.0 NODE_7392_length_282_cov_3.269504 gi|309264022|ref|XP_003086186.1| 96.36 110 3 1 3 332 177 285 1e-51 171 NODE_7392_length_282_cov_3.269504 gi|224994260|ref|NP_035159.3| 96.36 110 3 1 3 332 177 285 1e-51 171 NODE_7392_length_282_cov_3.269504 gi|59859885|ref|NP_001012321.1| 96.36 110 3 1 3 332 177 285 2e-51 171 NODE_7392_length_282_cov_3.269504 gi|9845502|ref|NP_002286.2| 96.36 110 3 1 3 332 177 285 2e-51 171 NODE_7392_length_282_cov_3.269504 gi|82905443|ref|XP_921694.1| 91.82 110 8 1 3 332 177 285 2e-47 160 NODE_7392_length_282_cov_3.269504 gi|490744582|ref|WP_004606890.1| 38.30 47 28 1 183 323 109 154 0.87 33.1 NODE_7464_length_104_cov_1.855769 gi|16306492|ref|NP_203698.1| 100.00 51 0 0 1 153 110 160 3e-29 109 NODE_7464_length_104_cov_1.855769 gi|4502709|ref|NP_001777.1| 100.00 51 0 0 1 153 167 217 7e-29 109 NODE_7464_length_104_cov_1.855769 gi|31542366|ref|NP_031685.2| 100.00 51 0 0 1 153 167 217 9e-29 108 NODE_7464_length_104_cov_1.855769 gi|4557439|ref|NP_001249.1| 76.47 51 12 0 1 153 166 216 4e-20 85.1 NODE_7464_length_104_cov_1.855769 gi|7949020|ref|NP_058036.1| 72.55 51 14 0 1 153 166 216 2e-19 83.2 NODE_7464_length_104_cov_1.855769 gi|16936528|ref|NP_001789.2| 72.55 51 14 0 1 153 166 216 2e-19 83.2 NODE_7464_length_104_cov_1.855769 gi|16332370|ref|NP_277027.1| 64.71 51 18 0 1 153 586 636 4e-17 79.3 NODE_7464_length_104_cov_1.855769 gi|16332358|ref|NP_277021.1| 64.71 51 18 0 1 153 588 638 4e-17 79.3 NODE_7464_length_104_cov_1.855769 gi|16332364|ref|NP_277024.1| 64.71 51 18 0 1 153 554 604 5e-17 79.0 NODE_7464_length_104_cov_1.855769 gi|16332372|ref|NP_277028.1| 64.71 51 18 0 1 153 577 627 5e-17 79.0 NODE_7482_length_126_cov_2.198413 gi|494138448|ref|WP_007078200.1| 34.00 50 30 1 165 25 20 69 4.0 29.6 NODE_7482_length_126_cov_2.198413 gi|47716521|ref|NP_848755.1| 32.08 53 32 2 162 10 40 90 7.1 28.9 NODE_7482_length_126_cov_2.198413 gi|489627568|ref|WP_003532008.1| 39.47 38 21 1 114 1 38 73 7.9 28.1 NODE_7482_length_126_cov_2.198413 gi|491906380|ref|WP_005663965.1| 59.09 22 9 0 84 19 287 308 8.2 28.5 NODE_7494_length_149_cov_2.013423 gi|33239451|ref|NP_872590.1| 98.46 65 1 0 197 3 97 161 5e-39 135 NODE_7494_length_149_cov_2.013423 gi|4505641|ref|NP_002583.1| 98.46 65 1 0 197 3 97 161 5e-39 135 NODE_7494_length_149_cov_2.013423 gi|7242171|ref|NP_035175.1| 96.92 65 2 0 197 3 97 161 1e-38 135 NODE_7494_length_149_cov_2.013423 gi|438000351|ref|YP_007250456.1| 47.69 65 32 1 197 3 97 159 3e-14 69.3 NODE_7494_length_149_cov_2.013423 gi|114680103|ref|YP_758516.1| 43.08 65 35 1 197 3 97 159 3e-13 66.2 NODE_7494_length_149_cov_2.013423 gi|9627791|ref|NP_054078.1| 43.08 65 35 1 197 3 97 159 4e-13 66.2 NODE_7494_length_149_cov_2.013423 gi|23577875|ref|NP_703039.1| 36.92 65 39 1 197 3 126 188 4e-11 61.2 NODE_7494_length_149_cov_2.013423 gi|73852490|ref|YP_293774.1| 31.75 63 43 0 191 3 97 159 2e-07 50.4 NODE_7494_length_149_cov_2.013423 gi|9629991|ref|NP_046209.1| 46.34 41 22 0 131 9 116 156 3e-07 50.1 NODE_7494_length_149_cov_2.013423 gi|472341269|ref|YP_007674788.1| 29.82 57 40 0 173 3 104 160 1e-06 48.5 NODE_7495_length_113_cov_1.407080 gi|493486652|ref|WP_006441429.1| 42.86 28 13 1 84 10 172 199 3.8 29.3 NODE_7505_length_132_cov_2.924242 gi|255003735|ref|NP_035417.2| 95.00 60 3 0 180 1 131 190 7e-34 121 NODE_7505_length_132_cov_2.924242 gi|15431288|ref|NP_009035.3| 95.00 60 3 0 180 1 131 190 7e-34 121 NODE_7505_length_132_cov_2.924242 gi|490752128|ref|WP_004614436.1| 35.19 54 35 0 4 165 138 191 1.3 31.2 NODE_7505_length_132_cov_2.924242 gi|490331127|ref|WP_004220549.1| 34.38 32 21 0 156 61 34 65 8.3 28.5 NODE_7505_length_132_cov_2.924242 gi|491504394|ref|WP_005362061.1| 37.50 32 20 0 156 61 34 65 8.3 28.5 NODE_7505_length_132_cov_2.924242 gi|491666453|ref|WP_005523168.1| 46.43 28 15 0 168 85 97 124 9.6 28.5 NODE_7517_length_154_cov_2.525974 gi|395132450|ref|NP_001257420.1| 92.54 67 5 0 2 202 16 82 4e-39 132 NODE_7517_length_154_cov_2.525974 gi|6912634|ref|NP_036555.1| 92.54 67 5 0 2 202 77 143 1e-38 133 NODE_7517_length_154_cov_2.525974 gi|31981945|ref|NP_033464.2| 92.54 67 5 0 2 202 77 143 2e-38 133 NODE_7517_length_154_cov_2.525974 gi|309263460|ref|XP_919283.3| 88.06 67 8 0 2 202 48 114 2e-36 126 NODE_7517_length_154_cov_2.525974 gi|148643490|ref|YP_001274003.1| 46.67 45 24 0 8 142 74 118 9e-06 44.7 NODE_7517_length_154_cov_2.525974 gi|493276901|ref|WP_006234696.1| 44.44 36 19 1 2 109 65 99 0.16 32.7 NODE_7517_length_154_cov_2.525974 gi|493206421|ref|WP_006193632.1| 40.00 40 21 1 2 112 5 44 0.33 32.3 NODE_7517_length_154_cov_2.525974 gi|492743068|ref|WP_005945231.1| 34.38 64 36 3 14 202 46 104 0.57 32.3 NODE_7517_length_154_cov_2.525974 gi|493774661|ref|WP_006723149.1| 44.44 36 19 1 2 109 101 135 0.63 31.6 NODE_7517_length_154_cov_2.525974 gi|490457136|ref|WP_004327884.1| 34.62 52 29 2 8 163 105 151 0.68 31.6 NODE_7519_length_130_cov_1.538462 gi|388684894|ref|YP_006382774.1| 33.93 56 31 3 160 5 731 784 6.8 28.9 NODE_7519_length_130_cov_1.538462 gi|40796179|ref|NP_955624.1| 35.48 31 16 1 20 112 21 47 7.9 28.5 NODE_7519_length_130_cov_1.538462 gi|493397567|ref|WP_006353681.1| 46.67 30 14 1 178 89 468 495 9.2 28.5 NODE_7548_length_125_cov_5.696000 gi|407261702|ref|XP_003946344.1| 100.00 57 0 0 173 3 21 77 5e-32 118 NODE_7548_length_125_cov_5.696000 gi|6681273|ref|NP_031932.1| 100.00 57 0 0 173 3 21 77 5e-32 119 NODE_7548_length_125_cov_5.696000 gi|4503475|ref|NP_001949.1| 100.00 57 0 0 173 3 21 77 5e-32 119 NODE_7548_length_125_cov_5.696000 gi|407261700|ref|XP_003946343.1| 100.00 57 0 0 173 3 21 77 6e-32 119 NODE_7548_length_125_cov_5.696000 gi|407261714|ref|XP_003946350.1| 100.00 57 0 0 173 3 21 77 2e-31 117 NODE_7548_length_125_cov_5.696000 gi|407261712|ref|XP_003946349.1| 100.00 57 0 0 173 3 21 77 2e-31 117 NODE_7548_length_125_cov_5.696000 gi|407261710|ref|XP_003946348.1| 100.00 57 0 0 173 3 21 77 2e-31 117 NODE_7548_length_125_cov_5.696000 gi|407261708|ref|XP_003946347.1| 100.00 57 0 0 173 3 21 77 2e-31 117 NODE_7548_length_125_cov_5.696000 gi|407261706|ref|XP_003946346.1| 100.00 57 0 0 173 3 21 77 2e-31 117 NODE_7548_length_125_cov_5.696000 gi|407261704|ref|XP_003946345.1| 100.00 57 0 0 173 3 21 77 2e-31 117 NODE_7591_length_136_cov_1.654412 gi|490429089|ref|WP_004301231.1| 48.72 39 19 1 65 181 95 132 0.19 33.5 NODE_7591_length_136_cov_1.654412 gi|490449690|ref|WP_004320581.1| 48.72 39 19 1 65 181 93 130 0.19 33.5 NODE_7591_length_136_cov_1.654412 gi|490980850|ref|WP_004842613.1| 38.64 44 22 1 182 66 230 273 0.37 32.7 NODE_7591_length_136_cov_1.654412 gi|490040882|ref|WP_003943281.1| 34.62 52 33 1 8 160 1 52 0.85 31.6 NODE_7591_length_136_cov_1.654412 gi|489089507|ref|WP_002999406.1| 40.48 42 24 1 170 48 455 496 0.96 31.6 NODE_7591_length_136_cov_1.654412 gi|120407054|ref|NP_766309.2| 42.86 35 19 1 46 150 62 95 2.3 30.4 NODE_7591_length_136_cov_1.654412 gi|490974918|ref|WP_004836706.1| 28.00 50 36 0 17 166 777 826 6.0 29.3 NODE_7591_length_136_cov_1.654412 gi|187829745|ref|NP_001120714.1| 30.00 60 33 2 173 3 47 100 6.8 28.1 NODE_7591_length_136_cov_1.654412 gi|492512723|ref|WP_005871524.1| 44.44 36 15 1 149 57 574 609 7.9 28.9 NODE_7606_length_123_cov_1.276423 gi|19527168|ref|NP_598709.1| 94.74 57 3 0 171 1 356 412 7e-30 114 NODE_7606_length_123_cov_1.276423 gi|190014588|ref|NP_001121689.1| 94.74 57 3 0 171 1 358 414 1e-29 113 NODE_7606_length_123_cov_1.276423 gi|19923653|ref|NP_150091.2| 94.74 57 3 0 171 1 358 414 1e-29 113 NODE_7606_length_123_cov_1.276423 gi|14249158|ref|NP_116020.1| 52.63 57 27 0 171 1 481 537 6e-12 64.7 NODE_7606_length_123_cov_1.276423 gi|48255931|ref|NP_001001520.1| 52.63 57 27 0 171 1 481 537 6e-12 64.7 NODE_7606_length_123_cov_1.276423 gi|6680201|ref|NP_032259.1| 51.79 56 27 0 171 4 477 532 2e-11 63.2 NODE_7606_length_123_cov_1.276423 gi|490477873|ref|WP_004348240.1| 43.24 37 21 0 7 117 117 153 1.7 30.8 NODE_7606_length_123_cov_1.276423 gi|489511235|ref|WP_003416087.1| 28.26 46 33 0 10 147 118 163 2.2 30.4 NODE_7606_length_123_cov_1.276423 gi|489580059|ref|WP_003484505.1| 45.83 24 13 0 73 2 80 103 8.8 28.1 NODE_7652_length_129_cov_1.798450 gi|309265792|ref|XP_003086606.1| 100.00 41 0 0 2 124 39 79 4e-20 83.2 NODE_7652_length_129_cov_1.798450 gi|6677775|ref|NP_033105.1| 100.00 41 0 0 2 124 39 79 4e-20 83.2 NODE_7652_length_129_cov_1.798450 gi|4506613|ref|NP_000974.1| 100.00 41 0 0 2 124 39 79 4e-20 83.2 NODE_7652_length_129_cov_1.798450 gi|407263678|ref|XP_003945522.1| 95.12 41 2 0 2 124 63 103 2e-18 79.7 NODE_7652_length_129_cov_1.798450 gi|407261857|ref|XP_003945935.1| 95.12 41 2 0 2 124 63 103 2e-18 79.7 NODE_7652_length_129_cov_1.798450 gi|309266196|ref|XP_003086720.1| 92.68 41 3 0 2 124 49 89 1e-17 77.0 NODE_7652_length_129_cov_1.798450 gi|149258340|ref|XP_001473369.1| 92.68 41 3 0 2 124 49 89 1e-17 77.0 NODE_7652_length_129_cov_1.798450 gi|13386010|ref|NP_080793.1| 70.73 41 11 1 2 124 34 73 2e-09 54.7 NODE_7652_length_129_cov_1.798450 gi|153791384|ref|NP_001093115.1| 70.73 41 11 1 2 124 34 73 2e-09 54.7 NODE_7652_length_129_cov_1.798450 gi|83001935|ref|XP_911947.1| 64.86 37 11 1 2 112 34 68 3e-06 45.4 NODE_7683_length_195_cov_2.876923 gi|46430508|ref|NP_997406.1| 100.00 64 0 0 192 1 31 94 2e-38 132 NODE_7683_length_195_cov_2.876923 gi|17105394|ref|NP_000975.2| 100.00 64 0 0 192 1 31 94 2e-38 132 NODE_7683_length_195_cov_2.876923 gi|309263233|ref|XP_003085999.1| 95.31 64 3 0 192 1 31 94 2e-36 127 NODE_7683_length_195_cov_2.876923 gi|149266479|ref|XP_001476183.1| 95.31 64 3 0 192 1 31 94 2e-36 127 NODE_7683_length_195_cov_2.876923 gi|94388507|ref|XP_001002269.1| 93.65 63 3 1 189 1 32 93 9e-34 120 NODE_7683_length_195_cov_2.876923 gi|407261812|ref|XP_003945909.1| 93.65 63 3 1 189 1 32 93 9e-34 122 NODE_7683_length_195_cov_2.876923 gi|94388502|ref|XP_001002232.1| 92.19 64 4 1 192 1 31 93 3e-33 118 NODE_7683_length_195_cov_2.876923 gi|94388474|ref|XP_989377.1| 92.19 64 4 1 192 1 31 93 3e-33 118 NODE_7683_length_195_cov_2.876923 gi|94388483|ref|XP_989631.1| 90.62 64 5 1 192 1 31 93 1e-32 117 NODE_7683_length_195_cov_2.876923 gi|94388464|ref|XP_989011.1| 90.62 64 5 1 192 1 31 93 1e-32 117 NODE_7758_length_125_cov_2.624000 gi|45496816|ref|NP_031691.1| 62.07 58 22 0 174 1 353 410 3e-17 80.1 NODE_7758_length_125_cov_2.624000 gi|83715978|ref|NP_001032898.1| 62.07 58 22 0 174 1 354 411 3e-17 80.1 NODE_7758_length_125_cov_2.624000 gi|14589891|ref|NP_001784.2| 60.34 58 23 0 174 1 362 419 1e-16 78.2 NODE_7758_length_125_cov_2.624000 gi|4757960|ref|NP_004351.1| 56.14 57 24 1 174 4 409 464 3e-16 77.4 NODE_7758_length_125_cov_2.624000 gi|7305007|ref|NP_038533.1| 56.36 55 24 0 174 10 389 443 3e-15 74.3 NODE_7758_length_125_cov_2.624000 gi|13435364|ref|NP_077740.1| 57.14 56 24 0 174 7 389 444 4e-15 73.9 NODE_7758_length_125_cov_2.624000 gi|13435366|ref|NP_004940.1| 57.14 56 24 0 174 7 389 444 4e-15 73.9 NODE_7758_length_125_cov_2.624000 gi|133778947|ref|NP_031908.3| 58.18 55 23 0 174 10 389 443 6e-15 73.6 NODE_7758_length_125_cov_2.624000 gi|6753374|ref|NP_033994.1| 54.55 55 24 1 174 10 411 464 2e-14 72.4 NODE_7758_length_125_cov_2.624000 gi|4826702|ref|NP_004939.1| 56.36 55 24 0 171 7 389 443 9e-14 70.1 NODE_7822_length_119_cov_2.504202 gi|55956788|ref|NP_005372.2| 92.00 50 4 0 1 150 601 650 2e-11 63.5 NODE_7822_length_119_cov_2.504202 gi|84875537|ref|NP_035010.3| 92.00 50 4 0 1 150 598 647 2e-11 63.2 NODE_7822_length_119_cov_2.504202 gi|488625962|ref|WP_002562669.1| 44.00 50 28 0 1 150 33 82 7e-05 41.6 NODE_7822_length_119_cov_2.504202 gi|496415133|ref|WP_009123980.1| 39.29 56 34 0 1 168 33 88 1e-04 40.4 NODE_7822_length_119_cov_2.504202 gi|492712191|ref|WP_005931209.1| 42.00 50 29 0 1 150 33 82 2e-04 40.4 NODE_7822_length_119_cov_2.504202 gi|496428757|ref|WP_009137604.1| 39.06 64 31 1 1 168 26 89 2e-04 40.0 NODE_7822_length_119_cov_2.504202 gi|492263401|ref|WP_005793284.1| 46.00 50 27 0 1 150 33 82 0.002 37.7 NODE_7822_length_119_cov_2.504202 gi|53714011|ref|YP_100003.1| 46.00 50 27 0 1 150 33 82 0.002 37.7 NODE_7822_length_119_cov_2.504202 gi|493898426|ref|WP_006844263.1| 34.55 55 36 0 1 165 33 87 0.002 37.0 NODE_7822_length_119_cov_2.504202 gi|490459166|ref|WP_004329831.1| 39.29 56 34 0 1 168 33 88 0.008 35.4 NODE_7842_length_107_cov_1.401869 gi|493962491|ref|WP_006905959.1| 44.44 27 15 0 63 143 90 116 5.2 29.3 NODE_7843_length_420_cov_3.121428 gi|6677777|ref|NP_033106.1| 100.00 142 0 0 45 470 1 142 9e-84 250 NODE_7843_length_420_cov_3.121428 gi|4506621|ref|NP_000978.1| 100.00 142 0 0 45 470 1 142 9e-84 250 NODE_7843_length_420_cov_3.121428 gi|7705813|ref|NP_057177.1| 98.59 142 2 0 45 470 1 142 8e-83 248 NODE_7843_length_420_cov_3.121428 gi|148642810|ref|YP_001273323.1| 48.91 92 46 1 81 356 7 97 1e-18 82.4 NODE_7843_length_420_cov_3.121428 gi|492469581|ref|WP_005855586.1| 36.71 79 47 2 308 75 325 401 0.15 36.6 NODE_7843_length_420_cov_3.121428 gi|495426100|ref|WP_008150797.1| 36.71 79 47 2 308 75 325 401 0.19 36.2 NODE_7843_length_420_cov_3.121428 gi|495430458|ref|WP_008155154.1| 36.71 79 47 2 308 75 325 401 0.20 36.2 NODE_7843_length_420_cov_3.121428 gi|494932940|ref|WP_007658974.1| 36.71 79 47 2 308 75 325 401 0.21 36.2 NODE_7843_length_420_cov_3.121428 gi|491878655|ref|WP_005648388.1| 36.71 79 47 2 308 75 325 401 0.22 36.2 NODE_7843_length_420_cov_3.121428 gi|491865721|ref|WP_005641366.1| 36.71 79 47 2 308 75 325 401 0.22 36.2 NODE_7864_length_229_cov_2.410480 gi|490333245|ref|WP_004222667.1| 41.86 43 25 0 242 114 58 100 0.018 37.0 NODE_7864_length_229_cov_2.410480 gi|493615916|ref|WP_006568160.1| 32.73 55 35 1 278 114 48 100 0.29 33.5 NODE_7864_length_229_cov_2.410480 gi|479158967|ref|YP_007788236.1| 32.73 55 35 1 278 114 48 100 0.49 32.7 NODE_7869_length_118_cov_2.050848 gi|31981515|ref|NP_035421.2| 89.09 55 6 0 167 3 150 204 3e-26 102 NODE_7869_length_118_cov_2.050848 gi|15431301|ref|NP_000962.2| 88.89 54 6 0 167 6 128 181 1e-25 100 NODE_7869_length_118_cov_2.050848 gi|27754134|ref|NP_079709.2| 59.26 54 22 0 164 3 127 180 8e-16 73.2 NODE_7869_length_118_cov_2.050848 gi|50053872|ref|NP_940888.2| 59.26 54 22 0 164 3 127 180 4e-15 70.9 NODE_7869_length_118_cov_2.050848 gi|89893787|ref|YP_517274.1| 40.54 37 19 1 27 137 109 142 1.1 30.8 NODE_7869_length_118_cov_2.050848 gi|497175784|ref|WP_009497348.1| 42.86 28 16 0 164 81 229 256 2.9 30.0 NODE_7869_length_118_cov_2.050848 gi|493620736|ref|WP_006572933.1| 36.59 41 26 0 24 146 273 313 3.2 30.0 NODE_7869_length_118_cov_2.050848 gi|9634637|ref|NP_038311.1| 41.94 31 18 0 110 18 102 132 3.2 29.3 NODE_7869_length_118_cov_2.050848 gi|281416421|ref|YP_003347445.1| 44.83 29 16 0 110 24 102 130 3.4 29.3 NODE_7869_length_118_cov_2.050848 gi|238801887|ref|YP_002925090.1| 41.94 31 18 0 110 18 102 132 4.5 28.9 NODE_7896_length_117_cov_1.709402 gi|255918141|ref|NP_001157617.1| 50.00 54 22 1 164 18 513 566 2e-05 45.4 NODE_7896_length_117_cov_1.709402 gi|255918141|ref|NP_001157617.1| 43.10 58 27 2 167 9 446 502 0.003 39.3 NODE_7896_length_117_cov_1.709402 gi|255918139|ref|NP_001157616.1| 50.00 54 22 1 164 18 513 566 2e-05 45.4 NODE_7896_length_117_cov_1.709402 gi|255918139|ref|NP_001157616.1| 43.10 58 27 2 167 9 446 502 0.003 39.3 NODE_7896_length_117_cov_1.709402 gi|41281612|ref|NP_115812.1| 50.00 54 22 1 164 18 513 566 2e-05 45.4 NODE_7896_length_117_cov_1.709402 gi|41281612|ref|NP_115812.1| 43.10 58 27 2 167 9 446 502 0.003 39.3 NODE_7896_length_117_cov_1.709402 gi|32469497|ref|NP_862902.1| 44.44 54 25 1 164 18 503 556 0.028 36.2 NODE_7896_length_117_cov_1.709402 gi|32469497|ref|NP_862902.1| 41.94 62 24 2 167 18 466 527 0.30 33.1 NODE_7896_length_117_cov_1.709402 gi|493486496|ref|WP_006441275.1| 44.00 25 14 0 164 90 96 120 3.0 29.6 NODE_7896_length_117_cov_1.709402 gi|386316836|ref|YP_006013000.1| 27.59 58 38 1 3 164 230 287 6.3 28.9 NODE_7896_length_117_cov_1.709402 gi|491906894|ref|WP_005664284.1| 55.00 20 9 0 73 14 236 255 8.7 28.5 NODE_7896_length_117_cov_1.709402 gi|489185142|ref|WP_003094567.1| 27.59 58 38 1 3 164 230 287 9.5 28.5 NODE_7912_length_187_cov_2.770053 gi|55956788|ref|NP_005372.2| 83.33 18 3 0 183 236 272 289 1.2 31.6 NODE_7913_length_149_cov_2.288591 gi|55956788|ref|NP_005372.2| 56.92 65 28 0 198 4 318 382 2e-15 75.1 NODE_7913_length_149_cov_2.288591 gi|55956788|ref|NP_005372.2| 53.85 26 12 0 138 61 601 626 3.8 30.0 NODE_7913_length_149_cov_2.288591 gi|84875537|ref|NP_035010.3| 56.92 65 28 0 198 4 320 384 3e-15 74.7 NODE_7913_length_149_cov_2.288591 gi|84875537|ref|NP_035010.3| 53.85 26 12 0 138 61 598 623 3.4 30.0 NODE_7913_length_149_cov_2.288591 gi|23346437|ref|NP_694693.1| 41.46 41 23 1 120 1 51 91 0.15 34.3 NODE_7913_length_149_cov_2.288591 gi|5032069|ref|NP_005841.1| 41.46 41 23 1 120 1 51 91 0.15 34.3 NODE_7913_length_149_cov_2.288591 gi|25121978|ref|NP_001342.2| 32.73 55 29 2 177 37 54 108 1.3 31.2 NODE_7913_length_149_cov_2.288591 gi|299829262|ref|NP_001177740.1| 32.73 55 29 2 177 37 74 128 1.4 31.2 NODE_7913_length_149_cov_2.288591 gi|489935237|ref|WP_003838546.1| 45.16 31 16 1 157 68 459 489 1.9 30.8 NODE_7913_length_149_cov_2.288591 gi|489939962|ref|WP_003843269.1| 45.16 31 16 1 157 68 459 489 2.0 30.8 NODE_7913_length_149_cov_2.288591 gi|25470890|ref|NP_733829.1| 22.22 63 44 1 177 4 127 189 2.1 30.4 NODE_7913_length_149_cov_2.288591 gi|169790818|ref|NP_573451.2| 22.22 63 44 1 177 4 126 188 2.1 30.4 NODE_7936_length_112_cov_1.339286 gi|5031749|ref|NP_005508.1| 96.55 29 1 0 109 23 1 29 1e-10 57.4 NODE_7936_length_112_cov_1.339286 gi|10835240|ref|NP_006344.1| 93.10 29 2 0 109 23 1 29 7e-10 55.1 NODE_7936_length_112_cov_1.339286 gi|407261273|ref|XP_003946212.1| 93.55 31 2 0 109 17 1 31 8e-10 55.1 NODE_7936_length_112_cov_1.339286 gi|149263574|ref|XP_001478610.1| 93.55 31 2 0 109 17 1 31 8e-10 55.1 NODE_7936_length_112_cov_1.339286 gi|8393534|ref|NP_058653.1| 93.55 31 2 0 109 17 1 31 8e-10 55.1 NODE_7936_length_112_cov_1.339286 gi|309268322|ref|XP_003084667.1| 93.55 31 2 0 109 17 1 31 1e-09 54.3 NODE_7936_length_112_cov_1.339286 gi|149267823|ref|XP_001478444.1| 82.76 29 5 0 109 23 1 29 5e-08 50.1 NODE_7936_length_112_cov_1.339286 gi|149267483|ref|XP_001480899.1| 82.76 29 5 0 109 23 1 29 5e-08 50.1 NODE_7936_length_112_cov_1.339286 gi|407262951|ref|XP_003945399.1| 90.00 30 2 1 106 17 240 268 8e-07 48.9 NODE_7936_length_112_cov_1.339286 gi|407261051|ref|XP_003946144.1| 90.00 30 2 1 106 17 240 268 8e-07 48.9 NODE_7948_length_125_cov_2.304000 gi|481019623|ref|YP_007877974.1| 44.83 29 15 1 149 63 59 86 5.7 28.9 NODE_7948_length_125_cov_2.304000 gi|491094259|ref|WP_004955865.1| 34.29 35 23 0 137 33 661 695 7.2 28.9 NODE_7956_length_500_cov_4.390000 gi|55956788|ref|NP_005372.2| 66.84 187 52 3 2 550 429 609 7e-64 215 NODE_7956_length_500_cov_4.390000 gi|55956788|ref|NP_005372.2| 37.21 129 74 3 149 523 389 514 3e-16 82.0 NODE_7956_length_500_cov_4.390000 gi|55956788|ref|NP_005372.2| 33.33 129 81 2 2 385 523 647 4e-08 57.0 NODE_7956_length_500_cov_4.390000 gi|55956788|ref|NP_005372.2| 26.40 125 78 4 167 529 309 423 0.22 37.0 NODE_7956_length_500_cov_4.390000 gi|84875537|ref|NP_035010.3| 63.98 186 54 3 2 550 431 606 1e-59 204 NODE_7956_length_500_cov_4.390000 gi|84875537|ref|NP_035010.3| 33.59 128 77 3 152 523 392 515 3e-12 69.7 NODE_7956_length_500_cov_4.390000 gi|84875537|ref|NP_035010.3| 33.33 129 77 2 2 385 524 644 1e-07 55.5 NODE_7956_length_500_cov_4.390000 gi|84875537|ref|NP_035010.3| 29.41 119 69 5 173 529 322 425 0.029 39.3 NODE_7956_length_500_cov_4.390000 gi|9994185|ref|NP_057174.1| 37.66 77 45 1 161 382 10 86 2e-09 59.7 NODE_7956_length_500_cov_4.390000 gi|493898426|ref|WP_006844263.1| 30.77 91 57 2 167 421 3 93 1e-08 55.1 NODE_7956_length_500_cov_4.390000 gi|4504715|ref|NP_003810.1| 27.69 195 122 5 2 538 138 329 7e-08 56.2 NODE_7956_length_500_cov_4.390000 gi|23346437|ref|NP_694693.1| 32.14 140 78 6 155 550 11 141 8e-08 55.8 NODE_7956_length_500_cov_4.390000 gi|5032069|ref|NP_005841.1| 32.14 140 78 6 155 550 11 141 8e-08 55.8 NODE_7956_length_500_cov_4.390000 gi|208431836|ref|NP_001129126.1| 27.69 195 122 5 2 538 138 329 8e-08 55.8 NODE_7956_length_500_cov_4.390000 gi|496427194|ref|WP_009136041.1| 29.59 98 63 3 164 439 2 99 1e-07 52.4 NODE_7956_length_500_cov_4.390000 gi|208431833|ref|NP_001129125.1| 27.69 195 122 5 2 538 138 329 1e-07 55.5 NODE_8004_length_261_cov_2.026820 gi|10863887|ref|NP_066924.1| 74.76 103 26 0 309 1 20 122 5e-52 169 NODE_8004_length_261_cov_2.026820 gi|7710002|ref|NP_057883.1| 73.79 103 27 0 309 1 20 122 2e-50 165 NODE_8004_length_261_cov_2.026820 gi|302318906|ref|NP_001180548.1| 62.14 103 39 0 309 1 20 122 2e-41 142 NODE_8004_length_261_cov_2.026820 gi|8393144|ref|NP_058583.1| 62.14 103 39 0 309 1 20 122 2e-41 142 NODE_8004_length_261_cov_2.026820 gi|297206813|ref|NP_001171952.1| 60.19 103 41 0 309 1 20 122 2e-40 137 NODE_8004_length_261_cov_2.026820 gi|297515502|ref|NP_001172046.1| 61.17 103 40 0 309 1 20 122 6e-40 139 NODE_8004_length_261_cov_2.026820 gi|297206811|ref|NP_001171951.1| 60.19 103 41 0 309 1 20 122 1e-39 137 NODE_8004_length_261_cov_2.026820 gi|153792186|ref|NP_001298.3| 60.19 103 41 0 309 1 20 122 1e-39 137 NODE_8004_length_261_cov_2.026820 gi|183979973|ref|NP_683763.2| 61.17 103 40 0 309 1 20 122 1e-39 138 NODE_8004_length_261_cov_2.026820 gi|183979975|ref|NP_001116867.1| 61.17 103 40 0 309 1 20 122 1e-39 137 NODE_8086_length_177_cov_1.694915 gi|493172907|ref|WP_006174984.1| 37.50 56 27 2 1 168 407 454 0.30 33.5 NODE_8086_length_177_cov_1.694915 gi|489954241|ref|WP_003857548.1| 35.71 56 28 2 1 168 407 454 0.54 32.7 NODE_8086_length_177_cov_1.694915 gi|493873627|ref|WP_006820074.1| 33.93 56 29 2 1 168 407 454 2.4 30.8 NODE_8086_length_177_cov_1.694915 gi|491361664|ref|WP_005219582.1| 34.15 41 24 1 31 153 24 61 7.2 29.3 NODE_8086_length_177_cov_1.694915 gi|497217900|ref|WP_009532162.1| 28.89 45 27 1 106 225 292 336 8.3 29.3 NODE_8086_length_177_cov_1.694915 gi|493735427|ref|WP_006684642.1| 30.36 56 31 2 1 168 407 454 9.3 28.9 NODE_8093_length_115_cov_1.582609 gi|219555707|ref|NP_001137232.1| 92.59 54 4 0 163 2 83 136 6e-31 112 NODE_8093_length_115_cov_1.582609 gi|29243942|ref|NP_808254.1| 94.44 54 3 0 163 2 53 106 2e-30 110 NODE_8093_length_115_cov_1.582609 gi|9966867|ref|NP_065123.1| 94.44 54 3 0 163 2 53 106 2e-30 110 NODE_8093_length_115_cov_1.582609 gi|262359900|ref|NP_001160068.1| 92.59 54 4 0 163 2 53 106 3e-30 110 NODE_8093_length_115_cov_1.582609 gi|262359898|ref|NP_001160067.1| 92.59 54 4 0 163 2 53 106 3e-30 110 NODE_8093_length_115_cov_1.582609 gi|262359896|ref|NP_001160066.1| 92.59 54 4 0 163 2 53 106 3e-30 110 NODE_8093_length_115_cov_1.582609 gi|262359894|ref|NP_001160065.1| 92.59 54 4 0 163 2 53 106 3e-30 110 NODE_8093_length_115_cov_1.582609 gi|262359891|ref|NP_001160064.1| 92.59 54 4 0 163 2 53 106 3e-30 110 NODE_8093_length_115_cov_1.582609 gi|262359889|ref|NP_001160063.1| 92.59 54 4 0 163 2 53 106 3e-30 110 NODE_8093_length_115_cov_1.582609 gi|262359887|ref|NP_001160062.1| 92.59 54 4 0 163 2 53 106 3e-30 110 NODE_8166_length_106_cov_3.820755 gi|494750693|ref|WP_007486101.1| 63.64 22 7 1 80 15 58 78 8.9 28.1 NODE_8166_length_106_cov_3.820755 gi|493930786|ref|WP_006875378.1| 40.00 30 18 0 51 140 35 64 9.1 26.6 NODE_8170_length_107_cov_1.467290 gi|491917641|ref|WP_005670950.1| 38.00 50 31 0 157 8 336 385 9e-05 43.5 NODE_8170_length_107_cov_1.467290 gi|46401749|ref|YP_006840.1| 34.48 29 19 0 121 35 22 50 1.2 29.3 NODE_8170_length_107_cov_1.467290 gi|490319206|ref|WP_004208699.1| 35.00 40 23 1 121 2 120 156 1.5 30.4 NODE_8170_length_107_cov_1.467290 gi|490375595|ref|WP_004255196.1| 30.77 39 27 0 133 17 174 212 3.0 29.6 NODE_8170_length_107_cov_1.467290 gi|493754408|ref|WP_006703291.1| 39.02 41 20 2 121 2 120 156 5.4 28.9 NODE_8191_length_149_cov_2.436242 gi|4503483|ref|NP_001952.1| 98.48 66 1 0 1 198 28 93 3e-36 134 NODE_8191_length_149_cov_2.436242 gi|33859482|ref|NP_031933.1| 98.48 66 1 0 1 198 28 93 4e-36 134 NODE_8191_length_149_cov_2.436242 gi|227908784|ref|NP_001153144.1| 59.62 52 21 0 1 156 28 79 7e-12 65.1 NODE_8191_length_149_cov_2.436242 gi|227908782|ref|NP_780526.2| 59.62 52 21 0 1 156 28 79 7e-12 65.1 NODE_8191_length_149_cov_2.436242 gi|94966754|ref|NP_078856.4| 59.62 52 21 0 1 156 28 79 8e-12 65.1 NODE_8191_length_149_cov_2.436242 gi|490132669|ref|WP_004033031.1| 39.66 58 35 0 1 174 24 81 1e-07 52.8 NODE_8191_length_149_cov_2.436242 gi|490960008|ref|WP_004821821.1| 43.55 62 33 2 1 186 16 75 1e-06 47.0 NODE_8191_length_149_cov_2.436242 gi|493646478|ref|WP_006598085.1| 46.55 58 30 1 1 174 18 74 4e-06 48.1 NODE_8191_length_149_cov_2.436242 gi|490970279|ref|WP_004832078.1| 43.10 58 32 1 1 174 17 73 9e-06 47.0 NODE_8191_length_149_cov_2.436242 gi|488927941|ref|WP_002839016.1| 42.37 59 33 1 1 177 17 74 1e-05 47.0 NODE_8196_length_109_cov_1.825688 gi|493895109|ref|WP_006841037.1| 41.67 36 21 0 10 117 22 57 1.4 30.4 NODE_8196_length_109_cov_1.825688 gi|488971639|ref|WP_002882570.1| 48.65 37 16 1 159 49 45 78 3.5 29.6 NODE_8196_length_109_cov_1.825688 gi|493135698|ref|WP_006154282.1| 44.74 38 18 1 159 46 45 79 6.6 28.1 NODE_8196_length_109_cov_1.825688 gi|446773341|ref|WP_000850597.1| 45.95 37 17 1 159 49 45 78 7.0 28.5 NODE_8196_length_109_cov_1.825688 gi|331266607|ref|YP_004326237.1| 45.95 37 17 1 159 49 45 78 7.0 28.5 NODE_8196_length_109_cov_1.825688 gi|446773313|ref|WP_000850569.1| 45.95 37 17 1 159 49 45 78 7.0 28.5 NODE_8196_length_109_cov_1.825688 gi|446773340|ref|WP_000850596.1| 45.95 37 17 1 159 49 45 78 7.4 28.5 NODE_8196_length_109_cov_1.825688 gi|446773314|ref|WP_000850570.1| 45.95 37 17 1 159 49 45 78 7.4 28.5 NODE_8196_length_109_cov_1.825688 gi|446714424|ref|WP_000791755.1| 45.95 37 17 1 159 49 45 78 7.4 28.5 NODE_8196_length_109_cov_1.825688 gi|446773343|ref|WP_000850599.1| 45.95 37 17 1 159 49 45 78 7.5 28.5 NODE_8227_length_113_cov_3.070796 gi|33859482|ref|NP_031933.1| 98.15 54 1 0 162 1 131 184 2e-28 111 NODE_8227_length_113_cov_3.070796 gi|4503483|ref|NP_001952.1| 98.15 54 1 0 162 1 131 184 6e-28 110 NODE_8227_length_113_cov_3.070796 gi|490132669|ref|WP_004033031.1| 58.00 50 21 0 159 10 116 165 2e-10 60.5 NODE_8227_length_113_cov_3.070796 gi|94966754|ref|NP_078856.4| 50.94 53 26 0 162 4 119 171 3e-10 60.1 NODE_8227_length_113_cov_3.070796 gi|94966752|ref|NP_001035700.1| 50.94 53 26 0 162 4 68 120 3e-10 60.1 NODE_8227_length_113_cov_3.070796 gi|227908784|ref|NP_001153144.1| 50.94 53 26 0 162 4 119 171 3e-10 60.1 NODE_8227_length_113_cov_3.070796 gi|227908782|ref|NP_780526.2| 50.94 53 26 0 162 4 119 171 3e-10 60.1 NODE_8227_length_113_cov_3.070796 gi|385298680|ref|NP_001245283.1| 38.00 50 31 0 153 4 224 273 6e-05 44.3 NODE_8227_length_113_cov_3.070796 gi|6755594|ref|NP_035561.1| 38.00 50 31 0 153 4 233 282 7e-05 44.3 NODE_8227_length_113_cov_3.070796 gi|158508674|ref|NP_001103465.1| 38.00 50 31 0 153 4 234 283 7e-05 44.3 NODE_8308_length_195_cov_2.666667 gi|46849812|ref|NP_034363.1| 86.42 81 11 0 244 2 2285 2365 1e-45 163 NODE_8308_length_195_cov_2.666667 gi|46849812|ref|NP_034363.1| 41.10 73 40 2 220 5 95 165 8e-13 68.9 NODE_8308_length_195_cov_2.666667 gi|46849812|ref|NP_034363.1| 31.17 77 51 1 229 5 181 257 7e-09 57.0 NODE_8308_length_195_cov_2.666667 gi|46849812|ref|NP_034363.1| 40.30 67 35 4 193 5 146 211 2e-05 47.0 NODE_8308_length_195_cov_2.666667 gi|46849812|ref|NP_034363.1| 31.48 54 35 1 184 29 525 578 0.001 41.2 NODE_8308_length_195_cov_2.666667 gi|46849812|ref|NP_034363.1| 25.35 71 49 1 202 2 472 542 0.002 40.8 NODE_8308_length_195_cov_2.666667 gi|46849812|ref|NP_034363.1| 40.48 42 24 1 217 92 559 599 0.003 40.0 NODE_8308_length_195_cov_2.666667 gi|46849812|ref|NP_034363.1| 24.27 103 46 2 217 5 230 332 0.042 36.6 NODE_8308_length_195_cov_2.666667 gi|47132557|ref|NP_997647.1| 82.72 81 14 0 244 2 2286 2366 2e-45 162 NODE_8308_length_195_cov_2.666667 gi|47132557|ref|NP_997647.1| 40.54 74 41 2 223 5 93 164 2e-12 67.8 NODE_8308_length_195_cov_2.666667 gi|47132557|ref|NP_997647.1| 32.47 77 50 1 229 5 180 256 3e-09 58.2 NODE_8308_length_195_cov_2.666667 gi|47132557|ref|NP_997647.1| 40.30 67 35 4 193 5 145 210 4e-05 45.8 NODE_8308_length_195_cov_2.666667 gi|47132557|ref|NP_997647.1| 33.33 54 34 1 184 29 525 578 3e-04 43.5 NODE_8308_length_195_cov_2.666667 gi|47132557|ref|NP_997647.1| 42.86 42 23 1 217 92 559 599 5e-04 42.7 NODE_8308_length_195_cov_2.666667 gi|47132557|ref|NP_997647.1| 25.35 71 49 1 202 2 472 542 0.001 41.6 NODE_8308_length_195_cov_2.666667 gi|47132557|ref|NP_997647.1| 24.04 104 46 2 217 5 229 332 0.11 35.4 NODE_8308_length_195_cov_2.666667 gi|16933542|ref|NP_002017.1| 82.72 81 14 0 244 2 2164 2244 3e-45 162 NODE_8308_length_195_cov_2.666667 gi|16933542|ref|NP_002017.1| 40.54 74 41 2 223 5 93 164 2e-12 67.8 NODE_8308_length_195_cov_2.666667 gi|16933542|ref|NP_002017.1| 32.47 77 50 1 229 5 180 256 3e-09 58.2 NODE_8308_length_195_cov_2.666667 gi|16933542|ref|NP_002017.1| 40.30 67 35 4 193 5 145 210 5e-05 45.8 NODE_8308_length_195_cov_2.666667 gi|16933542|ref|NP_002017.1| 33.33 54 34 1 184 29 525 578 3e-04 43.5 NODE_8308_length_195_cov_2.666667 gi|16933542|ref|NP_002017.1| 42.86 42 23 1 217 92 559 599 5e-04 42.4 NODE_8308_length_195_cov_2.666667 gi|16933542|ref|NP_002017.1| 25.35 71 49 1 202 2 472 542 0.001 41.6 NODE_8308_length_195_cov_2.666667 gi|16933542|ref|NP_002017.1| 24.04 104 46 2 217 5 229 332 0.11 35.0 NODE_8308_length_195_cov_2.666667 gi|47132553|ref|NP_997641.1| 82.72 81 14 0 244 2 2105 2185 4e-45 162 NODE_8308_length_195_cov_2.666667 gi|47132553|ref|NP_997641.1| 40.54 74 41 2 223 5 93 164 2e-12 67.4 NODE_8308_length_195_cov_2.666667 gi|47132553|ref|NP_997641.1| 32.47 77 50 1 229 5 180 256 4e-09 57.8 NODE_8308_length_195_cov_2.666667 gi|47132553|ref|NP_997641.1| 40.30 67 35 4 193 5 145 210 5e-05 45.4 NODE_8308_length_195_cov_2.666667 gi|47132553|ref|NP_997641.1| 33.33 54 34 1 184 29 525 578 3e-04 43.1 NODE_8308_length_195_cov_2.666667 gi|47132553|ref|NP_997641.1| 42.86 42 23 1 217 92 559 599 6e-04 42.4 NODE_8308_length_195_cov_2.666667 gi|47132553|ref|NP_997641.1| 25.35 71 49 1 202 2 472 542 0.001 41.6 NODE_8308_length_195_cov_2.666667 gi|47132553|ref|NP_997641.1| 24.04 104 46 2 217 5 229 332 0.13 35.0 NODE_8308_length_195_cov_2.666667 gi|47132555|ref|NP_997643.1| 82.72 81 14 0 244 2 2139 2219 7e-44 158 NODE_8308_length_195_cov_2.666667 gi|47132555|ref|NP_997643.1| 40.54 74 41 2 223 5 93 164 1e-11 65.5 NODE_8308_length_195_cov_2.666667 gi|47132555|ref|NP_997643.1| 32.47 77 50 1 229 5 180 256 4e-08 55.1 NODE_8308_length_195_cov_2.666667 gi|47132555|ref|NP_997643.1| 40.68 59 31 3 193 29 145 203 2e-04 43.5 NODE_8308_length_195_cov_2.666667 gi|47132555|ref|NP_997643.1| 33.33 54 34 1 184 29 525 578 0.002 40.4 NODE_8308_length_195_cov_2.666667 gi|47132555|ref|NP_997643.1| 25.00 68 47 1 193 2 475 542 0.004 39.7 NODE_8308_length_195_cov_2.666667 gi|47132555|ref|NP_997643.1| 42.86 42 23 1 217 92 559 599 0.015 38.1 NODE_8308_length_195_cov_2.666667 gi|47132555|ref|NP_997643.1| 23.53 102 45 1 211 5 231 332 1.0 32.0 NODE_8308_length_195_cov_2.666667 gi|47132549|ref|NP_997639.1| 83.75 80 13 0 241 2 1986 2065 8e-44 158 NODE_8308_length_195_cov_2.666667 gi|47132549|ref|NP_997639.1| 40.54 74 41 2 223 5 93 164 1e-11 65.5 NODE_8308_length_195_cov_2.666667 gi|47132549|ref|NP_997639.1| 32.47 77 50 1 229 5 180 256 3e-08 55.1 NODE_8308_length_195_cov_2.666667 gi|47132549|ref|NP_997639.1| 40.68 59 31 3 193 29 145 203 2e-04 43.5 NODE_8308_length_195_cov_2.666667 gi|47132549|ref|NP_997639.1| 33.33 54 34 1 184 29 525 578 0.002 40.4 NODE_8308_length_195_cov_2.666667 gi|47132549|ref|NP_997639.1| 25.37 67 46 1 193 5 475 541 0.004 39.7 NODE_8308_length_195_cov_2.666667 gi|47132549|ref|NP_997639.1| 42.86 42 23 1 217 92 559 599 0.015 38.1 NODE_8308_length_195_cov_2.666667 gi|47132549|ref|NP_997639.1| 23.53 102 45 1 211 5 231 332 1.0 32.3 NODE_8308_length_195_cov_2.666667 gi|47132547|ref|NP_473375.2| 40.54 74 41 2 223 5 93 164 7e-11 62.8 NODE_8308_length_195_cov_2.666667 gi|47132547|ref|NP_473375.2| 32.47 77 50 1 229 5 180 256 8e-08 53.5 NODE_8308_length_195_cov_2.666667 gi|47132547|ref|NP_473375.2| 40.68 59 31 3 193 29 145 203 0.001 41.6 NODE_8308_length_195_cov_2.666667 gi|47132547|ref|NP_473375.2| 33.33 54 34 1 184 29 525 578 0.006 38.9 NODE_8308_length_195_cov_2.666667 gi|47132547|ref|NP_473375.2| 25.35 71 49 1 202 2 472 542 0.011 38.1 NODE_8308_length_195_cov_2.666667 gi|47132547|ref|NP_473375.2| 42.86 42 23 1 217 92 559 599 0.023 37.4 NODE_8308_length_195_cov_2.666667 gi|47132547|ref|NP_473375.2| 33.33 45 30 0 223 89 227 271 2.6 30.8 NODE_8308_length_195_cov_2.666667 gi|27881494|ref|NP_775082.1| 30.14 73 37 4 229 23 1437 1499 3.5 30.4 NODE_8308_length_195_cov_2.666667 gi|16554449|ref|NP_003377.1| 30.14 73 37 4 229 23 1437 1499 3.5 30.4 NODE_8308_length_195_cov_2.666667 gi|116256333|ref|NP_009220.2| 34.62 52 33 1 166 11 607 657 3.5 30.4 NODE_8312_length_134_cov_2.686567 gi|495113824|ref|WP_007838643.1| 34.69 49 30 1 15 155 133 181 0.49 32.3 NODE_8312_length_134_cov_2.686567 gi|492328979|ref|WP_005811289.1| 39.47 38 19 1 183 70 207 240 1.5 30.8 NODE_8320_length_104_cov_1.432692 gi|133505571|ref|NP_898867.1| 76.00 50 12 0 152 3 371 420 1e-16 78.6 NODE_8320_length_104_cov_1.432692 gi|46049114|ref|NP_057279.2| 76.00 50 12 0 152 3 372 421 1e-16 78.2 NODE_8320_length_104_cov_1.432692 gi|261862322|ref|NP_001159879.1| 64.00 50 17 1 152 3 399 447 8e-12 64.3 NODE_8320_length_104_cov_1.432692 gi|261862320|ref|NP_001159878.1| 64.00 50 17 1 152 3 399 447 8e-12 64.3 NODE_8320_length_104_cov_1.432692 gi|6679597|ref|NP_033030.1| 64.00 50 17 1 152 3 399 447 8e-12 64.3 NODE_8320_length_104_cov_1.432692 gi|5032013|ref|NP_005724.1| 64.00 50 17 1 152 3 400 448 1e-11 63.9 NODE_8320_length_104_cov_1.432692 gi|6754472|ref|NP_004847.2| 57.14 49 21 0 149 3 330 378 3e-10 59.7 NODE_8320_length_104_cov_1.432692 gi|256985168|ref|NP_077207.3| 55.10 49 22 0 149 3 330 378 3e-10 59.7 NODE_8320_length_104_cov_1.432692 gi|20143967|ref|NP_612565.1| 57.14 49 21 0 149 3 330 378 4e-10 59.3 NODE_8320_length_104_cov_1.432692 gi|46852172|ref|NP_056069.2| 65.22 46 16 0 152 15 245 290 1e-08 55.1 NODE_8322_length_115_cov_1.800000 gi|156151392|ref|NP_001095867.1| 100.00 55 0 0 165 1 234 288 1e-29 113 NODE_8322_length_115_cov_1.800000 gi|156151396|ref|NP_001095869.1| 100.00 55 0 0 165 1 237 291 1e-29 113 NODE_8322_length_115_cov_1.800000 gi|33859724|ref|NP_083147.1| 100.00 55 0 0 165 1 335 389 3e-29 113 NODE_8322_length_115_cov_1.800000 gi|5031755|ref|NP_005817.1| 100.00 55 0 0 165 1 335 389 3e-29 113 NODE_8322_length_115_cov_1.800000 gi|156151394|ref|NP_001095868.1| 100.00 55 0 0 165 1 338 392 3e-29 113 NODE_8322_length_115_cov_1.800000 gi|29788787|ref|NP_062770.1| 87.27 55 7 0 165 1 332 386 2e-24 99.4 NODE_8322_length_115_cov_1.800000 gi|114145493|ref|NP_062640.2| 87.27 55 7 0 165 1 332 386 5e-24 98.6 NODE_8322_length_115_cov_1.800000 gi|228008400|ref|NP_001153149.1| 85.45 55 8 0 165 1 332 386 7e-24 98.2 NODE_8322_length_115_cov_1.800000 gi|228008293|ref|NP_001153148.1| 85.45 55 8 0 165 1 332 386 7e-24 98.2 NODE_8322_length_115_cov_1.800000 gi|359338991|ref|NP_001240700.1| 85.45 55 8 0 165 1 180 234 8e-24 96.3 NODE_8375_length_623_cov_5.855538 gi|251831117|ref|YP_003024036.1| 67.66 167 54 0 603 103 287 453 1e-58 201 NODE_8375_length_623_cov_5.855538 gi|34538608|ref|NP_904338.1| 64.21 190 68 0 672 103 264 453 4e-55 192 NODE_8375_length_623_cov_5.855538 gi|494060703|ref|WP_007002786.1| 52.25 111 53 0 603 271 293 403 8e-35 135 NODE_8375_length_623_cov_5.855538 gi|489880098|ref|WP_003783566.1| 52.73 110 52 0 579 250 309 418 2e-31 126 NODE_8375_length_623_cov_5.855538 gi|488718785|ref|WP_002642661.1| 52.78 108 51 0 579 256 309 416 7e-31 125 NODE_8375_length_623_cov_5.855538 gi|489884516|ref|WP_003787966.1| 52.78 108 51 0 579 256 309 416 8e-31 125 NODE_8375_length_623_cov_5.855538 gi|489919575|ref|WP_003822936.1| 51.85 108 52 0 579 256 309 416 2e-30 124 NODE_8375_length_623_cov_5.855538 gi|490654142|ref|WP_004519133.1| 50.00 116 58 0 603 256 176 291 3e-30 122 NODE_8375_length_623_cov_5.855538 gi|489895414|ref|WP_003798863.1| 48.31 118 61 0 603 250 301 418 3e-30 123 NODE_8375_length_623_cov_5.855538 gi|493897385|ref|WP_006843254.1| 54.55 110 50 0 603 274 291 400 6e-30 122 NODE_8402_length_121_cov_2.066116 gi|46849812|ref|NP_034363.1| 77.78 54 12 0 163 2 1668 1721 2e-19 87.0 NODE_8402_length_121_cov_2.066116 gi|46849812|ref|NP_034363.1| 36.36 55 34 1 169 5 1938 1991 0.001 40.8 NODE_8402_length_121_cov_2.066116 gi|46849812|ref|NP_034363.1| 45.95 37 20 0 118 8 1227 1263 0.031 36.2 NODE_8402_length_121_cov_2.066116 gi|46849812|ref|NP_034363.1| 41.30 46 27 0 163 26 1848 1893 0.053 35.8 NODE_8402_length_121_cov_2.066116 gi|46849812|ref|NP_034363.1| 39.53 43 26 0 148 20 1489 1531 0.081 35.0 NODE_8402_length_121_cov_2.066116 gi|46849812|ref|NP_034363.1| 37.21 43 27 0 148 20 850 892 0.14 34.3 NODE_8402_length_121_cov_2.066116 gi|46849812|ref|NP_034363.1| 44.12 34 19 0 121 20 2043 2076 2.2 30.4 NODE_8402_length_121_cov_2.066116 gi|46849812|ref|NP_034363.1| 48.15 27 14 0 100 20 1779 1805 7.0 28.9 NODE_8402_length_121_cov_2.066116 gi|46849812|ref|NP_034363.1| 29.27 41 29 0 154 32 1577 1617 7.6 28.9 NODE_8402_length_121_cov_2.066116 gi|47132555|ref|NP_997643.1| 77.78 54 12 0 163 2 1578 1631 2e-18 84.0 NODE_8402_length_121_cov_2.066116 gi|47132555|ref|NP_997643.1| 40.00 55 32 1 169 5 1848 1901 0.001 40.4 NODE_8402_length_121_cov_2.066116 gi|47132555|ref|NP_997643.1| 39.53 43 26 0 148 20 851 893 0.048 35.8 NODE_8402_length_121_cov_2.066116 gi|47132555|ref|NP_997643.1| 41.30 46 27 0 163 26 1758 1803 0.049 35.8 NODE_8402_length_121_cov_2.066116 gi|47132555|ref|NP_997643.1| 40.00 40 24 0 127 8 1225 1264 0.056 35.4 NODE_8402_length_121_cov_2.066116 gi|47132555|ref|NP_997643.1| 39.02 41 25 0 154 32 1487 1527 0.069 35.4 NODE_8402_length_121_cov_2.066116 gi|47132555|ref|NP_997643.1| 44.12 34 19 0 121 20 1953 1986 2.3 30.4 NODE_8402_length_121_cov_2.066116 gi|47132555|ref|NP_997643.1| 46.88 32 17 0 100 5 1689 1720 3.1 30.0 NODE_8402_length_121_cov_2.066116 gi|16933542|ref|NP_002017.1| 77.78 54 12 0 163 2 1578 1631 2e-18 83.6 NODE_8402_length_121_cov_2.066116 gi|16933542|ref|NP_002017.1| 40.00 55 32 1 169 5 1848 1901 0.001 40.8 NODE_8402_length_121_cov_2.066116 gi|16933542|ref|NP_002017.1| 39.53 43 26 0 148 20 851 893 0.048 35.8 NODE_8402_length_121_cov_2.066116 gi|16933542|ref|NP_002017.1| 41.30 46 27 0 163 26 1758 1803 0.049 35.8 NODE_8402_length_121_cov_2.066116 gi|16933542|ref|NP_002017.1| 40.00 40 24 0 127 8 1225 1264 0.056 35.4 NODE_8402_length_121_cov_2.066116 gi|16933542|ref|NP_002017.1| 39.02 41 25 0 154 32 1487 1527 0.070 35.4 NODE_8402_length_121_cov_2.066116 gi|16933542|ref|NP_002017.1| 44.12 34 19 0 121 20 1953 1986 2.3 30.4 NODE_8402_length_121_cov_2.066116 gi|16933542|ref|NP_002017.1| 46.88 32 17 0 100 5 1689 1720 3.1 30.0 NODE_8402_length_121_cov_2.066116 gi|47132557|ref|NP_997647.1| 77.78 54 12 0 163 2 1669 1722 3e-18 83.6 NODE_8402_length_121_cov_2.066116 gi|47132557|ref|NP_997647.1| 40.00 55 32 1 169 5 1939 1992 0.001 40.4 NODE_8402_length_121_cov_2.066116 gi|47132557|ref|NP_997647.1| 41.30 46 27 0 163 26 1849 1894 0.051 35.8 NODE_8402_length_121_cov_2.066116 gi|47132557|ref|NP_997647.1| 39.53 43 26 0 148 20 851 893 0.052 35.8 NODE_8402_length_121_cov_2.066116 gi|47132557|ref|NP_997647.1| 40.00 40 24 0 127 8 1225 1264 0.063 35.4 NODE_8402_length_121_cov_2.066116 gi|47132557|ref|NP_997647.1| 39.02 41 25 0 154 32 1578 1618 0.073 35.0 NODE_8402_length_121_cov_2.066116 gi|47132557|ref|NP_997647.1| 44.12 34 19 0 121 20 2044 2077 2.4 30.4 NODE_8402_length_121_cov_2.066116 gi|47132557|ref|NP_997647.1| 46.88 32 17 0 100 5 1780 1811 3.3 30.0 NODE_8402_length_121_cov_2.066116 gi|47132549|ref|NP_997639.1| 77.36 53 12 0 163 5 1578 1630 1e-17 81.6 NODE_8402_length_121_cov_2.066116 gi|47132549|ref|NP_997639.1| 40.00 55 32 1 169 5 1758 1811 0.001 40.8 NODE_8402_length_121_cov_2.066116 gi|47132549|ref|NP_997639.1| 41.30 46 27 0 163 26 1668 1713 0.046 35.8 NODE_8402_length_121_cov_2.066116 gi|47132549|ref|NP_997639.1| 39.53 43 26 0 148 20 851 893 0.046 35.8 NODE_8402_length_121_cov_2.066116 gi|47132549|ref|NP_997639.1| 40.00 40 24 0 127 8 1225 1264 0.054 35.4 NODE_8402_length_121_cov_2.066116 gi|47132549|ref|NP_997639.1| 39.02 41 25 0 154 32 1487 1527 0.068 35.4 NODE_8402_length_121_cov_2.066116 gi|47132549|ref|NP_997639.1| 44.12 34 19 0 121 20 1863 1896 2.2 30.4 NODE_8402_length_121_cov_2.066116 gi|47132553|ref|NP_997641.1| 77.36 53 12 0 163 5 1578 1630 1e-17 81.3 NODE_8402_length_121_cov_2.066116 gi|47132553|ref|NP_997641.1| 40.00 55 32 1 169 5 1758 1811 0.001 40.4 NODE_8402_length_121_cov_2.066116 gi|47132553|ref|NP_997641.1| 39.53 43 26 0 148 20 851 893 0.049 35.8 NODE_8402_length_121_cov_2.066116 gi|47132553|ref|NP_997641.1| 41.30 46 27 0 163 26 1668 1713 0.052 35.8 NODE_8402_length_121_cov_2.066116 gi|47132553|ref|NP_997641.1| 40.00 40 24 0 127 8 1225 1264 0.057 35.4 NODE_8402_length_121_cov_2.066116 gi|47132553|ref|NP_997641.1| 39.02 41 25 0 154 32 1487 1527 0.074 35.0 NODE_8402_length_121_cov_2.066116 gi|47132553|ref|NP_997641.1| 44.12 34 19 0 121 20 1863 1896 2.2 30.4 NODE_8402_length_121_cov_2.066116 gi|93141047|ref|NP_004361.3| 43.48 46 26 0 142 5 948 993 0.002 40.0 NODE_8402_length_121_cov_2.066116 gi|93141047|ref|NP_004361.3| 39.47 38 23 0 118 5 2165 2202 1.0 31.6 NODE_8402_length_121_cov_2.066116 gi|93141047|ref|NP_004361.3| 35.42 48 31 0 148 5 763 810 2.5 30.4 NODE_8402_length_121_cov_2.066116 gi|126722834|ref|NP_035737.2| 37.74 53 33 0 163 5 658 710 0.006 38.5 NODE_8402_length_121_cov_2.066116 gi|115647999|ref|NP_031764.2| 37.74 53 33 0 160 2 633 685 0.020 37.0 NODE_8402_length_121_cov_2.066116 gi|115647999|ref|NP_031764.2| 50.00 32 16 0 154 59 723 754 0.28 33.5 NODE_8402_length_121_cov_2.066116 gi|115647999|ref|NP_031764.2| 45.83 24 13 0 127 56 463 486 1.9 30.8 NODE_8402_length_121_cov_2.066116 gi|153946395|ref|NP_002151.2| 41.46 41 24 0 127 5 670 710 0.025 36.6 NODE_8402_length_121_cov_2.066116 gi|153946395|ref|NP_002151.2| 37.78 45 25 1 130 5 939 983 6.0 29.3 NODE_8402_length_121_cov_2.066116 gi|153946395|ref|NP_002151.2| 33.33 48 32 0 148 5 844 891 9.3 28.5 NODE_8433_length_196_cov_2.795918 gi|433652797|ref|YP_007296651.1| 60.00 20 8 0 137 78 241 260 7.4 29.3 NODE_8499_length_180_cov_5.250000 gi|393715095|ref|NP_001257329.1| 100.00 76 0 0 2 229 34 109 6e-47 160 NODE_8499_length_180_cov_5.250000 gi|57013276|ref|NP_006073.2| 100.00 76 0 0 2 229 69 144 1e-46 160 NODE_8499_length_180_cov_5.250000 gi|34740335|ref|NP_035784.1| 100.00 76 0 0 2 229 69 144 1e-46 160 NODE_8499_length_180_cov_5.250000 gi|393715091|ref|NP_001257328.1| 100.00 76 0 0 2 229 69 144 1e-46 160 NODE_8499_length_180_cov_5.250000 gi|17986283|ref|NP_006000.2| 100.00 76 0 0 2 229 69 144 1e-46 160 NODE_8499_length_180_cov_5.250000 gi|6755901|ref|NP_035783.1| 100.00 76 0 0 2 229 69 144 1e-46 160 NODE_8499_length_180_cov_5.250000 gi|6678469|ref|NP_033474.1| 100.00 76 0 0 2 229 69 144 1e-46 160 NODE_8499_length_180_cov_5.250000 gi|14389309|ref|NP_116093.1| 100.00 76 0 0 2 229 69 144 1e-46 160 NODE_8499_length_180_cov_5.250000 gi|82930689|ref|XP_909750.1| 97.37 76 2 0 2 229 68 143 1e-46 160 NODE_8499_length_180_cov_5.250000 gi|51765047|ref|XP_486246.1| 97.37 76 2 0 2 229 68 143 1e-46 160 NODE_8534_length_387_cov_3.046512 gi|410172476|ref|XP_003960507.1| 80.65 31 6 0 78 170 1 31 0.50 33.5 NODE_8534_length_387_cov_3.046512 gi|113420837|ref|XP_001126659.1| 80.65 31 6 0 78 170 1 31 0.50 33.5 NODE_8534_length_387_cov_3.046512 gi|7110705|ref|NP_032998.1| 83.87 31 5 0 78 170 1 31 3.1 31.6 NODE_8534_length_387_cov_3.046512 gi|151101407|ref|NP_001092755.1| 83.87 31 5 0 78 170 1 31 3.7 31.2 NODE_8534_length_387_cov_3.046512 gi|151101404|ref|NP_002814.3| 83.87 31 5 0 78 170 1 31 3.9 31.2 NODE_8560_length_276_cov_4.199275 gi|149273202|ref|XP_001476757.1| 87.50 96 12 0 39 326 1 96 6e-55 181 NODE_8560_length_276_cov_4.199275 gi|6679937|ref|NP_032110.1| 87.50 96 12 0 39 326 1 96 6e-55 181 NODE_8560_length_276_cov_4.199275 gi|407261725|ref|XP_001479421.4| 86.60 97 13 0 36 326 76 172 1e-54 182 NODE_8560_length_276_cov_4.199275 gi|7669492|ref|NP_002037.2| 88.42 95 11 0 42 326 4 98 1e-52 174 NODE_8560_length_276_cov_4.199275 gi|496426516|ref|WP_009135363.1| 61.05 95 36 1 42 326 4 97 1e-35 130 NODE_8560_length_276_cov_4.199275 gi|493397705|ref|WP_006353816.1| 62.50 96 35 1 42 326 3 98 2e-35 130 NODE_8560_length_276_cov_4.199275 gi|489623427|ref|WP_003527867.1| 59.38 96 38 1 42 326 3 98 2e-34 127 NODE_8560_length_276_cov_4.199275 gi|493929818|ref|WP_006874436.1| 62.50 96 35 1 42 326 3 98 4e-34 126 NODE_8560_length_276_cov_4.199275 gi|7657116|ref|NP_055179.1| 60.00 95 37 1 42 326 76 169 8e-34 126 NODE_8560_length_276_cov_4.199275 gi|493896295|ref|WP_006842178.1| 58.33 96 39 1 39 326 1 95 6e-33 123 NODE_8644_length_271_cov_2.169742 gi|124487199|ref|NP_001074632.1| 32.73 55 36 1 188 24 24 77 5.2 30.8 NODE_8644_length_271_cov_2.169742 gi|491920844|ref|WP_005673165.1| 45.00 40 20 1 113 232 35 72 8.5 30.0 NODE_8695_length_287_cov_2.369338 gi|358356404|ref|NP_001240312.1| 99.11 112 1 0 2 337 20 131 2e-61 194 NODE_8695_length_287_cov_2.369338 gi|358356402|ref|NP_001240311.1| 99.11 112 1 0 2 337 20 131 2e-61 194 NODE_8695_length_287_cov_2.369338 gi|358356398|ref|NP_001240309.1| 99.11 112 1 0 2 337 20 131 2e-61 194 NODE_8695_length_287_cov_2.369338 gi|358356396|ref|NP_001240308.1| 99.11 112 1 0 2 337 20 131 2e-61 194 NODE_8695_length_287_cov_2.369338 gi|15431293|ref|NP_002939.2| 99.11 112 1 0 2 337 20 131 2e-61 194 NODE_8695_length_287_cov_2.369338 gi|13385036|ref|NP_079862.1| 99.11 112 1 0 2 337 20 131 2e-61 194 NODE_8695_length_287_cov_2.369338 gi|149267527|ref|XP_001481087.1| 98.21 112 2 0 2 337 20 131 1e-60 192 NODE_8695_length_287_cov_2.369338 gi|309265700|ref|XP_003086580.1| 95.54 112 5 0 2 337 20 131 8e-60 189 NODE_8695_length_287_cov_2.369338 gi|149255418|ref|XP_001481082.1| 95.54 112 5 0 2 337 20 131 8e-60 189 NODE_8695_length_287_cov_2.369338 gi|358356407|ref|NP_001240313.1| 95.28 106 5 0 2 319 20 125 8e-54 172 NODE_8699_length_220_cov_3.086364 gi|149251177|ref|XP_001474740.1| 89.89 89 9 0 268 2 25 113 6e-32 117 NODE_8699_length_220_cov_3.086364 gi|33186863|ref|NP_058018.2| 91.01 89 8 0 268 2 25 113 8e-32 117 NODE_8699_length_220_cov_3.086364 gi|15431297|ref|NP_000968.2| 91.01 89 8 0 268 2 25 113 8e-32 117 NODE_8699_length_220_cov_3.086364 gi|15431295|ref|NP_150254.1| 91.01 89 8 0 268 2 25 113 8e-32 117 NODE_8699_length_220_cov_3.086364 gi|341604768|ref|NP_001230059.1| 73.03 89 5 1 268 2 25 94 7e-16 74.3 NODE_8699_length_220_cov_3.086364 gi|341604770|ref|NP_001230060.1| 89.23 65 7 0 268 74 25 89 2e-15 72.8 NODE_8699_length_220_cov_3.086364 gi|377836465|ref|XP_003689020.1| 52.38 63 9 1 190 2 51 92 1e-11 62.4 NODE_8699_length_220_cov_3.086364 gi|377834617|ref|XP_003689509.1| 52.38 63 9 1 190 2 51 92 1e-11 62.4 NODE_8699_length_220_cov_3.086364 gi|377836467|ref|XP_003689021.1| 62.50 40 14 1 190 74 51 90 3e-09 55.1 NODE_8699_length_220_cov_3.086364 gi|377834619|ref|XP_003689510.1| 62.50 40 14 1 190 74 51 90 3e-09 55.1 NODE_8717_length_103_cov_2.271845 gi|77539055|ref|NP_001029102.1| 97.96 49 1 0 148 2 1 49 2e-26 99.4 NODE_8717_length_103_cov_2.271845 gi|9845265|ref|NP_063936.1| 97.96 49 1 0 148 2 1 49 2e-26 99.4 NODE_8717_length_103_cov_2.271845 gi|4507761|ref|NP_003324.1| 97.96 49 1 0 148 2 1 49 2e-26 99.4 NODE_8717_length_103_cov_2.271845 gi|294459921|ref|NP_001170884.1| 97.96 49 1 0 148 2 1 49 2e-26 99.8 NODE_8717_length_103_cov_2.271845 gi|208022622|ref|NP_001129064.1| 97.96 49 1 0 148 2 1 49 2e-26 99.8 NODE_8717_length_103_cov_2.271845 gi|4506713|ref|NP_002945.1| 97.96 49 1 0 148 2 1 49 2e-26 99.8 NODE_8717_length_103_cov_2.271845 gi|40556034|ref|NP_955119.1| 95.92 49 2 0 148 2 1 49 2e-26 97.8 NODE_8717_length_103_cov_2.271845 gi|76443694|ref|NP_001029037.1| 97.96 49 1 0 148 2 1 49 2e-26 99.8 NODE_8717_length_103_cov_2.271845 gi|13195690|ref|NP_077239.1| 97.96 49 1 0 148 2 1 49 2e-26 99.8 NODE_8717_length_103_cov_2.271845 gi|94378076|ref|XP_001002242.1| 95.92 49 2 0 148 2 1 49 3e-25 96.7 NODE_8779_length_359_cov_2.512535 gi|255308899|ref|NP_038790.2| 95.56 135 6 0 3 407 170 304 8e-78 243 NODE_8779_length_359_cov_2.512535 gi|4506649|ref|NP_000958.1| 95.56 135 6 0 3 407 170 304 1e-77 243 NODE_8779_length_359_cov_2.512535 gi|76496472|ref|NP_001029025.1| 94.62 130 7 0 18 407 126 255 1e-73 231 NODE_8779_length_359_cov_2.512535 gi|309268181|ref|XP_001475783.2| 91.11 135 12 0 3 407 170 304 4e-72 228 NODE_8779_length_359_cov_2.512535 gi|13384820|ref|NP_079701.1| 76.30 135 32 0 3 407 3 137 3e-65 206 NODE_8779_length_359_cov_2.512535 gi|4826988|ref|NP_005052.1| 78.52 135 29 0 3 407 170 304 6e-64 207 NODE_8779_length_359_cov_2.512535 gi|255653009|ref|NP_001157417.1| 76.30 135 32 0 3 407 170 304 6e-63 204 NODE_8779_length_359_cov_2.512535 gi|309266996|ref|XP_001476854.2| 94.44 72 4 0 192 407 10 81 5e-42 144 NODE_8779_length_359_cov_2.512535 gi|148642822|ref|YP_001273335.1| 38.64 132 75 2 18 395 153 284 6e-14 72.0 NODE_8779_length_359_cov_2.512535 gi|491673190|ref|WP_005529332.1| 30.59 85 53 2 257 15 131 213 0.26 35.0 NODE_8789_length_102_cov_1.960784 gi|156151392|ref|NP_001095867.1| 98.00 50 1 0 1 150 175 224 2e-28 110 NODE_8789_length_102_cov_1.960784 gi|156151396|ref|NP_001095869.1| 98.00 50 1 0 1 150 178 227 2e-28 110 NODE_8789_length_102_cov_1.960784 gi|228008396|ref|NP_001153145.1| 98.00 50 1 0 1 150 175 224 3e-28 108 NODE_8789_length_102_cov_1.960784 gi|5031755|ref|NP_005817.1| 98.00 50 1 0 1 150 276 325 3e-28 110 NODE_8789_length_102_cov_1.960784 gi|359338991|ref|NP_001240700.1| 98.00 50 1 0 1 150 121 170 3e-28 108 NODE_8789_length_102_cov_1.960784 gi|156151394|ref|NP_001095868.1| 98.00 50 1 0 1 150 279 328 3e-28 110 NODE_8789_length_102_cov_1.960784 gi|33859724|ref|NP_083147.1| 98.00 50 1 0 1 150 276 325 3e-28 110 NODE_8789_length_102_cov_1.960784 gi|29788787|ref|NP_062770.1| 98.00 50 1 0 1 150 273 322 6e-28 108 NODE_8789_length_102_cov_1.960784 gi|228008400|ref|NP_001153149.1| 98.00 50 1 0 1 150 273 322 6e-28 108 NODE_8789_length_102_cov_1.960784 gi|228008293|ref|NP_001153148.1| 98.00 50 1 0 1 150 273 322 6e-28 108 NODE_8819_length_109_cov_3.183486 gi|31560385|ref|NP_062621.2| 94.23 52 3 0 157 2 30 81 2e-28 105 NODE_8819_length_109_cov_3.183486 gi|309264473|ref|XP_003086312.1| 94.23 52 3 0 157 2 30 81 2e-28 105 NODE_8819_length_109_cov_3.183486 gi|63487024|ref|XP_619762.1| 94.23 52 3 0 157 2 30 81 2e-28 105 NODE_8819_length_109_cov_3.183486 gi|309262452|ref|XP_003085811.1| 94.23 52 3 0 157 2 30 81 3e-28 104 NODE_8819_length_109_cov_3.183486 gi|149262567|ref|XP_001480448.1| 94.23 52 3 0 157 2 30 81 3e-28 104 NODE_8819_length_109_cov_3.183486 gi|18104948|ref|NP_000973.2| 92.31 52 4 0 157 2 30 81 4e-28 104 NODE_8819_length_109_cov_3.183486 gi|309270949|ref|XP_001480330.2| 92.31 52 4 0 157 2 30 81 9e-28 103 NODE_8819_length_109_cov_3.183486 gi|309272152|ref|XP_003085488.1| 92.31 52 4 0 157 2 30 81 1e-27 103 NODE_8819_length_109_cov_3.183486 gi|309265319|ref|XP_003086501.1| 92.31 52 4 0 157 2 30 81 1e-27 103 NODE_8819_length_109_cov_3.183486 gi|309265361|ref|XP_003086513.1| 92.31 52 4 0 157 2 56 107 2e-27 103 NODE_8822_length_167_cov_2.059880 gi|16933542|ref|NP_002017.1| 94.37 71 4 0 3 215 496 566 1e-41 151 NODE_8822_length_167_cov_2.059880 gi|16933542|ref|NP_002017.1| 38.36 73 40 2 3 215 167 236 9e-09 56.6 NODE_8822_length_167_cov_2.059880 gi|16933542|ref|NP_002017.1| 36.36 66 37 2 3 197 123 184 1e-07 53.1 NODE_8822_length_167_cov_2.059880 gi|16933542|ref|NP_002017.1| 39.34 61 35 1 3 185 213 271 1e-06 50.1 NODE_8822_length_167_cov_2.059880 gi|16933542|ref|NP_002017.1| 33.87 62 37 1 3 188 2202 2259 2e-05 46.2 NODE_8822_length_167_cov_2.059880 gi|16933542|ref|NP_002017.1| 44.26 61 29 3 3 185 2245 2300 3e-05 46.2 NODE_8822_length_167_cov_2.059880 gi|16933542|ref|NP_002017.1| 34.29 70 42 3 3 206 76 143 0.005 39.3 NODE_8822_length_167_cov_2.059880 gi|16933542|ref|NP_002017.1| 27.71 83 30 3 3 164 258 339 1.2 31.6 NODE_8822_length_167_cov_2.059880 gi|47132557|ref|NP_997647.1| 94.37 71 4 0 3 215 496 566 1e-41 151 NODE_8822_length_167_cov_2.059880 gi|47132557|ref|NP_997647.1| 38.36 73 40 2 3 215 167 236 9e-09 56.6 NODE_8822_length_167_cov_2.059880 gi|47132557|ref|NP_997647.1| 36.36 66 37 2 3 197 123 184 1e-07 53.1 NODE_8822_length_167_cov_2.059880 gi|47132557|ref|NP_997647.1| 39.34 61 35 1 3 185 213 271 2e-06 49.7 NODE_8822_length_167_cov_2.059880 gi|47132557|ref|NP_997647.1| 33.87 62 37 1 3 188 2324 2381 2e-05 46.2 NODE_8822_length_167_cov_2.059880 gi|47132557|ref|NP_997647.1| 44.26 61 29 3 3 185 2367 2422 3e-05 46.2 NODE_8822_length_167_cov_2.059880 gi|47132557|ref|NP_997647.1| 34.29 70 42 3 3 206 76 143 0.005 39.3 NODE_8822_length_167_cov_2.059880 gi|47132557|ref|NP_997647.1| 27.71 83 30 3 3 164 258 339 1.4 31.6 NODE_8822_length_167_cov_2.059880 gi|47132555|ref|NP_997643.1| 94.37 71 4 0 3 215 496 566 1e-41 151 NODE_8822_length_167_cov_2.059880 gi|47132555|ref|NP_997643.1| 38.36 73 40 2 3 215 167 236 9e-09 56.6 NODE_8822_length_167_cov_2.059880 gi|47132555|ref|NP_997643.1| 36.36 66 37 2 3 197 123 184 1e-07 53.1 NODE_8822_length_167_cov_2.059880 gi|47132555|ref|NP_997643.1| 39.34 61 35 1 3 185 213 271 1e-06 50.1 NODE_8822_length_167_cov_2.059880 gi|47132555|ref|NP_997643.1| 33.87 62 37 1 3 188 2177 2234 2e-05 46.2 NODE_8822_length_167_cov_2.059880 gi|47132555|ref|NP_997643.1| 44.26 61 29 3 3 185 2220 2275 3e-05 46.2 NODE_8822_length_167_cov_2.059880 gi|47132555|ref|NP_997643.1| 34.29 70 42 3 3 206 76 143 0.005 39.3 NODE_8822_length_167_cov_2.059880 gi|47132555|ref|NP_997643.1| 27.71 83 30 3 3 164 258 339 1.3 31.6 NODE_8822_length_167_cov_2.059880 gi|47132553|ref|NP_997641.1| 94.37 71 4 0 3 215 496 566 1e-41 151 NODE_8822_length_167_cov_2.059880 gi|47132553|ref|NP_997641.1| 38.36 73 40 2 3 215 167 236 9e-09 56.6 NODE_8822_length_167_cov_2.059880 gi|47132553|ref|NP_997641.1| 36.36 66 37 2 3 197 123 184 1e-07 53.1 NODE_8822_length_167_cov_2.059880 gi|47132553|ref|NP_997641.1| 39.34 61 35 1 3 185 213 271 1e-06 50.1 NODE_8822_length_167_cov_2.059880 gi|47132553|ref|NP_997641.1| 33.87 62 37 1 3 188 2143 2200 2e-05 46.2 NODE_8822_length_167_cov_2.059880 gi|47132553|ref|NP_997641.1| 44.26 61 29 3 3 185 2186 2241 3e-05 46.2 NODE_8822_length_167_cov_2.059880 gi|47132553|ref|NP_997641.1| 34.29 70 42 3 3 206 76 143 0.005 39.3 NODE_8822_length_167_cov_2.059880 gi|47132553|ref|NP_997641.1| 27.71 83 30 3 3 164 258 339 1.2 31.6 NODE_8822_length_167_cov_2.059880 gi|47132549|ref|NP_997639.1| 94.37 71 4 0 3 215 496 566 1e-41 151 NODE_8822_length_167_cov_2.059880 gi|47132549|ref|NP_997639.1| 38.36 73 40 2 3 215 167 236 8e-09 56.6 NODE_8822_length_167_cov_2.059880 gi|47132549|ref|NP_997639.1| 36.36 66 37 2 3 197 123 184 1e-07 53.5 NODE_8822_length_167_cov_2.059880 gi|47132549|ref|NP_997639.1| 39.34 61 35 1 3 185 213 271 1e-06 50.1 NODE_8822_length_167_cov_2.059880 gi|47132549|ref|NP_997639.1| 33.87 62 37 1 3 188 2023 2080 2e-05 46.6 NODE_8822_length_167_cov_2.059880 gi|47132549|ref|NP_997639.1| 44.26 61 29 3 3 185 2066 2121 3e-05 46.2 NODE_8822_length_167_cov_2.059880 gi|47132549|ref|NP_997639.1| 34.29 70 42 3 3 206 76 143 0.005 39.3 NODE_8822_length_167_cov_2.059880 gi|47132549|ref|NP_997639.1| 27.71 83 30 3 3 164 258 339 1.2 31.6 NODE_8822_length_167_cov_2.059880 gi|46849812|ref|NP_034363.1| 90.14 71 7 0 3 215 496 566 1e-40 148 NODE_8822_length_167_cov_2.059880 gi|46849812|ref|NP_034363.1| 38.36 73 40 2 3 215 168 237 1e-08 56.2 NODE_8822_length_167_cov_2.059880 gi|46849812|ref|NP_034363.1| 46.51 43 23 0 78 206 474 516 3e-07 52.0 NODE_8822_length_167_cov_2.059880 gi|46849812|ref|NP_034363.1| 34.85 66 38 2 3 197 124 185 7e-07 50.8 NODE_8822_length_167_cov_2.059880 gi|46849812|ref|NP_034363.1| 39.34 61 35 1 3 185 214 272 1e-06 50.1 NODE_8822_length_167_cov_2.059880 gi|46849812|ref|NP_034363.1| 44.26 61 29 3 3 185 2366 2421 3e-05 46.2 NODE_8822_length_167_cov_2.059880 gi|46849812|ref|NP_034363.1| 32.26 62 38 1 3 188 2323 2380 2e-04 43.5 NODE_8822_length_167_cov_2.059880 gi|46849812|ref|NP_034363.1| 34.29 70 42 3 3 206 77 144 0.004 39.7 NODE_8822_length_167_cov_2.059880 gi|46849812|ref|NP_034363.1| 32.50 40 27 0 90 209 2305 2344 1.8 31.2 NODE_8822_length_167_cov_2.059880 gi|47132547|ref|NP_473375.2| 94.37 71 4 0 3 215 496 566 2e-40 144 NODE_8822_length_167_cov_2.059880 gi|47132547|ref|NP_473375.2| 38.36 73 40 2 3 215 167 236 1e-08 55.8 NODE_8822_length_167_cov_2.059880 gi|47132547|ref|NP_473375.2| 36.36 66 37 2 3 197 123 184 2e-07 52.4 NODE_8822_length_167_cov_2.059880 gi|47132547|ref|NP_473375.2| 39.34 61 35 1 3 185 213 271 2e-06 48.9 NODE_8822_length_167_cov_2.059880 gi|47132547|ref|NP_473375.2| 34.29 70 42 3 3 206 76 143 0.004 39.3 NODE_8822_length_167_cov_2.059880 gi|47132547|ref|NP_473375.2| 27.71 83 30 3 3 164 258 339 1.9 30.8 NODE_8822_length_167_cov_2.059880 gi|311992845|ref|YP_004009712.1| 30.61 49 32 1 188 48 27 75 0.018 35.4 NODE_8822_length_167_cov_2.059880 gi|495645093|ref|WP_008369672.1| 31.58 38 26 0 75 188 82 119 0.64 32.0 NODE_8822_length_167_cov_2.059880 gi|489892444|ref|WP_003795894.1| 43.18 44 22 1 194 72 909 952 1.3 31.6 NODE_8839_length_109_cov_10.449541 gi|304361742|ref|NP_899228.4| 98.00 50 1 0 3 152 869 918 1.5 30.8 NODE_8839_length_109_cov_10.449541 gi|304361742|ref|NP_899228.4| 92.31 13 1 0 119 157 815 827 3.1 30.0 NODE_8839_length_109_cov_10.449541 gi|157266285|ref|NP_001096133.1| 92.31 13 1 0 119 157 490 502 3.2 30.0 NODE_8839_length_109_cov_10.449541 gi|282721104|ref|NP_001164226.1| 92.31 13 1 0 119 157 490 502 3.2 29.6 NODE_8839_length_109_cov_10.449541 gi|282721102|ref|NP_775909.2| 92.31 13 1 0 119 157 490 502 3.2 29.6 NODE_8839_length_109_cov_10.449541 gi|92110019|ref|NP_060410.2| 92.31 13 1 0 119 157 1032 1044 3.2 30.0 NODE_8839_length_109_cov_10.449541 gi|92110019|ref|NP_060410.2| 70.00 50 14 1 2 148 1087 1136 5.0 29.3 NODE_8839_length_109_cov_10.449541 gi|14149997|ref|NP_115640.1| 92.31 13 1 0 119 157 471 483 3.6 29.6 NODE_8839_length_109_cov_10.449541 gi|374088176|ref|NP_001243346.1| 92.31 13 1 0 119 157 401 413 3.8 29.6 NODE_8839_length_109_cov_10.449541 gi|374088174|ref|NP_001243345.1| 92.31 13 1 0 119 157 459 471 4.1 29.6 NODE_8839_length_109_cov_10.449541 gi|221218991|ref|NP_001137461.1| 84.62 13 2 0 119 157 410 422 8.0 28.5 NODE_8839_length_109_cov_10.449541 gi|221136848|ref|NP_001137460.1| 84.62 13 2 0 119 157 410 422 8.3 28.5 NODE_8872_length_148_cov_1.418919 gi|74229034|ref|NP_852658.2| 98.15 54 1 0 198 37 647 700 6e-29 114 NODE_8872_length_148_cov_1.418919 gi|5453998|ref|NP_006382.1| 98.15 54 1 0 198 37 647 700 6e-29 114 NODE_8872_length_148_cov_1.418919 gi|300360505|ref|NP_001177924.1| 75.93 54 13 0 198 37 442 495 2e-21 92.4 NODE_8872_length_148_cov_1.418919 gi|53759103|ref|NP_006381.2| 75.93 54 13 0 198 37 647 700 3e-21 92.4 NODE_8872_length_148_cov_1.418919 gi|124487445|ref|NP_001074582.1| 74.07 54 14 0 198 37 647 700 1e-20 90.5 NODE_8872_length_148_cov_1.418919 gi|289522103|ref|YP_003475889.1| 42.50 40 18 1 171 52 1895 1929 0.75 32.3 NODE_8872_length_148_cov_1.418919 gi|490512243|ref|WP_004377850.1| 37.14 35 22 0 69 173 93 127 2.5 30.4 NODE_8872_length_148_cov_1.418919 gi|62327636|ref|YP_224218.1| 36.36 44 23 1 183 52 1849 1887 6.3 29.3 NODE_8909_length_237_cov_2.299578 gi|488755457|ref|WP_002678722.1| 77.78 18 3 1 235 285 38 55 5.0 30.0 NODE_8909_length_237_cov_2.299578 gi|490452970|ref|WP_004323817.1| 52.00 25 12 0 190 264 785 809 9.6 29.6 NODE_8938_length_126_cov_2.841270 gi|490416432|ref|WP_004288922.1| 41.03 39 19 2 167 63 396 434 3.8 29.6 NODE_8938_length_126_cov_2.841270 gi|494109638|ref|WP_007050422.1| 30.56 36 25 0 49 156 337 372 9.9 28.5 NODE_8955_length_269_cov_2.520446 gi|332164781|ref|NP_001193728.1| 96.23 106 4 0 318 1 298 403 4e-66 214 NODE_8955_length_269_cov_2.520446 gi|33286422|ref|NP_872271.1| 96.23 106 4 0 318 1 293 398 4e-66 214 NODE_8955_length_269_cov_2.520446 gi|33286420|ref|NP_872270.1| 96.23 106 4 0 318 1 293 398 4e-66 214 NODE_8955_length_269_cov_2.520446 gi|332164777|ref|NP_001193726.1| 96.23 106 4 0 318 1 219 324 7e-66 212 NODE_8955_length_269_cov_2.520446 gi|359807367|ref|NP_001240812.1| 96.23 106 4 0 318 1 293 398 2e-65 213 NODE_8955_length_269_cov_2.520446 gi|332164775|ref|NP_001193725.1| 96.23 106 4 0 318 1 367 472 2e-65 214 NODE_8955_length_269_cov_2.520446 gi|33286418|ref|NP_002645.3| 96.23 106 4 0 318 1 293 398 2e-65 213 NODE_8955_length_269_cov_2.520446 gi|332164779|ref|NP_001193727.1| 96.23 106 4 0 318 1 278 383 2e-65 213 NODE_8955_length_269_cov_2.520446 gi|31981562|ref|NP_035229.2| 96.23 106 4 0 318 1 293 398 3e-65 213 NODE_8955_length_269_cov_2.520446 gi|32967597|ref|NP_870986.1| 89.62 106 11 0 318 1 305 410 1e-61 203 NODE_8981_length_113_cov_1.796460 gi|6753374|ref|NP_033994.1| 90.48 21 2 0 57 119 864 884 1e-06 49.3 NODE_8981_length_113_cov_1.796460 gi|4757960|ref|NP_004351.1| 90.48 21 2 0 57 119 862 882 1e-06 49.3 NODE_8981_length_113_cov_1.796460 gi|14589891|ref|NP_001784.2| 85.71 21 3 0 57 119 809 829 8e-06 47.0 NODE_8981_length_113_cov_1.796460 gi|83715978|ref|NP_001032898.1| 85.71 21 3 0 57 119 802 822 9e-06 46.6 NODE_8981_length_113_cov_1.796460 gi|45496816|ref|NP_031691.1| 85.71 21 3 0 57 119 801 821 9e-06 46.6 NODE_8981_length_113_cov_1.796460 gi|356640224|ref|NP_001239268.1| 76.19 21 5 0 57 119 822 842 1e-04 43.5 NODE_8981_length_113_cov_1.796460 gi|356640221|ref|NP_001239267.1| 76.19 21 5 0 57 119 859 879 1e-04 43.5 NODE_8981_length_113_cov_1.796460 gi|14589893|ref|NP_001785.2| 76.19 21 5 0 57 119 896 916 1e-04 43.5 NODE_8981_length_113_cov_1.796460 gi|6753376|ref|NP_033997.1| 76.19 21 5 0 57 119 893 913 1e-04 43.5 NODE_8981_length_113_cov_1.796460 gi|161760627|ref|NP_031690.3| 75.00 20 5 0 57 116 887 906 6e-04 41.2 NODE_8997_length_112_cov_1.812500 gi|18250296|ref|NP_077180.1| 100.00 53 0 0 160 2 29 81 5e-31 112 NODE_8997_length_112_cov_1.812500 gi|4506619|ref|NP_000977.1| 100.00 53 0 0 160 2 29 81 5e-31 112 NODE_8997_length_112_cov_1.812500 gi|407263600|ref|XP_003945506.1| 100.00 53 0 0 160 2 29 81 9e-31 109 NODE_8997_length_112_cov_1.812500 gi|38348464|ref|NP_941011.1| 39.29 56 29 2 160 5 29 83 0.020 35.4 NODE_8997_length_112_cov_1.812500 gi|10047102|ref|NP_057388.1| 37.50 56 30 2 160 5 29 83 0.030 35.0 NODE_8997_length_112_cov_1.812500 gi|358356833|ref|YP_004934584.1| 30.00 40 28 0 129 10 23 62 1.7 29.6 NODE_8997_length_112_cov_1.812500 gi|496136446|ref|WP_008860953.1| 35.29 34 22 0 58 159 543 576 4.3 29.6 NODE_8997_length_112_cov_1.812500 gi|494757251|ref|WP_007492659.1| 26.92 52 35 1 147 1 113 164 4.6 29.3 NODE_9004_length_129_cov_2.860465 gi|378548190|ref|NP_001243731.1| 100.00 59 0 0 178 2 85 143 5e-33 119 NODE_9004_length_129_cov_2.860465 gi|15718687|ref|NP_000996.2| 100.00 59 0 0 178 2 85 143 5e-33 119 NODE_9004_length_129_cov_2.860465 gi|6755372|ref|NP_036182.1| 100.00 59 0 0 178 2 85 143 5e-33 119 NODE_9004_length_129_cov_2.860465 gi|386869503|ref|NP_001247435.1| 98.31 59 1 0 178 2 101 159 3e-32 117 NODE_9004_length_129_cov_2.860465 gi|386869506|ref|NP_001247436.1| 100.00 17 0 0 52 2 1 17 0.001 38.1 NODE_9004_length_129_cov_2.860465 gi|148642816|ref|YP_001273329.1| 50.00 32 16 0 97 2 105 136 0.007 37.7 NODE_9004_length_129_cov_2.860465 gi|490187839|ref|WP_004086440.1| 48.78 41 21 0 127 5 117 157 0.051 35.0 NODE_9004_length_129_cov_2.860465 gi|490974928|ref|WP_004836716.1| 35.09 57 37 0 175 5 102 158 0.10 34.3 NODE_9004_length_129_cov_2.860465 gi|490965088|ref|WP_004826894.1| 33.33 57 38 0 175 5 102 158 0.15 33.5 NODE_9004_length_129_cov_2.860465 gi|184155985|ref|YP_001844325.1| 39.02 41 25 0 127 5 116 156 0.30 32.7 NODE_9018_length_131_cov_1.786260 gi|149258501|ref|XP_001475977.1| 96.55 58 2 0 6 179 265 322 5e-31 116 NODE_9018_length_131_cov_1.786260 gi|19526818|ref|NP_598429.1| 96.55 58 2 0 6 179 265 322 6e-31 115 NODE_9018_length_131_cov_1.786260 gi|407261592|ref|XP_003946312.1| 96.55 58 2 0 6 179 265 322 6e-31 115 NODE_9018_length_131_cov_1.786260 gi|47132595|ref|NP_998776.1| 96.55 58 2 0 6 179 269 326 5e-30 113 NODE_9018_length_131_cov_1.786260 gi|4505775|ref|NP_002626.1| 96.55 58 2 0 6 179 269 326 5e-30 113 NODE_9018_length_131_cov_1.786260 gi|6031192|ref|NP_005879.1| 96.55 58 2 0 6 179 270 327 6e-30 113 NODE_9018_length_131_cov_1.786260 gi|490517994|ref|WP_004383519.1| 41.94 31 17 1 69 158 1 31 1.4 28.9 NODE_9018_length_131_cov_1.786260 gi|490986958|ref|WP_004848691.1| 34.29 35 23 0 72 176 8 42 3.6 29.6 NODE_9018_length_131_cov_1.786260 gi|492422285|ref|WP_005838958.1| 30.43 46 32 0 179 42 96 141 5.1 29.3 NODE_9018_length_131_cov_1.786260 gi|315064796|ref|YP_004063671.1| 37.50 40 24 1 60 176 1797 1836 5.2 29.3 NODE_9050_length_309_cov_9.757281 gi|34538601|ref|NP_904331.1| 66.67 114 38 0 354 13 107 220 2e-54 176 NODE_9050_length_309_cov_9.757281 gi|251831110|ref|YP_003024029.1| 68.42 114 36 0 354 13 107 220 9e-51 167 NODE_9050_length_309_cov_9.757281 gi|494060890|ref|WP_007002973.1| 48.25 114 59 0 351 10 152 265 2e-30 116 NODE_9050_length_309_cov_9.757281 gi|490319117|ref|WP_004208610.1| 48.25 114 58 1 351 13 192 305 1e-29 115 NODE_9050_length_309_cov_9.757281 gi|488801868|ref|WP_002714274.1| 49.06 106 49 2 354 37 148 248 9e-29 111 NODE_9050_length_309_cov_9.757281 gi|492887322|ref|WP_006022899.1| 48.11 106 50 2 354 37 148 248 2e-28 110 NODE_9050_length_309_cov_9.757281 gi|493248465|ref|WP_006216866.1| 44.64 112 55 3 351 37 129 240 4e-25 102 NODE_9050_length_309_cov_9.757281 gi|493432514|ref|WP_006388092.1| 48.78 82 42 0 282 37 171 252 1e-24 101 NODE_9050_length_309_cov_9.757281 gi|488804984|ref|WP_002717390.1| 45.61 114 57 2 354 13 147 255 1e-22 95.1 NODE_9050_length_309_cov_9.757281 gi|491913834|ref|WP_005668116.1| 45.45 77 42 0 270 40 186 262 2e-19 87.0 NODE_9075_length_257_cov_2.883269 gi|13385652|ref|NP_080423.1| 97.85 93 2 0 280 2 1 93 2e-60 188 NODE_9075_length_257_cov_2.883269 gi|4506697|ref|NP_001014.1| 97.85 93 2 0 280 2 1 93 2e-60 188 NODE_9075_length_257_cov_2.883269 gi|226246671|ref|NP_001139699.1| 97.85 93 2 0 280 2 1 93 3e-60 188 NODE_9075_length_257_cov_2.883269 gi|148642957|ref|YP_001273470.1| 40.00 75 45 0 232 8 1 75 3e-14 68.6 NODE_9075_length_257_cov_2.883269 gi|489036778|ref|WP_002947121.1| 34.67 75 48 1 232 8 1 74 7e-08 51.2 NODE_9075_length_257_cov_2.883269 gi|220903934|ref|YP_002479246.1| 33.77 77 50 1 238 8 4 79 1e-07 50.8 NODE_9075_length_257_cov_2.883269 gi|490403557|ref|WP_004278047.1| 32.89 76 48 2 232 8 27 100 6e-07 48.9 NODE_9075_length_257_cov_2.883269 gi|479167565|ref|YP_007796064.1| 37.50 72 44 1 223 8 6 76 7e-07 48.5 NODE_9075_length_257_cov_2.883269 gi|57236893|ref|YP_179846.1| 30.67 75 51 1 232 8 1 74 8e-07 48.5 NODE_9075_length_257_cov_2.883269 gi|386761316|ref|YP_006234951.1| 31.17 77 52 1 232 2 1 76 1e-06 47.8 NODE_9116_length_132_cov_3.045455 gi|157277969|ref|NP_444493.1| 88.24 17 2 0 131 181 2 18 0.010 37.4 NODE_9116_length_132_cov_3.045455 gi|34740329|ref|NP_919223.1| 93.33 15 1 0 137 181 26 40 0.095 34.7 NODE_9116_length_132_cov_3.045455 gi|37674277|ref|NP_932758.1| 93.33 15 1 0 137 181 26 40 0.095 34.7 NODE_9116_length_132_cov_3.045455 gi|31559916|ref|NP_666242.2| 93.33 15 1 0 137 181 26 40 0.095 34.7 NODE_9116_length_132_cov_3.045455 gi|260304980|ref|NP_001159443.1| 77.78 18 4 0 128 181 2 19 0.53 32.3 NODE_9116_length_132_cov_3.045455 gi|14043070|ref|NP_112420.1| 77.78 18 4 0 128 181 2 19 0.63 32.0 NODE_9116_length_132_cov_3.045455 gi|85060507|ref|NP_001034218.1| 77.78 18 4 0 128 181 2 19 0.63 32.0 NODE_9116_length_132_cov_3.045455 gi|6754220|ref|NP_034577.1| 77.78 18 4 0 128 181 2 19 0.63 32.0 NODE_9116_length_132_cov_3.045455 gi|4504445|ref|NP_002127.1| 77.78 18 4 0 128 181 2 19 0.63 32.0 NODE_9116_length_132_cov_3.045455 gi|58761498|ref|NP_001011725.1| 77.78 18 4 0 128 181 2 19 0.69 32.0 NODE_9133_length_153_cov_1.150327 gi|5454088|ref|NP_006392.1| 67.31 52 17 0 44 199 1 52 7e-17 76.6 NODE_9133_length_153_cov_1.150327 gi|40254600|ref|NP_033802.2| 67.31 52 17 0 44 199 1 52 7e-15 70.9 NODE_9133_length_153_cov_1.150327 gi|18700032|ref|NP_570959.1| 63.46 52 19 0 44 199 1 52 8e-15 70.9 NODE_9133_length_153_cov_1.150327 gi|5453880|ref|NP_006296.1| 63.46 52 19 0 44 199 1 52 7e-14 68.2 NODE_9133_length_153_cov_1.150327 gi|210147569|ref|NP_001129950.1| 63.46 52 19 0 44 199 1 52 2e-12 63.9 NODE_9133_length_153_cov_1.150327 gi|13569879|ref|NP_112182.1| 63.46 52 19 0 44 199 1 52 3e-12 63.9 NODE_9133_length_153_cov_1.150327 gi|359279956|ref|NP_001240686.1| 59.62 52 21 0 44 199 1 52 2e-11 61.6 NODE_9133_length_153_cov_1.150327 gi|254587996|ref|NP_075699.3| 59.62 52 21 0 44 199 1 52 2e-11 61.6 NODE_9133_length_153_cov_1.150327 gi|6912604|ref|NP_036535.1| 56.86 51 22 0 44 196 1 51 5e-11 60.1 NODE_9133_length_153_cov_1.150327 gi|21071028|ref|NP_036536.2| 53.85 52 24 0 44 199 1 52 1e-10 58.5 NODE_9165_length_116_cov_1.715517 gi|145046220|ref|NP_647466.2| 50.98 51 21 2 160 8 384 430 2e-05 45.8 NODE_9165_length_116_cov_1.715517 gi|169636420|ref|NP_001207.2| 45.10 51 22 2 160 8 408 452 0.006 38.1 NODE_9165_length_116_cov_1.715517 gi|493593396|ref|WP_006546195.1| 50.00 26 13 0 123 46 486 511 1.5 30.8 NODE_9165_length_116_cov_1.715517 gi|488752328|ref|WP_002675610.1| 44.00 25 14 0 164 90 273 297 1.5 30.8 NODE_9165_length_116_cov_1.715517 gi|488744766|ref|WP_002668107.1| 44.00 25 14 0 164 90 273 297 1.5 30.8 NODE_9165_length_116_cov_1.715517 gi|7304955|ref|NP_038517.1| 43.14 51 23 2 163 26 212 261 1.6 30.8 NODE_9165_length_116_cov_1.715517 gi|498383651|ref|WP_010697807.1| 44.00 25 14 0 164 90 273 297 1.6 30.8 NODE_9165_length_116_cov_1.715517 gi|488778528|ref|WP_002690935.1| 44.00 25 14 0 164 90 273 297 1.6 30.8 NODE_9165_length_116_cov_1.715517 gi|42527670|ref|NP_972768.1| 44.00 25 14 0 164 90 273 297 1.6 30.8 NODE_9165_length_116_cov_1.715517 gi|498381448|ref|WP_010695604.1| 44.00 25 14 0 164 90 273 297 1.8 30.8 NODE_9187_length_137_cov_2.737226 gi|31980648|ref|NP_058054.2| 96.77 62 2 0 187 2 441 502 1e-34 127 NODE_9187_length_137_cov_2.737226 gi|32189394|ref|NP_001677.2| 96.77 62 2 0 187 2 441 502 2e-34 127 NODE_9187_length_137_cov_2.737226 gi|490822334|ref|WP_004684425.1| 83.87 62 10 0 187 2 382 443 2e-28 110 NODE_9187_length_137_cov_2.737226 gi|490775292|ref|WP_004637488.1| 83.87 62 10 0 187 2 382 443 3e-28 109 NODE_9187_length_137_cov_2.737226 gi|387120966|ref|YP_006286849.1| 83.87 62 10 0 187 2 375 436 6e-28 108 NODE_9187_length_137_cov_2.737226 gi|490936225|ref|WP_004798063.1| 82.26 62 11 0 187 2 382 443 1e-27 107 NODE_9187_length_137_cov_2.737226 gi|162286755|ref|YP_001083240.2| 82.26 62 11 0 187 2 382 443 1e-27 107 NODE_9187_length_137_cov_2.737226 gi|491158888|ref|WP_005017275.1| 82.26 62 11 0 187 2 382 443 1e-27 107 NODE_9187_length_137_cov_2.737226 gi|251793675|ref|YP_003008405.1| 82.26 62 11 0 187 2 375 436 5e-27 105 NODE_9187_length_137_cov_2.737226 gi|489895224|ref|WP_003798673.1| 82.26 62 11 0 187 2 382 443 5e-27 105 NODE_9198_length_510_cov_4.376471 gi|320461711|ref|NP_001189360.1| 89.29 140 15 0 2 421 60 199 5e-90 269 NODE_9198_length_510_cov_4.376471 gi|32455266|ref|NP_859048.1| 89.29 140 15 0 2 421 60 199 5e-90 269 NODE_9198_length_510_cov_4.376471 gi|32455264|ref|NP_859047.1| 89.29 140 15 0 2 421 60 199 5e-90 269 NODE_9198_length_510_cov_4.376471 gi|4505591|ref|NP_002565.1| 89.29 140 15 0 2 421 60 199 5e-90 269 NODE_9198_length_510_cov_4.376471 gi|6754976|ref|NP_035164.1| 88.57 140 16 0 2 421 60 199 9e-89 266 NODE_9198_length_510_cov_4.376471 gi|377835575|ref|XP_003688912.1| 87.14 140 18 0 2 421 60 199 1e-86 261 NODE_9198_length_510_cov_4.376471 gi|377834422|ref|XP_003689480.1| 87.14 140 18 0 2 421 60 199 1e-86 261 NODE_9198_length_510_cov_4.376471 gi|32189392|ref|NP_005800.3| 74.29 140 36 0 2 421 59 198 2e-75 233 NODE_9198_length_510_cov_4.376471 gi|148747558|ref|NP_035693.3| 72.86 140 38 0 2 421 59 198 6e-75 231 NODE_9198_length_510_cov_4.376471 gi|7948999|ref|NP_058044.1| 70.80 137 40 0 5 415 136 272 2e-65 209 NODE_9328_length_226_cov_3.637168 gi|33859482|ref|NP_031933.1| 97.44 78 2 0 235 2 320 397 1e-45 162 NODE_9328_length_226_cov_3.637168 gi|4503483|ref|NP_001952.1| 97.44 78 2 0 235 2 320 397 1e-45 161 NODE_9328_length_226_cov_3.637168 gi|217272894|ref|NP_001136077.1| 31.17 77 53 0 232 2 366 442 1e-05 47.4 NODE_9328_length_226_cov_3.637168 gi|6755594|ref|NP_035561.1| 31.17 77 53 0 232 2 400 476 1e-05 47.4 NODE_9328_length_226_cov_3.637168 gi|385298678|ref|NP_001245282.1| 31.17 77 53 0 232 2 401 477 1e-05 47.4 NODE_9328_length_226_cov_3.637168 gi|217272892|ref|NP_004238.3| 31.17 77 53 0 232 2 401 477 1e-05 47.4 NODE_9328_length_226_cov_3.637168 gi|158508674|ref|NP_001103465.1| 31.17 77 53 0 232 2 401 477 1e-05 47.4 NODE_9328_length_226_cov_3.637168 gi|385298680|ref|NP_001245283.1| 31.17 77 53 0 232 2 391 467 2e-05 47.4 NODE_9328_length_226_cov_3.637168 gi|490132669|ref|WP_004033031.1| 34.29 70 38 1 220 11 225 286 1e-04 44.7 NODE_9328_length_226_cov_3.637168 gi|227908784|ref|NP_001153144.1| 32.81 64 35 2 217 50 331 394 0.80 32.7 NODE_9356_length_159_cov_1.257862 gi|493248865|ref|WP_006217062.1| 91.30 23 2 0 208 140 272 294 1e-05 45.8 NODE_9356_length_159_cov_1.257862 gi|491906484|ref|WP_005664033.1| 91.30 23 2 0 208 140 262 284 3e-05 44.7 NODE_9356_length_159_cov_1.257862 gi|493431167|ref|WP_006386767.1| 86.96 23 3 0 208 140 272 294 4e-05 44.7 NODE_9356_length_159_cov_1.257862 gi|491911804|ref|WP_005666697.1| 91.30 23 2 0 208 140 260 282 5e-05 44.3 NODE_9356_length_159_cov_1.257862 gi|492548958|ref|WP_005882265.1| 91.30 23 2 0 208 140 260 282 6e-05 43.9 NODE_9356_length_159_cov_1.257862 gi|495815720|ref|WP_008540299.1| 82.61 23 4 0 208 140 264 286 1e-04 43.5 NODE_9356_length_159_cov_1.257862 gi|492539463|ref|WP_005878499.1| 82.61 23 4 0 208 140 237 259 3e-04 42.0 NODE_9356_length_159_cov_1.257862 gi|489879301|ref|WP_003782774.1| 82.61 23 4 0 208 140 261 283 6e-04 41.2 NODE_9356_length_159_cov_1.257862 gi|490654012|ref|WP_004519003.1| 82.61 23 4 0 208 140 262 284 6e-04 41.2 NODE_9356_length_159_cov_1.257862 gi|489847300|ref|WP_003750989.1| 82.61 23 4 0 208 140 262 284 6e-04 41.2 NODE_9391_length_274_cov_3.521898 gi|489885574|ref|WP_003789024.1| 33.33 51 32 2 14 163 209 258 0.72 33.1 NODE_9391_length_274_cov_3.521898 gi|494130065|ref|WP_007069832.1| 37.04 54 31 2 20 175 26 78 2.2 32.0 NODE_9391_length_274_cov_3.521898 gi|46397375|ref|NP_060620.2| 38.10 42 25 1 284 162 82 123 2.7 31.6 NODE_9391_length_274_cov_3.521898 gi|37059808|ref|NP_080015.3| 38.10 42 25 1 284 162 82 123 2.7 31.6 NODE_9391_length_274_cov_3.521898 gi|491653759|ref|WP_005510479.1| 36.73 49 27 1 83 229 100 144 3.5 31.2 NODE_9391_length_274_cov_3.521898 gi|491653759|ref|WP_005510479.1| 33.33 60 27 3 29 169 93 152 5.6 30.8 NODE_9391_length_274_cov_3.521898 gi|490362255|ref|WP_004242018.1| 31.67 60 35 2 17 178 1145 1204 3.7 31.2 NODE_9391_length_274_cov_3.521898 gi|493579915|ref|WP_006532998.1| 33.90 59 27 2 230 54 33 79 5.0 30.8 NODE_9391_length_274_cov_3.521898 gi|472339611|ref|YP_007673145.1| 29.03 62 42 1 317 132 112 171 5.5 30.8 NODE_9391_length_274_cov_3.521898 gi|491540951|ref|WP_005398570.1| 43.24 37 21 0 143 33 34 70 7.6 30.4 NODE_9391_length_274_cov_3.521898 gi|494181537|ref|WP_007116906.1| 46.43 28 15 0 218 135 192 219 9.4 30.0 NODE_9428_length_103_cov_1.194175 gi|126032348|ref|NP_004658.3| 45.45 22 12 0 26 91 4770 4791 8.9 28.5 NODE_9428_length_103_cov_1.194175 gi|134288898|ref|NP_034548.2| 45.45 22 12 0 26 91 4772 4793 8.9 28.5 NODE_9428_length_103_cov_1.194175 gi|489099774|ref|WP_003009643.1| 42.86 28 16 0 123 40 196 223 9.6 28.1 NODE_9428_length_103_cov_1.194175 gi|489088586|ref|WP_002998487.1| 42.86 28 16 0 123 40 196 223 9.6 28.1 NODE_9481_length_126_cov_1.912698 gi|34486094|ref|NP_038535.2| 93.10 58 4 0 174 1 161 218 3e-21 91.3 NODE_9481_length_126_cov_1.912698 gi|289577116|ref|NP_001166176.1| 93.10 58 4 0 174 1 161 218 4e-21 91.3 NODE_9481_length_126_cov_1.912698 gi|289577080|ref|NP_001409.3| 93.10 58 4 0 174 1 161 218 4e-21 91.3 NODE_9481_length_126_cov_1.912698 gi|110630015|ref|NP_001035221.1| 93.10 58 4 0 174 1 161 218 4e-21 91.3 NODE_9481_length_126_cov_1.912698 gi|289577114|ref|NP_001036024.3| 93.10 58 4 0 174 1 161 218 4e-21 91.3 NODE_9481_length_126_cov_1.912698 gi|56699434|ref|NP_001005331.1| 40.30 67 28 1 168 4 836 902 5e-05 45.1 NODE_9481_length_126_cov_1.912698 gi|56699432|ref|NP_666053.2| 40.30 67 28 1 168 4 843 909 5e-05 45.1 NODE_9481_length_126_cov_1.912698 gi|38201623|ref|NP_937884.1| 40.30 67 28 1 168 4 839 905 5e-05 44.7 NODE_9481_length_126_cov_1.912698 gi|302699247|ref|NP_001181876.1| 40.30 67 28 1 168 4 846 912 5e-05 44.7 NODE_9481_length_126_cov_1.912698 gi|302699245|ref|NP_001181875.1| 40.30 67 28 1 168 4 846 912 5e-05 44.7 NODE_9523_length_160_cov_2.100000 gi|491490995|ref|WP_005348729.1| 57.89 19 8 0 108 164 50 68 1.3 30.4 NODE_9523_length_160_cov_2.100000 gi|150004710|ref|YP_001299454.1| 32.43 37 25 0 203 93 470 506 1.9 30.8 NODE_9523_length_160_cov_2.100000 gi|9626876|ref|NP_041146.1| 29.82 57 38 1 205 41 149 205 4.3 29.6 NODE_9523_length_160_cov_2.100000 gi|489517744|ref|WP_003422556.1| 61.11 18 7 0 153 206 162 179 5.9 29.3 NODE_9523_length_160_cov_2.100000 gi|116284394|ref|NP_079005.3| 46.15 39 18 2 84 191 826 864 7.7 29.3 NODE_9523_length_160_cov_2.100000 gi|116284396|ref|NP_001070654.1| 46.15 39 18 2 84 191 834 872 7.7 29.3 NODE_9523_length_160_cov_2.100000 gi|224831241|ref|NP_001139281.1| 46.15 39 18 2 84 191 867 905 7.7 29.3 NODE_9523_length_160_cov_2.100000 gi|26248871|ref|NP_754911.1| 33.33 45 29 1 203 72 596 640 7.8 29.3 NODE_9523_length_160_cov_2.100000 gi|488947213|ref|WP_002858288.1| 38.78 49 25 1 167 36 223 271 9.2 28.9 NODE_9523_length_160_cov_2.100000 gi|489066779|ref|WP_002976774.1| 44.00 25 14 0 85 11 146 170 9.7 28.5 NODE_9533_length_115_cov_1.739130 gi|161621271|ref|NP_001104548.1| 41.67 36 14 1 29 115 290 325 1.7 30.8 NODE_9533_length_115_cov_1.739130 gi|161621269|ref|NP_035061.3| 41.67 36 14 1 29 115 290 325 1.7 30.8 NODE_9533_length_115_cov_1.739130 gi|491471372|ref|WP_005329126.1| 48.15 27 14 0 2 82 5 31 5.9 28.9 NODE_9533_length_115_cov_1.739130 gi|491466013|ref|WP_005323776.1| 48.15 27 14 0 2 82 18 44 6.3 28.9 NODE_9533_length_115_cov_1.739130 gi|491650733|ref|WP_005507455.1| 45.83 24 13 0 8 79 288 311 7.3 28.9 NODE_9533_length_115_cov_1.739130 gi|491871039|ref|WP_005644219.1| 44.44 27 14 1 156 76 217 242 8.9 28.5 NODE_9533_length_115_cov_1.739130 gi|21389473|ref|NP_653239.1| 38.89 36 20 1 2 109 12 45 9.3 28.1 NODE_9533_length_115_cov_1.739130 gi|491648115|ref|WP_005505641.1| 45.83 24 13 0 8 79 287 310 9.4 28.5 NODE_9571_length_191_cov_2.418848 gi|492247394|ref|WP_005789090.1| 24.68 77 57 1 8 238 28 103 0.97 31.6 NODE_9571_length_191_cov_2.418848 gi|492259722|ref|WP_005792610.1| 24.68 77 57 1 8 238 30 105 1.1 31.6 NODE_9571_length_191_cov_2.418848 gi|494177798|ref|WP_007115528.1| 45.45 33 17 1 29 124 267 299 1.1 32.0 NODE_9571_length_191_cov_2.418848 gi|490747450|ref|WP_004609758.1| 33.33 39 26 0 50 166 22 60 2.1 31.2 NODE_9571_length_191_cov_2.418848 gi|491061077|ref|WP_004922711.1| 42.42 33 19 0 142 240 3 35 2.8 30.4 NODE_9571_length_191_cov_2.418848 gi|490502877|ref|WP_004368968.1| 51.85 27 13 0 26 106 442 468 3.4 30.4 NODE_9571_length_191_cov_2.418848 gi|493963437|ref|WP_006906891.1| 36.96 46 25 2 107 238 116 159 3.9 30.0 NODE_9571_length_191_cov_2.418848 gi|49237332|ref|YP_031613.1| 42.86 42 20 1 5 118 22 63 4.7 29.6 NODE_9571_length_191_cov_2.418848 gi|491057703|ref|WP_004919340.1| 34.04 47 30 1 50 190 378 423 6.1 29.6 NODE_9571_length_191_cov_2.418848 gi|488982132|ref|WP_002892951.1| 38.89 36 20 2 95 199 95 129 7.5 28.9 metaMix/inst/extdata/dat1/remove.sh0000644000176200001440000000024513403500106016740 0ustar liggesusers#for k in `cat removeID.tab`; do # # # sed "/${k}/d" blastOut.tab > blastOut_nomouse.tab # # #done grep -vFf removeID.tab blastOut.tab > blastOut_nomouse.tab metaMix/inst/extdata/dat1/blastOut.tab0000644000176200001440000032453013403500106017402 0ustar liggesusersNODE_1597_length_349_cov_49.601719 gi|38018023|ref|NP_937947.1| 99.25 133 1 0 399 1 4175 4307 4e-83 274 NODE_1597_length_349_cov_49.601719 gi|253756606|ref|YP_003038519.1| 98.50 133 2 0 399 1 4175 4307 1e-82 272 NODE_1597_length_349_cov_49.601719 gi|253756607|ref|YP_003038518.1| 98.50 133 2 0 399 1 4175 4307 2e-82 272 NODE_1597_length_349_cov_49.601719 gi|253756581|ref|YP_003038496.1| 97.74 133 3 0 399 1 4175 4307 3e-82 271 NODE_1597_length_349_cov_49.601719 gi|15081555|ref|NP_150074.1| 97.74 133 3 0 399 1 4175 4307 3e-82 271 NODE_1597_length_349_cov_49.601719 gi|253756594|ref|YP_003038508.1| 97.74 133 3 0 399 1 4175 4307 3e-82 271 NODE_1597_length_349_cov_49.601719 gi|253756595|ref|YP_003038507.1| 97.74 133 3 0 399 1 4175 4307 4e-82 271 NODE_1597_length_349_cov_49.601719 gi|253756582|ref|YP_003038495.1| 97.74 133 3 0 399 1 4175 4307 4e-82 271 NODE_1597_length_349_cov_49.601719 gi|26008080|ref|NP_150073.2| 97.74 133 3 0 399 1 4175 4307 4e-82 271 NODE_1597_length_349_cov_49.601719 gi|167600355|ref|YP_001671997.1| 96.99 133 4 0 399 1 4221 4353 6e-82 270 NODE_1607_length_290_cov_156.668961 gi|38018025|ref|NP_937949.1| 94.69 113 5 1 338 3 99 211 7e-68 217 NODE_1607_length_290_cov_156.668961 gi|253756597|ref|YP_003038510.1| 90.27 113 10 1 338 3 99 211 2e-63 205 NODE_1607_length_290_cov_156.668961 gi|253756584|ref|YP_003038498.1| 89.38 113 11 1 338 3 99 211 7e-63 204 NODE_1607_length_290_cov_156.668961 gi|253756609|ref|YP_003038521.1| 89.38 113 11 1 338 3 99 211 1e-62 203 NODE_1607_length_290_cov_156.668961 gi|15081546|ref|NP_150076.1| 89.38 113 11 1 338 3 99 211 1e-62 203 NODE_1607_length_290_cov_156.668961 gi|394935453|ref|YP_005454244.1| 87.61 113 13 1 338 3 99 211 7e-61 199 NODE_1607_length_290_cov_156.668961 gi|85718617|ref|YP_459951.1| 83.19 113 18 1 338 3 99 211 4e-58 192 NODE_1607_length_290_cov_156.668961 gi|167600357|ref|YP_001671999.1| 58.41 113 46 1 338 3 98 210 1e-36 134 NODE_1607_length_290_cov_156.668961 gi|60115394|ref|YP_209232.1| 56.76 111 47 1 338 9 104 214 4e-36 133 NODE_1607_length_290_cov_156.668961 gi|253750534|ref|YP_003029847.1| 56.76 111 47 1 338 9 104 214 2e-34 129 NODE_1713_length_191_cov_280.675385 gi|38018026|ref|NP_937950.1| 95.00 80 4 0 1 240 159 238 4e-47 167 NODE_1713_length_191_cov_280.675385 gi|253756610|ref|YP_003038522.1| 88.75 80 9 0 1 240 153 232 5e-43 155 NODE_1713_length_191_cov_280.675385 gi|253756598|ref|YP_003038511.1| 87.50 80 10 0 1 240 153 232 3e-42 153 NODE_1713_length_191_cov_280.675385 gi|15081547|ref|NP_150077.1| 86.25 80 11 0 1 240 153 232 1e-41 151 NODE_1713_length_191_cov_280.675385 gi|253756585|ref|YP_003038499.1| 86.25 80 11 0 1 240 153 232 2e-41 150 NODE_1713_length_191_cov_280.675385 gi|394935454|ref|YP_005454245.1| 85.00 80 12 0 1 240 152 231 1e-40 148 NODE_1713_length_191_cov_280.675385 gi|85718618|ref|YP_459952.1| 83.75 80 13 0 1 240 153 232 3e-40 147 NODE_1713_length_191_cov_280.675385 gi|167600358|ref|YP_001672000.1| 65.00 80 28 0 1 240 153 232 5e-33 126 NODE_1713_length_191_cov_280.675385 gi|56807326|ref|YP_173238.1| 57.50 80 33 1 1 240 144 222 2e-24 102 NODE_1713_length_191_cov_280.675385 gi|253750535|ref|YP_003029848.1| 49.38 81 40 1 1 240 146 226 1e-20 90.9 NODE_1715_length_142_cov_213.845078 gi|38018026|ref|NP_937950.1| 92.06 63 5 0 191 3 244 306 2e-32 124 NODE_1715_length_142_cov_213.845078 gi|253756598|ref|YP_003038511.1| 80.95 63 8 1 191 3 238 296 1e-26 107 NODE_1715_length_142_cov_213.845078 gi|15081547|ref|NP_150077.1| 80.95 63 8 1 191 3 238 296 1e-26 107 NODE_1715_length_142_cov_213.845078 gi|253756585|ref|YP_003038499.1| 80.95 63 8 1 191 3 238 296 1e-26 107 NODE_1715_length_142_cov_213.845078 gi|253756610|ref|YP_003038522.1| 79.37 63 9 1 191 3 238 296 4e-26 106 NODE_1715_length_142_cov_213.845078 gi|394935454|ref|YP_005454245.1| 80.95 63 8 1 191 3 237 295 4e-26 106 NODE_1715_length_142_cov_213.845078 gi|167600358|ref|YP_001672000.1| 69.84 63 15 1 191 3 238 296 4e-23 97.8 NODE_1715_length_142_cov_213.845078 gi|85718618|ref|YP_459952.1| 69.84 63 15 1 191 3 238 296 2e-22 95.5 NODE_1715_length_142_cov_213.845078 gi|56807326|ref|YP_173238.1| 63.08 65 22 1 191 3 228 292 1e-18 84.7 NODE_1715_length_142_cov_213.845078 gi|9629814|ref|NP_045300.1| 52.38 63 30 0 191 3 232 294 5e-15 73.9 NODE_1766_length_314_cov_463.656036 gi|394935454|ref|YP_005454245.1| 96.67 120 4 0 3 362 908 1027 3e-71 237 NODE_1766_length_314_cov_463.656036 gi|85718618|ref|YP_459952.1| 95.00 120 6 0 3 362 895 1014 2e-70 234 NODE_1766_length_314_cov_463.656036 gi|38018026|ref|NP_937950.1| 97.50 120 3 0 3 362 907 1026 5e-70 234 NODE_1766_length_314_cov_463.656036 gi|253756598|ref|YP_003038511.1| 94.17 120 7 0 3 362 909 1028 9e-69 230 NODE_1766_length_314_cov_463.656036 gi|15081547|ref|NP_150077.1| 94.17 120 7 0 3 362 909 1028 9e-69 230 NODE_1766_length_314_cov_463.656036 gi|253756585|ref|YP_003038499.1| 94.17 120 7 0 3 362 909 1028 1e-68 230 NODE_1766_length_314_cov_463.656036 gi|253756610|ref|YP_003038522.1| 92.50 120 9 0 3 362 909 1028 5e-68 228 NODE_1766_length_314_cov_463.656036 gi|167600358|ref|YP_001672000.1| 90.68 118 11 0 9 362 911 1028 1e-66 224 NODE_1766_length_314_cov_463.656036 gi|56807326|ref|YP_173238.1| 81.51 119 22 0 6 362 901 1019 7e-60 205 NODE_1766_length_314_cov_463.656036 gi|9629814|ref|NP_045300.1| 81.90 116 21 0 15 362 869 984 6e-59 202 NODE_2060_length_233_cov_764.030029 gi|38018026|ref|NP_937950.1| 95.70 93 4 0 3 281 1178 1270 1e-54 189 NODE_2060_length_233_cov_764.030029 gi|394935454|ref|YP_005454245.1| 92.47 93 7 0 3 281 1179 1271 2e-52 182 NODE_2060_length_233_cov_764.030029 gi|253756610|ref|YP_003038522.1| 92.47 93 7 0 3 281 1180 1272 6e-52 181 NODE_2060_length_233_cov_764.030029 gi|253756598|ref|YP_003038511.1| 91.40 93 8 0 3 281 1180 1272 2e-51 180 NODE_2060_length_233_cov_764.030029 gi|253756585|ref|YP_003038499.1| 91.30 92 8 0 6 281 1181 1272 1e-50 177 NODE_2060_length_233_cov_764.030029 gi|15081547|ref|NP_150077.1| 91.40 93 8 0 3 281 1180 1272 1e-50 177 NODE_2060_length_233_cov_764.030029 gi|167600358|ref|YP_001672000.1| 89.25 93 10 0 3 281 1180 1272 3e-50 176 NODE_2060_length_233_cov_764.030029 gi|85718618|ref|YP_459952.1| 84.95 93 14 0 3 281 1166 1258 3e-48 171 NODE_2060_length_233_cov_764.030029 gi|9629814|ref|NP_045300.1| 71.58 95 25 1 3 281 1136 1230 8e-40 146 NODE_2060_length_233_cov_764.030029 gi|60115395|ref|YP_209233.1| 71.58 95 25 1 3 281 1188 1282 2e-39 145 NODE_2345_length_1115_cov_56.699551 gi|26008090|ref|NP_742138.1| 98.97 388 4 0 2 1165 433 820 0.0 803 NODE_2345_length_1115_cov_56.699551 gi|85719076|ref|YP_459941.1| 94.59 388 21 0 2 1165 433 820 0.0 769 NODE_2345_length_1115_cov_56.699551 gi|25121569|ref|NP_740616.1| 93.56 388 25 0 2 1165 433 820 0.0 769 NODE_2345_length_1115_cov_56.699551 gi|60145599|ref|NP_001012452.1| 92.53 388 29 0 2 1165 433 820 0.0 762 NODE_2345_length_1115_cov_56.699551 gi|38018023|ref|NP_937947.1| 100.00 388 0 0 2 1165 4802 5189 0.0 815 NODE_2345_length_1115_cov_56.699551 gi|253756595|ref|YP_003038507.1| 98.97 388 4 0 2 1165 4802 5189 0.0 806 NODE_2345_length_1115_cov_56.699551 gi|26008080|ref|NP_150073.2| 98.97 388 4 0 2 1165 4802 5189 0.0 806 NODE_2345_length_1115_cov_56.699551 gi|253756582|ref|YP_003038495.1| 98.97 388 4 0 2 1165 4802 5189 0.0 806 NODE_2345_length_1115_cov_56.699551 gi|253756607|ref|YP_003038518.1| 98.97 388 4 0 2 1165 4802 5189 0.0 806 NODE_2345_length_1115_cov_56.699551 gi|167600354|ref|YP_001671996.1| 98.97 388 4 0 2 1165 4848 5235 0.0 806 NODE_2652_length_118_cov_2.500000 gi|314953946|ref|YP_004063986.1| 40.91 44 25 1 134 3 903 945 7.9 28.9 NODE_2652_length_118_cov_2.500000 gi|9632197|ref|NP_048906.1| 38.71 31 18 1 7 96 81 111 9.8 27.7 NODE_2838_length_139_cov_133.841721 gi|38018025|ref|NP_937949.1| 96.77 62 2 0 187 2 38 99 5e-35 127 NODE_2838_length_139_cov_133.841721 gi|253756609|ref|YP_003038521.1| 93.55 62 4 0 187 2 38 99 1e-33 124 NODE_2838_length_139_cov_133.841721 gi|85718617|ref|YP_459951.1| 93.55 62 4 0 187 2 38 99 1e-33 124 NODE_2838_length_139_cov_133.841721 gi|394935453|ref|YP_005454244.1| 91.94 62 5 0 187 2 38 99 3e-33 123 NODE_2838_length_139_cov_133.841721 gi|253756597|ref|YP_003038510.1| 90.32 62 6 0 187 2 38 99 5e-32 119 NODE_2838_length_139_cov_133.841721 gi|15081546|ref|NP_150076.1| 90.32 62 6 0 187 2 38 99 5e-32 119 NODE_2838_length_139_cov_133.841721 gi|253756584|ref|YP_003038498.1| 88.71 62 7 0 187 2 38 99 8e-32 119 NODE_2838_length_139_cov_133.841721 gi|167600357|ref|YP_001671999.1| 88.71 62 7 0 187 2 37 98 5e-31 117 NODE_2838_length_139_cov_133.841721 gi|56807325|ref|YP_173237.1| 69.35 62 19 0 187 2 32 93 1e-22 93.2 NODE_2838_length_139_cov_133.841721 gi|60115394|ref|YP_209232.1| 64.52 62 22 0 187 2 43 104 5e-21 89.4 NODE_2854_length_149_cov_752.966431 gi|167600358|ref|YP_001672000.1| 96.97 66 2 0 2 199 1274 1339 1e-37 139 NODE_2854_length_149_cov_752.966431 gi|253756598|ref|YP_003038511.1| 96.97 66 2 0 2 199 1274 1339 2e-37 139 NODE_2854_length_149_cov_752.966431 gi|15081547|ref|NP_150077.1| 96.97 66 2 0 2 199 1274 1339 2e-37 138 NODE_2854_length_149_cov_752.966431 gi|253756585|ref|YP_003038499.1| 96.97 66 2 0 2 199 1274 1339 2e-37 138 NODE_2854_length_149_cov_752.966431 gi|394935454|ref|YP_005454245.1| 96.97 66 2 0 2 199 1273 1338 2e-37 138 NODE_2854_length_149_cov_752.966431 gi|85718618|ref|YP_459952.1| 96.97 66 2 0 2 199 1260 1325 3e-37 138 NODE_2854_length_149_cov_752.966431 gi|38018026|ref|NP_937950.1| 98.48 66 1 0 2 199 1272 1337 3e-37 138 NODE_2854_length_149_cov_752.966431 gi|56807326|ref|YP_173238.1| 76.56 64 15 0 8 199 1269 1332 9e-29 114 NODE_2854_length_149_cov_752.966431 gi|253756610|ref|YP_003038522.1| 94.55 55 3 0 2 166 1274 1328 1e-27 110 NODE_2854_length_149_cov_752.966431 gi|9629814|ref|NP_045300.1| 83.02 53 9 0 8 166 1234 1286 8e-24 99.8 NODE_2981_length_212_cov_275.750000 gi|38018026|ref|NP_937950.1| 96.55 87 3 0 2 262 392 478 5e-51 178 NODE_2981_length_212_cov_275.750000 gi|15081547|ref|NP_150077.1| 96.55 87 3 0 2 262 382 468 6e-51 178 NODE_2981_length_212_cov_275.750000 gi|253756585|ref|YP_003038499.1| 96.55 87 3 0 2 262 382 468 7e-51 178 NODE_2981_length_212_cov_275.750000 gi|253756610|ref|YP_003038522.1| 95.40 87 4 0 2 262 382 468 3e-50 176 NODE_2981_length_212_cov_275.750000 gi|253756598|ref|YP_003038511.1| 94.25 87 5 0 2 262 382 468 9e-50 174 NODE_2981_length_212_cov_275.750000 gi|394935454|ref|YP_005454245.1| 93.10 87 6 0 2 262 381 467 2e-49 174 NODE_2981_length_212_cov_275.750000 gi|167600358|ref|YP_001672000.1| 78.16 87 18 1 2 262 382 467 9e-40 146 NODE_2981_length_212_cov_275.750000 gi|85718618|ref|YP_459952.1| 76.71 73 17 0 2 220 382 454 3e-33 127 NODE_2981_length_212_cov_275.750000 gi|60115395|ref|YP_209233.1| 60.76 79 31 0 2 238 380 458 1e-29 117 NODE_2981_length_212_cov_275.750000 gi|56807326|ref|YP_173238.1| 67.12 73 24 0 2 220 378 450 1e-28 114 NODE_3045_length_866_cov_8.483833 gi|34538598|ref|NP_904328.1| 69.07 291 90 0 914 42 26 316 5e-92 283 NODE_3045_length_866_cov_8.483833 gi|251831107|ref|YP_003024026.1| 67.01 291 96 0 914 42 26 316 5e-83 260 NODE_3045_length_866_cov_8.483833 gi|494060707|ref|WP_007002790.1| 44.13 281 150 2 914 93 39 319 3e-52 181 NODE_3045_length_866_cov_8.483833 gi|496406861|ref|WP_009115725.1| 40.61 293 157 4 914 84 44 335 5e-42 155 NODE_3045_length_866_cov_8.483833 gi|496410681|ref|WP_009119545.1| 40.61 293 157 4 914 84 43 334 5e-42 154 NODE_3045_length_866_cov_8.483833 gi|489880086|ref|WP_003783554.1| 41.46 287 152 3 914 102 52 338 1e-41 154 NODE_3045_length_866_cov_8.483833 gi|489884532|ref|WP_003787982.1| 40.96 293 156 4 914 84 52 343 2e-41 153 NODE_3045_length_866_cov_8.483833 gi|491919997|ref|WP_005672482.1| 41.61 298 153 4 914 84 48 345 3e-41 153 NODE_3045_length_866_cov_8.483833 gi|489919582|ref|WP_003822943.1| 41.46 287 152 3 914 102 51 337 4e-41 152 NODE_3045_length_866_cov_8.483833 gi|488718793|ref|WP_002642669.1| 40.20 296 143 4 914 102 52 338 5e-40 149 NODE_3126_length_177_cov_47.276836 gi|26008095|ref|NP_742170.1| 98.67 75 1 0 2 226 247 321 5e-24 99.0 NODE_3126_length_177_cov_47.276836 gi|253756606|ref|YP_003038519.1| 100.00 75 0 0 2 226 2997 3071 2e-23 99.4 NODE_3126_length_177_cov_47.276836 gi|38018023|ref|NP_937947.1| 100.00 75 0 0 2 226 2997 3071 2e-23 99.4 NODE_3126_length_177_cov_47.276836 gi|253756607|ref|YP_003038518.1| 100.00 75 0 0 2 226 2997 3071 3e-23 99.0 NODE_3126_length_177_cov_47.276836 gi|15081555|ref|NP_150074.1| 98.67 75 1 0 2 226 2997 3071 3e-23 99.0 NODE_3126_length_177_cov_47.276836 gi|253756594|ref|YP_003038508.1| 98.67 75 1 0 2 226 2997 3071 3e-23 99.0 NODE_3126_length_177_cov_47.276836 gi|253756581|ref|YP_003038496.1| 98.67 75 1 0 2 226 2997 3071 3e-23 99.0 NODE_3126_length_177_cov_47.276836 gi|253756595|ref|YP_003038507.1| 98.67 75 1 0 2 226 2997 3071 4e-23 98.6 NODE_3126_length_177_cov_47.276836 gi|253756582|ref|YP_003038495.1| 98.67 75 1 0 2 226 2997 3071 4e-23 98.6 NODE_3126_length_177_cov_47.276836 gi|26008080|ref|NP_150073.2| 98.67 75 1 0 2 226 2997 3071 4e-23 98.6 NODE_3187_length_311_cov_218.842438 gi|38018026|ref|NP_937950.1| 87.07 116 13 1 351 4 1 114 1e-56 196 NODE_3187_length_311_cov_218.842438 gi|253756598|ref|YP_003038511.1| 87.93 116 10 1 351 4 1 112 6e-56 194 NODE_3187_length_311_cov_218.842438 gi|15081547|ref|NP_150077.1| 87.93 116 10 1 351 4 1 112 7e-56 194 NODE_3187_length_311_cov_218.842438 gi|253756585|ref|YP_003038499.1| 87.93 116 10 1 351 4 1 112 9e-56 193 NODE_3187_length_311_cov_218.842438 gi|394935454|ref|YP_005454245.1| 86.21 116 12 1 351 4 1 112 5e-55 191 NODE_3187_length_311_cov_218.842438 gi|253756610|ref|YP_003038522.1| 86.21 116 12 1 351 4 1 112 2e-54 189 NODE_3187_length_311_cov_218.842438 gi|85718618|ref|YP_459952.1| 76.07 117 24 1 351 1 1 113 3e-50 177 NODE_3187_length_311_cov_218.842438 gi|167600358|ref|YP_001672000.1| 70.69 116 30 1 351 4 1 112 3e-45 163 NODE_3187_length_311_cov_218.842438 gi|60115395|ref|YP_209233.1| 57.39 115 46 1 351 7 1 112 7e-35 134 NODE_3187_length_311_cov_218.842438 gi|56807326|ref|YP_173238.1| 56.41 117 46 2 351 1 1 112 2e-34 132 NODE_3192_length_109_cov_357.678894 gi|38018023|ref|NP_937947.1| 98.08 52 1 0 2 157 1462 1513 1e-26 107 NODE_3192_length_109_cov_357.678894 gi|253756607|ref|YP_003038518.1| 96.15 52 2 0 2 157 1462 1513 9e-26 105 NODE_3192_length_109_cov_357.678894 gi|253756582|ref|YP_003038495.1| 96.15 52 2 0 2 157 1462 1513 9e-26 105 NODE_3192_length_109_cov_357.678894 gi|26008080|ref|NP_150073.2| 96.15 52 2 0 2 157 1462 1513 9e-26 105 NODE_3192_length_109_cov_357.678894 gi|253756595|ref|YP_003038507.1| 96.15 52 2 0 2 157 1462 1513 9e-26 105 NODE_3192_length_109_cov_357.678894 gi|253756606|ref|YP_003038519.1| 96.15 52 2 0 2 157 1462 1513 1e-25 104 NODE_3192_length_109_cov_357.678894 gi|253756581|ref|YP_003038496.1| 96.15 52 2 0 2 157 1462 1513 1e-25 104 NODE_3192_length_109_cov_357.678894 gi|15081555|ref|NP_150074.1| 96.15 52 2 0 2 157 1462 1513 1e-25 104 NODE_3192_length_109_cov_357.678894 gi|253756594|ref|YP_003038508.1| 96.15 52 2 0 2 157 1462 1513 1e-25 104 NODE_3192_length_109_cov_357.678894 gi|26008083|ref|NP_742169.1| 96.15 52 2 0 2 157 611 662 6e-25 102 NODE_3220_length_578_cov_94.439445 gi|26008094|ref|NP_742142.1| 98.97 195 2 0 1 585 105 299 4e-139 399 NODE_3220_length_578_cov_94.439445 gi|38018023|ref|NP_937947.1| 100.00 195 0 0 1 585 6901 7095 2e-128 408 NODE_3220_length_578_cov_94.439445 gi|253756595|ref|YP_003038507.1| 98.97 195 2 0 1 585 6900 7094 1e-126 403 NODE_3220_length_578_cov_94.439445 gi|253756582|ref|YP_003038495.1| 98.97 195 2 0 1 585 6900 7094 1e-126 403 NODE_3220_length_578_cov_94.439445 gi|26008080|ref|NP_150073.2| 98.97 195 2 0 1 585 6900 7094 1e-126 403 NODE_3220_length_578_cov_94.439445 gi|85718615|ref|YP_459949.1| 98.46 195 3 0 1 585 6901 7095 4e-125 398 NODE_3220_length_578_cov_94.439445 gi|253756607|ref|YP_003038518.1| 97.95 195 4 0 1 585 6900 7094 1e-124 397 NODE_3220_length_578_cov_94.439445 gi|394935459|ref|YP_005454239.1| 97.44 195 5 0 1 585 6957 7151 1e-124 397 NODE_3220_length_578_cov_94.439445 gi|167600354|ref|YP_001671996.1| 96.41 195 7 0 1 585 6934 7128 2e-122 390 NODE_3220_length_578_cov_94.439445 gi|25121573|ref|NP_740620.1| 85.05 194 29 0 1 582 105 298 1e-121 354 NODE_3221_length_169_cov_100.307693 gi|38018024|ref|NP_937948.1| 98.48 66 1 0 20 217 1 66 1e-39 138 NODE_3221_length_169_cov_100.307693 gi|253756596|ref|YP_003038509.1| 95.45 66 3 0 20 217 1 66 5e-39 136 NODE_3221_length_169_cov_100.307693 gi|253756583|ref|YP_003038497.1| 95.45 66 3 0 20 217 1 66 5e-39 136 NODE_3221_length_169_cov_100.307693 gi|15081545|ref|NP_150075.1| 95.45 66 3 0 20 217 1 66 5e-39 136 NODE_3221_length_169_cov_100.307693 gi|253756608|ref|YP_003038520.1| 92.42 66 5 0 20 217 1 66 1e-37 132 NODE_3221_length_169_cov_100.307693 gi|85718616|ref|YP_459950.1| 89.39 66 7 0 20 217 1 66 3e-35 124 NODE_3221_length_169_cov_100.307693 gi|167600356|ref|YP_001671998.1| 64.62 65 23 0 20 214 1 65 6e-25 99.4 NODE_3221_length_169_cov_100.307693 gi|11192310|ref|NP_068669.1| 58.73 63 26 0 26 214 13 75 4e-21 88.6 NODE_3221_length_169_cov_100.307693 gi|253750533|ref|YP_003029846.1| 56.72 67 29 0 14 214 1 67 5e-21 88.6 NODE_3221_length_169_cov_100.307693 gi|394935449|ref|YP_005454240.1| 88.37 43 5 0 20 148 1 43 2e-20 82.4 NODE_3229_length_202_cov_723.222778 gi|85718618|ref|YP_459952.1| 98.80 83 1 0 251 3 1062 1144 6e-48 169 NODE_3229_length_202_cov_723.222778 gi|38018026|ref|NP_937950.1| 100.00 83 0 0 251 3 1074 1156 6e-48 169 NODE_3229_length_202_cov_723.222778 gi|253756585|ref|YP_003038499.1| 98.80 83 1 0 251 3 1076 1158 1e-47 169 NODE_3229_length_202_cov_723.222778 gi|15081547|ref|NP_150077.1| 98.80 83 1 0 251 3 1076 1158 1e-47 168 NODE_3229_length_202_cov_723.222778 gi|253756610|ref|YP_003038522.1| 98.80 83 1 0 251 3 1076 1158 2e-47 168 NODE_3229_length_202_cov_723.222778 gi|253756598|ref|YP_003038511.1| 98.80 83 1 0 251 3 1076 1158 2e-47 168 NODE_3229_length_202_cov_723.222778 gi|394935454|ref|YP_005454245.1| 98.80 83 1 0 251 3 1075 1157 3e-47 167 NODE_3229_length_202_cov_723.222778 gi|167600358|ref|YP_001672000.1| 92.77 83 6 0 251 3 1076 1158 6e-45 160 NODE_3229_length_202_cov_723.222778 gi|253750535|ref|YP_003029848.1| 89.16 83 9 0 251 3 1068 1150 2e-43 156 NODE_3229_length_202_cov_723.222778 gi|60115395|ref|YP_209233.1| 86.75 83 11 0 251 3 1084 1166 4e-43 155 NODE_3236_length_163_cov_391.503082 gi|38018026|ref|NP_937950.1| 90.41 73 4 2 213 1 494 565 1e-34 130 NODE_3236_length_163_cov_391.503082 gi|253756610|ref|YP_003038522.1| 74.70 83 8 3 210 1 485 567 7e-30 117 NODE_3236_length_163_cov_391.503082 gi|253756585|ref|YP_003038499.1| 73.49 83 9 3 210 1 485 567 3e-29 115 NODE_3236_length_163_cov_391.503082 gi|15081547|ref|NP_150077.1| 73.49 83 9 3 210 1 485 567 3e-29 115 NODE_3236_length_163_cov_391.503082 gi|253756598|ref|YP_003038511.1| 74.70 83 8 3 210 1 485 567 4e-29 115 NODE_3236_length_163_cov_391.503082 gi|394935454|ref|YP_005454245.1| 68.29 82 13 3 207 1 485 566 1e-25 105 NODE_3236_length_163_cov_391.503082 gi|167600358|ref|YP_001672000.1| 50.60 83 27 3 207 1 485 567 5e-15 74.3 NODE_3236_length_163_cov_391.503082 gi|56807326|ref|YP_173238.1| 42.17 83 30 3 207 1 473 551 1e-07 53.1 NODE_3236_length_163_cov_391.503082 gi|85718618|ref|YP_459952.1| 35.80 81 33 4 207 1 480 553 8e-05 44.7 NODE_3236_length_163_cov_391.503082 gi|253750535|ref|YP_003029848.1| 33.73 83 37 4 210 1 477 554 4e-04 42.4 NODE_3407_length_174_cov_2.557471 gi|489240182|ref|WP_003148409.1| 40.48 42 18 1 219 115 30 71 5.7 29.6 NODE_3407_length_174_cov_2.557471 gi|495171955|ref|WP_007896750.1| 40.54 37 22 0 83 193 349 385 7.4 29.3 NODE_3407_length_174_cov_2.557471 gi|269797424|ref|YP_003311324.1| 30.77 52 33 1 64 210 217 268 7.4 29.3 NODE_3407_length_174_cov_2.557471 gi|491530222|ref|WP_005387845.1| 30.77 52 33 1 64 210 217 268 9.5 28.9 NODE_3501_length_336_cov_52.416668 gi|26008090|ref|NP_742138.1| 98.44 128 2 0 386 3 77 204 1e-82 267 NODE_3501_length_336_cov_52.416668 gi|38018023|ref|NP_937947.1| 100.00 128 0 0 386 3 4446 4573 4e-82 271 NODE_3501_length_336_cov_52.416668 gi|167600354|ref|YP_001671996.1| 99.22 128 1 0 386 3 4492 4619 1e-81 269 NODE_3501_length_336_cov_52.416668 gi|253756607|ref|YP_003038518.1| 98.44 128 2 0 386 3 4446 4573 2e-81 268 NODE_3501_length_336_cov_52.416668 gi|253756595|ref|YP_003038507.1| 98.44 128 2 0 386 3 4446 4573 2e-81 268 NODE_3501_length_336_cov_52.416668 gi|26008080|ref|NP_150073.2| 98.44 128 2 0 386 3 4446 4573 2e-81 268 NODE_3501_length_336_cov_52.416668 gi|253756582|ref|YP_003038495.1| 98.44 128 2 0 386 3 4446 4573 2e-81 268 NODE_3501_length_336_cov_52.416668 gi|85718615|ref|YP_459949.1| 97.66 128 3 0 386 3 4446 4573 2e-80 266 NODE_3501_length_336_cov_52.416668 gi|394935459|ref|YP_005454239.1| 88.28 128 15 0 386 3 4506 4633 1e-72 244 NODE_3501_length_336_cov_52.416668 gi|25121569|ref|NP_740616.1| 77.34 128 29 0 386 3 77 204 2e-63 213 NODE_3502_length_463_cov_51.583153 gi|38018023|ref|NP_937947.1| 98.85 87 1 0 263 3 4375 4461 2e-92 181 NODE_3502_length_463_cov_51.583153 gi|38018023|ref|NP_937947.1| 98.82 85 1 0 511 257 4292 4376 2e-92 179 NODE_3502_length_463_cov_51.583153 gi|253756607|ref|YP_003038518.1| 98.84 86 1 0 511 254 4292 4377 3e-90 182 NODE_3502_length_463_cov_51.583153 gi|253756607|ref|YP_003038518.1| 94.25 87 5 0 263 3 4375 4461 3e-90 172 NODE_3502_length_463_cov_51.583153 gi|85718615|ref|YP_459949.1| 97.67 86 2 0 511 254 4292 4377 5e-90 181 NODE_3502_length_463_cov_51.583153 gi|85718615|ref|YP_459949.1| 94.25 87 5 0 263 3 4375 4461 5e-90 172 NODE_3502_length_463_cov_51.583153 gi|26008080|ref|NP_150073.2| 97.67 86 2 0 511 254 4292 4377 5e-90 181 NODE_3502_length_463_cov_51.583153 gi|26008080|ref|NP_150073.2| 94.25 87 5 0 263 3 4375 4461 5e-90 172 NODE_3502_length_463_cov_51.583153 gi|253756582|ref|YP_003038495.1| 97.67 86 2 0 511 254 4292 4377 6e-90 181 NODE_3502_length_463_cov_51.583153 gi|253756582|ref|YP_003038495.1| 94.25 87 5 0 263 3 4375 4461 6e-90 172 NODE_3502_length_463_cov_51.583153 gi|253756595|ref|YP_003038507.1| 97.67 86 2 0 511 254 4292 4377 6e-90 181 NODE_3502_length_463_cov_51.583153 gi|253756595|ref|YP_003038507.1| 94.25 87 5 0 263 3 4375 4461 6e-90 172 NODE_3502_length_463_cov_51.583153 gi|167600354|ref|YP_001671996.1| 96.51 86 3 0 511 254 4338 4423 2e-89 179 NODE_3502_length_463_cov_51.583153 gi|167600354|ref|YP_001671996.1| 94.25 87 5 0 263 3 4421 4507 2e-89 171 NODE_3502_length_463_cov_51.583153 gi|394935459|ref|YP_005454239.1| 91.86 86 7 0 511 254 4352 4437 1e-83 173 NODE_3502_length_463_cov_51.583153 gi|394935459|ref|YP_005454239.1| 86.05 86 12 0 263 6 4435 4520 1e-83 158 NODE_3502_length_463_cov_51.583153 gi|26007546|ref|NP_068668.2| 88.37 86 10 0 511 254 4379 4464 3e-76 167 NODE_3502_length_463_cov_51.583153 gi|26007546|ref|NP_068668.2| 74.71 87 22 0 263 3 4462 4548 3e-76 139 NODE_3502_length_463_cov_51.583153 gi|253750532|ref|YP_003029844.1| 87.21 86 11 0 511 254 4373 4458 1e-75 165 NODE_3502_length_463_cov_51.583153 gi|253750532|ref|YP_003029844.1| 74.71 87 22 0 263 3 4456 4542 1e-75 139 NODE_3600_length_758_cov_23.003958 gi|34538600|ref|NP_904330.1| 74.50 251 64 0 3 755 264 514 9e-122 365 NODE_3600_length_758_cov_23.003958 gi|251831109|ref|YP_003024028.1| 72.69 249 68 0 3 749 264 512 1e-114 347 NODE_3600_length_758_cov_23.003958 gi|488801869|ref|WP_002714275.1| 53.78 251 114 1 3 749 251 501 5e-75 244 NODE_3600_length_758_cov_23.003958 gi|492887319|ref|WP_006022898.1| 54.18 251 113 1 3 749 288 538 3e-74 243 NODE_3600_length_758_cov_23.003958 gi|488804983|ref|WP_002717389.1| 53.88 245 111 1 3 731 291 535 1e-73 242 NODE_3600_length_758_cov_23.003958 gi|490319116|ref|WP_004208609.1| 52.65 245 114 1 3 731 309 553 2e-72 239 NODE_3600_length_758_cov_23.003958 gi|494060889|ref|WP_007002972.1| 52.03 246 116 1 3 734 286 531 2e-70 233 NODE_3600_length_758_cov_23.003958 gi|488806148|ref|WP_002718554.1| 52.03 246 116 2 3 734 289 534 8e-68 226 NODE_3600_length_758_cov_23.003958 gi|493432515|ref|WP_006388093.1| 44.22 251 138 1 3 749 285 535 1e-55 194 NODE_3600_length_758_cov_23.003958 gi|493248467|ref|WP_006216867.1| 43.82 251 139 1 3 749 285 535 6e-55 192 NODE_3624_length_129_cov_271.782959 gi|38018023|ref|NP_937947.1| 100.00 59 0 0 179 3 1630 1688 2e-32 124 NODE_3624_length_129_cov_271.782959 gi|85718615|ref|YP_459949.1| 94.92 59 3 0 179 3 1630 1688 4e-29 115 NODE_3624_length_129_cov_271.782959 gi|26008083|ref|NP_742169.1| 93.22 59 4 0 179 3 779 837 7e-29 114 NODE_3624_length_129_cov_271.782959 gi|253756594|ref|YP_003038508.1| 93.22 59 4 0 179 3 1630 1688 1e-28 114 NODE_3624_length_129_cov_271.782959 gi|15081555|ref|NP_150074.1| 93.22 59 4 0 179 3 1630 1688 1e-28 114 NODE_3624_length_129_cov_271.782959 gi|253756581|ref|YP_003038496.1| 93.22 59 4 0 179 3 1630 1688 1e-28 114 NODE_3624_length_129_cov_271.782959 gi|253756595|ref|YP_003038507.1| 93.22 59 4 0 179 3 1630 1688 1e-28 114 NODE_3624_length_129_cov_271.782959 gi|26008080|ref|NP_150073.2| 93.22 59 4 0 179 3 1630 1688 1e-28 114 NODE_3624_length_129_cov_271.782959 gi|253756606|ref|YP_003038519.1| 93.22 59 4 0 179 3 1630 1688 1e-28 114 NODE_3624_length_129_cov_271.782959 gi|253756582|ref|YP_003038495.1| 93.22 59 4 0 179 3 1630 1688 1e-28 114 NODE_3737_length_1036_cov_70.698845 gi|38018023|ref|NP_937947.1| 99.45 362 2 0 1 1086 6266 6627 0.0 728 NODE_3737_length_1036_cov_70.698845 gi|253756595|ref|YP_003038507.1| 98.34 361 6 0 1 1083 6266 6626 0.0 719 NODE_3737_length_1036_cov_70.698845 gi|253756582|ref|YP_003038495.1| 98.34 361 6 0 1 1083 6266 6626 0.0 719 NODE_3737_length_1036_cov_70.698845 gi|26008080|ref|NP_150073.2| 98.34 361 6 0 1 1083 6266 6626 0.0 719 NODE_3737_length_1036_cov_70.698845 gi|253756607|ref|YP_003038518.1| 97.78 361 8 0 1 1083 6266 6626 0.0 715 NODE_3737_length_1036_cov_70.698845 gi|85718615|ref|YP_459949.1| 97.24 362 10 0 1 1086 6266 6627 0.0 714 NODE_3737_length_1036_cov_70.698845 gi|167600354|ref|YP_001671996.1| 91.69 361 26 1 1 1083 6308 6664 0.0 669 NODE_3737_length_1036_cov_70.698845 gi|394935459|ref|YP_005454239.1| 90.70 355 33 0 1 1065 6322 6676 0.0 655 NODE_3737_length_1036_cov_70.698845 gi|26007546|ref|NP_068668.2| 81.16 361 68 0 1 1083 6350 6710 0.0 602 NODE_3737_length_1036_cov_70.698845 gi|253750532|ref|YP_003029844.1| 80.95 357 68 0 1 1071 6344 6700 0.0 595 NODE_3758_length_116_cov_364.594818 gi|38018026|ref|NP_937950.1| 96.36 55 2 0 165 1 313 367 7e-30 116 NODE_3758_length_116_cov_364.594818 gi|394935454|ref|YP_005454245.1| 92.73 55 4 0 165 1 302 356 9e-29 113 NODE_3758_length_116_cov_364.594818 gi|15081547|ref|NP_150077.1| 92.73 55 4 0 165 1 303 357 1e-28 113 NODE_3758_length_116_cov_364.594818 gi|253756598|ref|YP_003038511.1| 92.73 55 4 0 165 1 303 357 1e-28 113 NODE_3758_length_116_cov_364.594818 gi|253756610|ref|YP_003038522.1| 92.73 55 4 0 165 1 303 357 1e-28 113 NODE_3758_length_116_cov_364.594818 gi|253756585|ref|YP_003038499.1| 92.73 55 4 0 165 1 303 357 1e-28 112 NODE_3758_length_116_cov_364.594818 gi|85718618|ref|YP_459952.1| 85.45 55 8 0 165 1 303 357 2e-26 106 NODE_3758_length_116_cov_364.594818 gi|167600358|ref|YP_001672000.1| 74.55 55 14 0 165 1 303 357 5e-22 94.0 NODE_3758_length_116_cov_364.594818 gi|9629814|ref|NP_045300.1| 74.55 55 14 0 165 1 301 355 1e-21 93.2 NODE_3758_length_116_cov_364.594818 gi|60115395|ref|YP_209233.1| 72.73 55 15 0 165 1 301 355 2e-21 92.4 NODE_3792_length_227_cov_68.550659 gi|38018023|ref|NP_937947.1| 98.91 92 1 0 2 277 4084 4175 6e-54 188 NODE_3792_length_227_cov_68.550659 gi|15081555|ref|NP_150074.1| 97.83 92 2 0 2 277 4084 4175 3e-53 186 NODE_3792_length_227_cov_68.550659 gi|253756581|ref|YP_003038496.1| 97.83 92 2 0 2 277 4084 4175 4e-53 186 NODE_3792_length_227_cov_68.550659 gi|253756606|ref|YP_003038519.1| 97.83 92 2 0 2 277 4084 4175 4e-53 186 NODE_3792_length_227_cov_68.550659 gi|253756594|ref|YP_003038508.1| 97.83 92 2 0 2 277 4084 4175 4e-53 186 NODE_3792_length_227_cov_68.550659 gi|167600355|ref|YP_001671997.1| 97.83 92 2 0 2 277 4130 4221 4e-53 186 NODE_3792_length_227_cov_68.550659 gi|167600354|ref|YP_001671996.1| 97.83 92 2 0 2 277 4130 4221 4e-53 186 NODE_3792_length_227_cov_68.550659 gi|253756582|ref|YP_003038495.1| 97.83 92 2 0 2 277 4084 4175 5e-53 185 NODE_3792_length_227_cov_68.550659 gi|253756607|ref|YP_003038518.1| 97.83 92 2 0 2 277 4084 4175 5e-53 185 NODE_3792_length_227_cov_68.550659 gi|253756595|ref|YP_003038507.1| 97.83 92 2 0 2 277 4084 4175 5e-53 185 NODE_3818_length_247_cov_68.971657 gi|26008085|ref|NP_742133.1| 94.95 99 5 0 297 1 50 148 4e-59 190 NODE_3818_length_247_cov_68.971657 gi|38018023|ref|NP_937947.1| 98.99 99 1 0 297 1 3599 3697 1e-57 199 NODE_3818_length_247_cov_68.971657 gi|253756594|ref|YP_003038508.1| 94.95 99 5 0 297 1 3599 3697 2e-55 192 NODE_3818_length_247_cov_68.971657 gi|15081555|ref|NP_150074.1| 94.95 99 5 0 297 1 3599 3697 2e-55 192 NODE_3818_length_247_cov_68.971657 gi|253756581|ref|YP_003038496.1| 94.95 99 5 0 297 1 3599 3697 2e-55 192 NODE_3818_length_247_cov_68.971657 gi|253756606|ref|YP_003038519.1| 94.95 99 5 0 297 1 3599 3697 2e-55 192 NODE_3818_length_247_cov_68.971657 gi|253756582|ref|YP_003038495.1| 94.95 99 5 0 297 1 3599 3697 3e-55 192 NODE_3818_length_247_cov_68.971657 gi|253756595|ref|YP_003038507.1| 94.95 99 5 0 297 1 3599 3697 3e-55 192 NODE_3818_length_247_cov_68.971657 gi|26008080|ref|NP_150073.2| 94.95 99 5 0 297 1 3599 3697 3e-55 192 NODE_3818_length_247_cov_68.971657 gi|253756607|ref|YP_003038518.1| 94.95 99 5 0 297 1 3599 3697 3e-55 192 NODE_3849_length_112_cov_551.357117 gi|38018023|ref|NP_937947.1| 98.15 54 1 0 1 162 1289 1342 4e-18 83.2 NODE_3849_length_112_cov_551.357117 gi|26008083|ref|NP_742169.1| 96.30 54 2 0 1 162 438 491 3e-17 80.5 NODE_3849_length_112_cov_551.357117 gi|253756594|ref|YP_003038508.1| 96.30 54 2 0 1 162 1289 1342 3e-17 80.9 NODE_3849_length_112_cov_551.357117 gi|253756581|ref|YP_003038496.1| 96.30 54 2 0 1 162 1289 1342 3e-17 80.5 NODE_3849_length_112_cov_551.357117 gi|15081555|ref|NP_150074.1| 96.30 54 2 0 1 162 1289 1342 3e-17 80.5 NODE_3849_length_112_cov_551.357117 gi|253756606|ref|YP_003038519.1| 96.30 54 2 0 1 162 1289 1342 3e-17 80.5 NODE_3849_length_112_cov_551.357117 gi|85718615|ref|YP_459949.1| 96.30 54 2 0 1 162 1289 1342 3e-17 80.5 NODE_3849_length_112_cov_551.357117 gi|253756595|ref|YP_003038507.1| 96.30 54 2 0 1 162 1289 1342 3e-17 80.5 NODE_3849_length_112_cov_551.357117 gi|253756582|ref|YP_003038495.1| 96.30 54 2 0 1 162 1289 1342 3e-17 80.5 NODE_3849_length_112_cov_551.357117 gi|26008080|ref|NP_150073.2| 96.30 54 2 0 1 162 1289 1342 3e-17 80.5 NODE_3862_length_193_cov_173.751297 gi|38018023|ref|NP_937947.1| 98.75 80 1 0 3 242 2060 2139 4e-44 159 NODE_3862_length_193_cov_173.751297 gi|26008083|ref|NP_742169.1| 92.50 80 6 0 3 242 1209 1288 4e-41 150 NODE_3862_length_193_cov_173.751297 gi|15081555|ref|NP_150074.1| 92.50 80 6 0 3 242 2060 2139 6e-41 150 NODE_3862_length_193_cov_173.751297 gi|26008080|ref|NP_150073.2| 92.50 80 6 0 3 242 2060 2139 8e-41 149 NODE_3862_length_193_cov_173.751297 gi|253756594|ref|YP_003038508.1| 91.25 80 7 0 3 242 2060 2139 1e-40 149 NODE_3862_length_193_cov_173.751297 gi|253756595|ref|YP_003038507.1| 91.25 80 7 0 3 242 2060 2139 2e-40 148 NODE_3862_length_193_cov_173.751297 gi|253756581|ref|YP_003038496.1| 91.25 80 7 0 3 242 2060 2139 4e-40 147 NODE_3862_length_193_cov_173.751297 gi|253756582|ref|YP_003038495.1| 91.25 80 7 0 3 242 2060 2139 5e-40 147 NODE_3862_length_193_cov_173.751297 gi|253756606|ref|YP_003038519.1| 90.00 80 8 0 3 242 2060 2139 2e-39 145 NODE_3862_length_193_cov_173.751297 gi|253756607|ref|YP_003038518.1| 90.00 80 8 0 3 242 2060 2139 2e-39 145 NODE_3883_length_163_cov_166.533737 gi|38018023|ref|NP_937947.1| 98.57 70 1 0 211 2 2230 2299 2e-40 148 NODE_3883_length_163_cov_166.533737 gi|26008083|ref|NP_742169.1| 98.57 70 1 0 211 2 1379 1448 2e-40 147 NODE_3883_length_163_cov_166.533737 gi|253756594|ref|YP_003038508.1| 98.57 70 1 0 211 2 2230 2299 3e-40 147 NODE_3883_length_163_cov_166.533737 gi|253756581|ref|YP_003038496.1| 98.57 70 1 0 211 2 2230 2299 3e-40 147 NODE_3883_length_163_cov_166.533737 gi|15081555|ref|NP_150074.1| 98.57 70 1 0 211 2 2230 2299 3e-40 147 NODE_3883_length_163_cov_166.533737 gi|253756595|ref|YP_003038507.1| 98.57 70 1 0 211 2 2230 2299 4e-40 147 NODE_3883_length_163_cov_166.533737 gi|253756582|ref|YP_003038495.1| 98.57 70 1 0 211 2 2230 2299 4e-40 147 NODE_3883_length_163_cov_166.533737 gi|26008080|ref|NP_150073.2| 98.57 70 1 0 211 2 2230 2299 4e-40 147 NODE_3883_length_163_cov_166.533737 gi|167600355|ref|YP_001671997.1| 97.14 70 2 0 211 2 2276 2345 9e-40 146 NODE_3883_length_163_cov_166.533737 gi|167600354|ref|YP_001671996.1| 97.14 70 2 0 211 2 2276 2345 1e-39 145 NODE_3903_length_1067_cov_9.381443 gi|34538610|ref|NP_904340.1| 71.77 372 105 0 1116 1 3 374 2e-174 499 NODE_3903_length_1067_cov_9.381443 gi|251831119|ref|YP_003024038.1| 69.81 371 112 0 1113 1 4 374 7e-156 451 NODE_3903_length_1067_cov_9.381443 gi|494061236|ref|WP_007003318.1| 49.07 375 187 2 1113 1 18 392 2e-106 327 NODE_3903_length_1067_cov_9.381443 gi|488802282|ref|WP_002714688.1| 47.75 377 189 3 1113 1 17 391 8e-102 323 NODE_3903_length_1067_cov_9.381443 gi|492875618|ref|WP_006018984.1| 46.68 377 193 3 1113 1 17 391 8e-102 323 NODE_3903_length_1067_cov_9.381443 gi|488804222|ref|WP_002716628.1| 47.59 374 192 2 1113 4 17 390 4e-99 316 NODE_3903_length_1067_cov_9.381443 gi|490318665|ref|WP_004208160.1| 46.21 383 194 4 1113 1 19 401 1e-91 289 NODE_3903_length_1067_cov_9.381443 gi|489840120|ref|WP_003743825.1| 40.58 382 200 7 1098 34 21 402 9e-69 230 NODE_3903_length_1067_cov_9.381443 gi|489879342|ref|WP_003782815.1| 42.23 341 171 6 1113 169 16 356 4e-68 228 NODE_3903_length_1067_cov_9.381443 gi|488717304|ref|WP_002641180.1| 42.36 347 173 8 1113 154 17 363 7e-67 225 NODE_3927_length_241_cov_381.448120 gi|38018026|ref|NP_937950.1| 94.79 96 5 0 2 289 562 657 2e-55 191 NODE_3927_length_241_cov_381.448120 gi|394935454|ref|YP_005454245.1| 92.71 96 7 0 2 289 563 658 4e-55 191 NODE_3927_length_241_cov_381.448120 gi|253756585|ref|YP_003038499.1| 90.62 96 9 0 2 289 564 659 7e-55 189 NODE_3927_length_241_cov_381.448120 gi|15081547|ref|NP_150077.1| 90.62 96 9 0 2 289 564 659 8e-55 189 NODE_3927_length_241_cov_381.448120 gi|253756598|ref|YP_003038511.1| 90.62 96 9 0 2 289 564 659 1e-54 189 NODE_3927_length_241_cov_381.448120 gi|253756610|ref|YP_003038522.1| 88.54 96 11 0 2 289 564 659 3e-53 185 NODE_3927_length_241_cov_381.448120 gi|167600358|ref|YP_001672000.1| 71.88 96 27 0 2 289 564 659 9e-43 155 NODE_3927_length_241_cov_381.448120 gi|85718618|ref|YP_459952.1| 72.92 96 26 0 2 289 550 645 1e-42 155 NODE_3927_length_241_cov_381.448120 gi|253750535|ref|YP_003029848.1| 62.89 97 35 1 2 289 551 647 3e-34 130 NODE_3927_length_241_cov_381.448120 gi|60115395|ref|YP_209233.1| 59.00 100 37 2 2 289 561 660 4e-31 122 NODE_3950_length_493_cov_447.586212 gi|38018026|ref|NP_937950.1| 98.33 180 3 0 541 2 726 905 5e-114 360 NODE_3950_length_493_cov_447.586212 gi|253756610|ref|YP_003038522.1| 95.00 180 9 0 541 2 728 907 7e-110 348 NODE_3950_length_493_cov_447.586212 gi|253756585|ref|YP_003038499.1| 94.44 180 10 0 541 2 728 907 8e-110 348 NODE_3950_length_493_cov_447.586212 gi|15081547|ref|NP_150077.1| 94.44 180 10 0 541 2 728 907 2e-109 347 NODE_3950_length_493_cov_447.586212 gi|253756598|ref|YP_003038511.1| 94.44 180 10 0 541 2 728 907 2e-109 347 NODE_3950_length_493_cov_447.586212 gi|394935454|ref|YP_005454245.1| 93.89 180 11 0 541 2 727 906 6e-109 345 NODE_3950_length_493_cov_447.586212 gi|85718618|ref|YP_459952.1| 87.22 180 23 0 541 2 714 893 8e-103 328 NODE_3950_length_493_cov_447.586212 gi|167600358|ref|YP_001672000.1| 82.78 180 31 0 541 2 728 907 2e-96 310 NODE_3950_length_493_cov_447.586212 gi|253750535|ref|YP_003029848.1| 68.33 180 57 0 541 2 716 895 2e-79 263 NODE_3950_length_493_cov_447.586212 gi|60115395|ref|YP_209233.1| 67.22 180 59 0 541 2 729 908 7e-79 261 NODE_3954_length_225_cov_85.515556 gi|26008094|ref|NP_742142.1| 100.00 91 0 0 1 273 12 102 2e-59 190 NODE_3954_length_225_cov_85.515556 gi|38018023|ref|NP_937947.1| 100.00 91 0 0 1 273 6808 6898 1e-58 201 NODE_3954_length_225_cov_85.515556 gi|253756607|ref|YP_003038518.1| 100.00 91 0 0 1 273 6807 6897 1e-58 201 NODE_3954_length_225_cov_85.515556 gi|253756582|ref|YP_003038495.1| 100.00 91 0 0 1 273 6807 6897 1e-58 201 NODE_3954_length_225_cov_85.515556 gi|26008080|ref|NP_150073.2| 100.00 91 0 0 1 273 6807 6897 1e-58 201 NODE_3954_length_225_cov_85.515556 gi|253756595|ref|YP_003038507.1| 100.00 91 0 0 1 273 6807 6897 1e-58 201 NODE_3954_length_225_cov_85.515556 gi|85718615|ref|YP_459949.1| 100.00 91 0 0 1 273 6808 6898 1e-58 201 NODE_3954_length_225_cov_85.515556 gi|167600354|ref|YP_001671996.1| 97.80 91 2 0 1 273 6841 6931 1e-57 198 NODE_3954_length_225_cov_85.515556 gi|394935459|ref|YP_005454239.1| 95.60 91 4 0 1 273 6864 6954 8e-57 196 NODE_3954_length_225_cov_85.515556 gi|60115406|ref|YP_209243.1| 89.01 91 10 0 1 273 12 102 2e-53 175 NODE_3974_length_370_cov_90.656754 gi|26008091|ref|NP_742139.1| 99.29 140 1 0 420 1 22 161 3e-97 299 NODE_3974_length_370_cov_90.656754 gi|38018023|ref|NP_937947.1| 100.00 140 0 0 420 1 5319 5458 1e-91 298 NODE_3974_length_370_cov_90.656754 gi|26008080|ref|NP_150073.2| 99.29 140 1 0 420 1 5319 5458 2e-91 298 NODE_3974_length_370_cov_90.656754 gi|253756582|ref|YP_003038495.1| 99.29 140 1 0 420 1 5319 5458 3e-91 298 NODE_3974_length_370_cov_90.656754 gi|253756595|ref|YP_003038507.1| 99.29 140 1 0 420 1 5319 5458 3e-91 298 NODE_3974_length_370_cov_90.656754 gi|253756607|ref|YP_003038518.1| 99.29 140 1 0 420 1 5319 5458 3e-91 298 NODE_3974_length_370_cov_90.656754 gi|167600354|ref|YP_001671996.1| 99.29 140 1 0 420 1 5365 5504 3e-91 298 NODE_3974_length_370_cov_90.656754 gi|85718615|ref|YP_459949.1| 98.57 140 2 0 420 1 5319 5458 5e-91 297 NODE_3974_length_370_cov_90.656754 gi|25121570|ref|NP_740617.1| 92.14 140 11 0 420 1 22 161 9e-91 282 NODE_3974_length_370_cov_90.656754 gi|394935459|ref|YP_005454239.1| 97.86 140 3 0 420 1 5379 5518 2e-90 295 NODE_4055_length_206_cov_71.718445 gi|38018023|ref|NP_937947.1| 100.00 85 0 0 1 255 3477 3561 2e-50 177 NODE_4055_length_206_cov_71.718445 gi|85718615|ref|YP_459949.1| 97.65 85 2 0 1 255 3477 3561 5e-49 173 NODE_4055_length_206_cov_71.718445 gi|253756607|ref|YP_003038518.1| 97.65 85 2 0 1 255 3477 3561 1e-48 172 NODE_4055_length_206_cov_71.718445 gi|253756582|ref|YP_003038495.1| 97.65 85 2 0 1 255 3477 3561 1e-48 172 NODE_4055_length_206_cov_71.718445 gi|26008080|ref|NP_150073.2| 97.65 85 2 0 1 255 3477 3561 1e-48 172 NODE_4055_length_206_cov_71.718445 gi|167600354|ref|YP_001671996.1| 97.65 85 2 0 1 255 3523 3607 1e-48 172 NODE_4055_length_206_cov_71.718445 gi|253756595|ref|YP_003038507.1| 96.47 85 3 0 1 255 3477 3561 2e-48 172 NODE_4055_length_206_cov_71.718445 gi|253756606|ref|YP_003038519.1| 97.65 85 2 0 1 255 3477 3561 2e-48 171 NODE_4055_length_206_cov_71.718445 gi|253756581|ref|YP_003038496.1| 97.65 85 2 0 1 255 3477 3561 2e-48 171 NODE_4055_length_206_cov_71.718445 gi|15081555|ref|NP_150074.1| 97.65 85 2 0 1 255 3477 3561 8e-48 170 NODE_4128_length_290_cov_40.872414 gi|26008087|ref|NP_742135.1| 98.21 112 2 0 338 3 58 169 7e-74 225 NODE_4128_length_290_cov_40.872414 gi|38018023|ref|NP_937947.1| 100.00 112 0 0 338 3 3983 4094 2e-67 228 NODE_4128_length_290_cov_40.872414 gi|25121566|ref|NP_740613.1| 90.18 112 11 0 338 3 55 166 2e-67 209 NODE_4128_length_290_cov_40.872414 gi|85719069|ref|YP_460020.1| 87.50 112 14 0 338 3 55 166 2e-67 208 NODE_4128_length_290_cov_40.872414 gi|15081555|ref|NP_150074.1| 98.21 112 2 0 338 3 3983 4094 1e-66 225 NODE_4128_length_290_cov_40.872414 gi|253756581|ref|YP_003038496.1| 98.21 112 2 0 338 3 3983 4094 1e-66 225 NODE_4128_length_290_cov_40.872414 gi|253756594|ref|YP_003038508.1| 98.21 112 2 0 338 3 3983 4094 1e-66 225 NODE_4128_length_290_cov_40.872414 gi|253756606|ref|YP_003038519.1| 98.21 112 2 0 338 3 3983 4094 1e-66 225 NODE_4128_length_290_cov_40.872414 gi|167600355|ref|YP_001671997.1| 98.21 112 2 0 338 3 4029 4140 2e-66 225 NODE_4128_length_290_cov_40.872414 gi|253756607|ref|YP_003038518.1| 98.21 112 2 0 338 3 3983 4094 2e-66 225 NODE_4157_length_1497_cov_6.110220 gi|34538607|ref|NP_904337.1| 57.53 365 155 0 1103 9 59 423 9e-86 280 NODE_4157_length_1497_cov_6.110220 gi|251831116|ref|YP_003024035.1| 60.81 347 136 0 1049 9 77 423 9e-81 266 NODE_4157_length_1497_cov_6.110220 gi|488803228|ref|WP_002715634.1| 35.01 337 208 5 1109 105 83 410 6e-24 109 NODE_4157_length_1497_cov_6.110220 gi|492880177|ref|WP_006020755.1| 35.01 337 208 5 1109 105 83 410 7e-24 109 NODE_4157_length_1497_cov_6.110220 gi|488799188|ref|WP_002711594.1| 35.31 337 207 5 1109 105 86 413 8e-24 109 NODE_4157_length_1497_cov_6.110220 gi|494060702|ref|WP_007002785.1| 34.49 345 215 5 1145 117 73 408 2e-23 108 NODE_4157_length_1497_cov_6.110220 gi|490654140|ref|WP_004519131.1| 32.93 334 211 5 1109 126 81 407 8e-21 100 NODE_4157_length_1497_cov_6.110220 gi|489773080|ref|WP_003676981.1| 32.93 334 211 5 1109 126 81 407 2e-20 99.4 NODE_4157_length_1497_cov_6.110220 gi|489844193|ref|WP_003747888.1| 32.63 334 212 5 1109 126 81 407 2e-20 99.4 NODE_4157_length_1497_cov_6.110220 gi|488144434|ref|WP_002215642.1| 32.63 334 212 5 1109 126 81 407 3e-20 98.6 NODE_4164_length_250_cov_71.987999 gi|26008092|ref|NP_742140.1| 98.99 99 1 0 2 298 29 127 7e-63 206 NODE_4164_length_250_cov_71.987999 gi|253756595|ref|YP_003038507.1| 98.99 99 1 0 2 298 5929 6027 7e-60 205 NODE_4164_length_250_cov_71.987999 gi|253756582|ref|YP_003038495.1| 98.99 99 1 0 2 298 5929 6027 7e-60 205 NODE_4164_length_250_cov_71.987999 gi|26008080|ref|NP_150073.2| 98.99 99 1 0 2 298 5929 6027 7e-60 205 NODE_4164_length_250_cov_71.987999 gi|253756607|ref|YP_003038518.1| 98.99 99 1 0 2 298 5929 6027 8e-60 205 NODE_4164_length_250_cov_71.987999 gi|38018023|ref|NP_937947.1| 98.99 99 1 0 2 298 5929 6027 8e-60 205 NODE_4164_length_250_cov_71.987999 gi|85718615|ref|YP_459949.1| 97.98 99 2 0 2 298 5929 6027 5e-59 203 NODE_4164_length_250_cov_71.987999 gi|60115404|ref|YP_209241.1| 86.87 99 13 0 2 298 27 125 2e-56 189 NODE_4164_length_250_cov_71.987999 gi|25121571|ref|NP_740618.1| 86.87 99 13 0 2 298 29 127 7e-56 187 NODE_4164_length_250_cov_71.987999 gi|394935459|ref|YP_005454239.1| 89.90 99 10 0 2 298 5985 6083 2e-55 192 NODE_4225_length_322_cov_158.403732 gi|38018024|ref|NP_937948.1| 99.19 124 1 0 1 372 143 266 1e-87 263 NODE_4225_length_322_cov_158.403732 gi|253756608|ref|YP_003038520.1| 94.35 124 7 0 1 372 143 266 2e-82 250 NODE_4225_length_322_cov_158.403732 gi|253756596|ref|YP_003038509.1| 93.55 124 8 0 1 372 143 266 3e-82 249 NODE_4225_length_322_cov_158.403732 gi|253756583|ref|YP_003038497.1| 93.55 124 8 0 1 372 143 266 3e-82 249 NODE_4225_length_322_cov_158.403732 gi|15081545|ref|NP_150075.1| 91.94 124 10 0 1 372 143 266 3e-81 247 NODE_4225_length_322_cov_158.403732 gi|167600356|ref|YP_001671998.1| 72.13 122 34 0 4 369 144 265 3e-62 198 NODE_4225_length_322_cov_158.403732 gi|253750533|ref|YP_003029846.1| 46.72 122 60 1 19 369 142 263 3e-32 120 NODE_4225_length_322_cov_158.403732 gi|60115393|ref|YP_209231.1| 46.72 122 60 1 19 369 142 263 1e-31 119 NODE_4225_length_322_cov_158.403732 gi|394935452|ref|YP_005454243.1| 87.10 62 5 1 187 372 1 59 3e-31 112 NODE_4225_length_322_cov_158.403732 gi|11192310|ref|NP_068669.1| 46.28 121 60 1 22 369 151 271 3e-30 115 NODE_4240_length_404_cov_133.896042 gi|38018025|ref|NP_937949.1| 96.03 151 6 0 454 2 211 361 3e-99 299 NODE_4240_length_404_cov_133.896042 gi|253756584|ref|YP_003038498.1| 95.36 151 7 0 454 2 211 361 3e-99 299 NODE_4240_length_404_cov_133.896042 gi|15081546|ref|NP_150076.1| 95.36 151 7 0 454 2 211 361 4e-99 299 NODE_4240_length_404_cov_133.896042 gi|253756609|ref|YP_003038521.1| 94.70 151 8 0 454 2 211 361 3e-98 297 NODE_4240_length_404_cov_133.896042 gi|253756597|ref|YP_003038510.1| 94.70 151 8 0 454 2 211 361 4e-98 296 NODE_4240_length_404_cov_133.896042 gi|394935453|ref|YP_005454244.1| 94.04 151 9 0 454 2 211 361 3e-97 294 NODE_4240_length_404_cov_133.896042 gi|85718617|ref|YP_459951.1| 90.73 151 14 0 454 2 211 361 5e-95 288 NODE_4240_length_404_cov_133.896042 gi|167600357|ref|YP_001671999.1| 71.52 151 43 0 454 2 210 360 1e-71 228 NODE_4240_length_404_cov_133.896042 gi|253750534|ref|YP_003029847.1| 61.18 152 53 2 439 2 226 377 2e-55 186 NODE_4240_length_404_cov_133.896042 gi|11192311|ref|NP_068670.1| 57.89 152 58 2 439 2 99 250 7e-54 179 NODE_4243_length_386_cov_71.272018 gi|38018023|ref|NP_937947.1| 100.00 144 0 0 3 434 5191 5334 2e-92 301 NODE_4243_length_386_cov_71.272018 gi|253756595|ref|YP_003038507.1| 98.61 144 2 0 3 434 5191 5334 4e-91 297 NODE_4243_length_386_cov_71.272018 gi|253756582|ref|YP_003038495.1| 98.61 144 2 0 3 434 5191 5334 4e-91 297 NODE_4243_length_386_cov_71.272018 gi|26008080|ref|NP_150073.2| 98.61 144 2 0 3 434 5191 5334 4e-91 297 NODE_4243_length_386_cov_71.272018 gi|253756607|ref|YP_003038518.1| 98.61 144 2 0 3 434 5191 5334 4e-91 297 NODE_4243_length_386_cov_71.272018 gi|394935459|ref|YP_005454239.1| 98.61 144 2 0 3 434 5251 5394 5e-91 297 NODE_4243_length_386_cov_71.272018 gi|167600354|ref|YP_001671996.1| 98.61 144 2 0 3 434 5237 5380 5e-91 297 NODE_4243_length_386_cov_71.272018 gi|85718615|ref|YP_459949.1| 97.92 144 3 0 3 434 5191 5334 2e-90 296 NODE_4243_length_386_cov_71.272018 gi|253750532|ref|YP_003029844.1| 94.44 144 8 0 3 434 5272 5415 7e-87 285 NODE_4243_length_386_cov_71.272018 gi|26007546|ref|NP_068668.2| 93.75 144 9 0 3 434 5278 5421 1e-86 285 NODE_4282_length_145_cov_155.027588 gi|38018024|ref|NP_937948.1| 100.00 28 0 0 193 110 251 278 5e-12 63.2 NODE_4282_length_145_cov_155.027588 gi|38018025|ref|NP_937949.1| 96.77 31 1 0 95 3 1 31 8e-12 63.9 NODE_4282_length_145_cov_155.027588 gi|394935453|ref|YP_005454244.1| 93.55 31 2 0 95 3 1 31 3e-11 62.4 NODE_4282_length_145_cov_155.027588 gi|253756609|ref|YP_003038521.1| 90.32 31 3 0 95 3 1 31 4e-11 62.0 NODE_4282_length_145_cov_155.027588 gi|253756584|ref|YP_003038498.1| 90.32 31 3 0 95 3 1 31 5e-11 62.0 NODE_4282_length_145_cov_155.027588 gi|15081546|ref|NP_150076.1| 90.32 31 3 0 95 3 1 31 5e-11 61.6 NODE_4282_length_145_cov_155.027588 gi|253756597|ref|YP_003038510.1| 90.32 31 3 0 95 3 1 31 6e-11 61.6 NODE_4282_length_145_cov_155.027588 gi|253756608|ref|YP_003038520.1| 88.89 27 3 0 193 113 251 277 2e-08 53.9 NODE_4282_length_145_cov_155.027588 gi|15081545|ref|NP_150075.1| 88.89 27 3 0 193 113 251 277 2e-08 53.9 NODE_4282_length_145_cov_155.027588 gi|253756596|ref|YP_003038509.1| 88.89 27 3 0 193 113 251 277 2e-08 53.9 NODE_4487_length_453_cov_43.684326 gi|26008090|ref|NP_742138.1| 99.40 167 1 0 501 1 205 371 2e-114 353 NODE_4487_length_453_cov_43.684326 gi|38018023|ref|NP_937947.1| 100.00 167 0 0 501 1 4574 4740 2e-111 357 NODE_4487_length_453_cov_43.684326 gi|253756582|ref|YP_003038495.1| 99.40 167 1 0 501 1 4574 4740 6e-111 355 NODE_4487_length_453_cov_43.684326 gi|26008080|ref|NP_150073.2| 99.40 167 1 0 501 1 4574 4740 6e-111 355 NODE_4487_length_453_cov_43.684326 gi|85718615|ref|YP_459949.1| 99.40 167 1 0 501 1 4574 4740 6e-111 355 NODE_4487_length_453_cov_43.684326 gi|253756595|ref|YP_003038507.1| 99.40 167 1 0 501 1 4574 4740 6e-111 355 NODE_4487_length_453_cov_43.684326 gi|253756607|ref|YP_003038518.1| 99.40 167 1 0 501 1 4574 4740 7e-111 355 NODE_4487_length_453_cov_43.684326 gi|167600354|ref|YP_001671996.1| 96.41 167 6 0 501 1 4620 4786 3e-108 348 NODE_4487_length_453_cov_43.684326 gi|394935459|ref|YP_005454239.1| 94.61 167 9 0 501 1 4634 4800 2e-107 345 NODE_4487_length_453_cov_43.684326 gi|25121569|ref|NP_740616.1| 87.43 167 21 0 501 1 205 371 7e-101 317 NODE_4518_length_558_cov_97.378136 gi|38018023|ref|NP_937947.1| 99.01 202 2 0 606 1 6612 6813 6e-121 386 NODE_4518_length_558_cov_97.378136 gi|85718615|ref|YP_459949.1| 96.53 202 7 0 606 1 6612 6813 2e-117 376 NODE_4518_length_558_cov_97.378136 gi|253756607|ref|YP_003038518.1| 96.52 201 6 1 603 1 6613 6812 4e-116 372 NODE_4518_length_558_cov_97.378136 gi|253756595|ref|YP_003038507.1| 96.52 201 6 1 603 1 6613 6812 5e-116 372 NODE_4518_length_558_cov_97.378136 gi|253756582|ref|YP_003038495.1| 96.02 201 7 1 603 1 6613 6812 1e-115 371 NODE_4518_length_558_cov_97.378136 gi|26008080|ref|NP_150073.2| 96.02 201 7 1 603 1 6613 6812 1e-115 371 NODE_4518_length_558_cov_97.378136 gi|167600354|ref|YP_001671996.1| 95.00 200 5 1 600 1 6652 6846 1e-112 362 NODE_4518_length_558_cov_97.378136 gi|26008093|ref|NP_742141.1| 95.65 184 7 1 603 52 192 374 1e-111 332 NODE_4518_length_558_cov_97.378136 gi|394935459|ref|YP_005454239.1| 88.12 202 24 0 606 1 6668 6869 3e-98 320 NODE_4518_length_558_cov_97.378136 gi|26007546|ref|NP_068668.2| 78.50 200 42 1 600 1 6698 6896 3e-91 300 NODE_4564_length_261_cov_64.168579 gi|26008084|ref|NP_742132.1| 99.03 103 1 0 309 1 1 103 4e-68 213 NODE_4564_length_261_cov_64.168579 gi|167600355|ref|YP_001671997.1| 99.03 103 1 0 309 1 3293 3395 3e-63 215 NODE_4564_length_261_cov_64.168579 gi|15081555|ref|NP_150074.1| 99.03 103 1 0 309 1 3247 3349 4e-63 215 NODE_4564_length_261_cov_64.168579 gi|253756594|ref|YP_003038508.1| 99.03 103 1 0 309 1 3247 3349 4e-63 215 NODE_4564_length_261_cov_64.168579 gi|253756581|ref|YP_003038496.1| 99.03 103 1 0 309 1 3247 3349 4e-63 215 NODE_4564_length_261_cov_64.168579 gi|253756606|ref|YP_003038519.1| 99.03 103 1 0 309 1 3247 3349 4e-63 215 NODE_4564_length_261_cov_64.168579 gi|253756582|ref|YP_003038495.1| 99.03 103 1 0 309 1 3247 3349 5e-63 214 NODE_4564_length_261_cov_64.168579 gi|26008080|ref|NP_150073.2| 99.03 103 1 0 309 1 3247 3349 5e-63 214 NODE_4564_length_261_cov_64.168579 gi|253756595|ref|YP_003038507.1| 99.03 103 1 0 309 1 3247 3349 6e-63 214 NODE_4564_length_261_cov_64.168579 gi|253756607|ref|YP_003038518.1| 99.03 103 1 0 309 1 3247 3349 6e-63 214 NODE_4565_length_451_cov_47.064301 gi|253756606|ref|YP_003038519.1| 98.80 167 2 0 1 501 3096 3262 2e-108 348 NODE_4565_length_451_cov_47.064301 gi|167600355|ref|YP_001671997.1| 98.20 167 3 0 1 501 3142 3308 4e-108 347 NODE_4565_length_451_cov_47.064301 gi|253756581|ref|YP_003038496.1| 98.20 167 3 0 1 501 3096 3262 4e-108 347 NODE_4565_length_451_cov_47.064301 gi|253756594|ref|YP_003038508.1| 98.20 167 3 0 1 501 3096 3262 4e-108 347 NODE_4565_length_451_cov_47.064301 gi|15081555|ref|NP_150074.1| 98.20 167 3 0 1 501 3096 3262 4e-108 347 NODE_4565_length_451_cov_47.064301 gi|253756607|ref|YP_003038518.1| 98.80 167 2 0 1 501 3096 3262 4e-108 347 NODE_4565_length_451_cov_47.064301 gi|38018023|ref|NP_937947.1| 98.80 167 2 0 1 501 3096 3262 4e-108 347 NODE_4565_length_451_cov_47.064301 gi|253756595|ref|YP_003038507.1| 98.20 167 3 0 1 501 3096 3262 8e-108 347 NODE_4565_length_451_cov_47.064301 gi|253756582|ref|YP_003038495.1| 98.20 167 3 0 1 501 3096 3262 8e-108 347 NODE_4565_length_451_cov_47.064301 gi|26008080|ref|NP_150073.2| 98.20 167 3 0 1 501 3096 3262 8e-108 347 NODE_4615_length_136_cov_46.544117 gi|26008091|ref|NP_742139.1| 100.00 61 0 0 185 3 186 246 3e-34 127 NODE_4615_length_136_cov_46.544117 gi|167600354|ref|YP_001671996.1| 100.00 61 0 0 185 3 5529 5589 3e-33 127 NODE_4615_length_136_cov_46.544117 gi|85718615|ref|YP_459949.1| 100.00 61 0 0 185 3 5483 5543 3e-33 127 NODE_4615_length_136_cov_46.544117 gi|253756595|ref|YP_003038507.1| 100.00 61 0 0 185 3 5483 5543 3e-33 127 NODE_4615_length_136_cov_46.544117 gi|253756582|ref|YP_003038495.1| 100.00 61 0 0 185 3 5483 5543 3e-33 127 NODE_4615_length_136_cov_46.544117 gi|26008080|ref|NP_150073.2| 100.00 61 0 0 185 3 5483 5543 3e-33 127 NODE_4615_length_136_cov_46.544117 gi|38018023|ref|NP_937947.1| 100.00 61 0 0 185 3 5483 5543 3e-33 127 NODE_4615_length_136_cov_46.544117 gi|253756607|ref|YP_003038518.1| 100.00 61 0 0 185 3 5483 5543 4e-33 126 NODE_4615_length_136_cov_46.544117 gi|394935459|ref|YP_005454239.1| 98.36 61 1 0 185 3 5543 5603 5e-33 126 NODE_4615_length_136_cov_46.544117 gi|25121570|ref|NP_740617.1| 91.80 61 5 0 185 3 186 246 1e-31 120 NODE_4640_length_153_cov_1.307190 gi|493308571|ref|WP_006266084.1| 37.10 62 39 0 202 17 333 394 0.003 39.3 NODE_4640_length_153_cov_1.307190 gi|493304973|ref|WP_006262529.1| 37.10 62 39 0 202 17 333 394 0.004 39.3 NODE_4640_length_153_cov_1.307190 gi|493300186|ref|WP_006257801.1| 37.10 62 39 0 202 17 333 394 0.004 39.3 NODE_4640_length_153_cov_1.307190 gi|489079252|ref|WP_002989190.1| 35.38 65 42 0 196 2 335 399 0.004 38.9 NODE_4640_length_153_cov_1.307190 gi|489088389|ref|WP_002998290.1| 41.94 62 36 0 202 17 333 394 0.008 38.1 NODE_4640_length_153_cov_1.307190 gi|490516256|ref|WP_004381808.1| 72.73 22 6 0 202 137 276 297 0.023 36.6 NODE_4640_length_153_cov_1.307190 gi|494222853|ref|WP_007135001.1| 42.50 40 23 0 202 83 276 315 0.037 36.2 NODE_4640_length_153_cov_1.307190 gi|489099428|ref|WP_003009297.1| 40.32 62 37 0 202 17 333 394 0.040 36.2 NODE_4640_length_153_cov_1.307190 gi|490512353|ref|WP_004377959.1| 42.50 40 23 0 202 83 276 315 0.079 35.0 NODE_4640_length_153_cov_1.307190 gi|490506982|ref|WP_004373026.1| 42.50 40 23 0 202 83 276 315 0.082 35.0 NODE_4642_length_542_cov_46.265682 gi|38018023|ref|NP_937947.1| 99.49 196 1 0 590 3 3788 3983 2e-125 399 NODE_4642_length_542_cov_46.265682 gi|85718615|ref|YP_459949.1| 97.96 196 4 0 590 3 3788 3983 1e-122 390 NODE_4642_length_542_cov_46.265682 gi|253756594|ref|YP_003038508.1| 97.45 196 5 0 590 3 3788 3983 1e-122 390 NODE_4642_length_542_cov_46.265682 gi|167600355|ref|YP_001671997.1| 97.45 196 5 0 590 3 3834 4029 1e-122 390 NODE_4642_length_542_cov_46.265682 gi|253756606|ref|YP_003038519.1| 97.45 196 5 0 590 3 3788 3983 2e-122 390 NODE_4642_length_542_cov_46.265682 gi|15081555|ref|NP_150074.1| 97.45 196 5 0 590 3 3788 3983 2e-122 390 NODE_4642_length_542_cov_46.265682 gi|253756581|ref|YP_003038496.1| 97.45 196 5 0 590 3 3788 3983 2e-122 390 NODE_4642_length_542_cov_46.265682 gi|253756595|ref|YP_003038507.1| 97.45 196 5 0 590 3 3788 3983 3e-122 389 NODE_4642_length_542_cov_46.265682 gi|26008080|ref|NP_150073.2| 97.45 196 5 0 590 3 3788 3983 3e-122 389 NODE_4642_length_542_cov_46.265682 gi|253756607|ref|YP_003038518.1| 97.45 196 5 0 590 3 3788 3983 3e-122 389 NODE_4736_length_116_cov_134.034485 gi|38018024|ref|NP_937948.1| 98.18 55 1 0 1 165 51 105 1e-30 114 NODE_4736_length_116_cov_134.034485 gi|253756596|ref|YP_003038509.1| 92.73 55 4 0 1 165 51 105 3e-29 110 NODE_4736_length_116_cov_134.034485 gi|253756583|ref|YP_003038497.1| 92.73 55 4 0 1 165 51 105 3e-29 110 NODE_4736_length_116_cov_134.034485 gi|15081545|ref|NP_150075.1| 92.73 55 4 0 1 165 51 105 3e-29 110 NODE_4736_length_116_cov_134.034485 gi|85718616|ref|YP_459950.1| 90.91 55 5 0 1 165 51 105 8e-29 107 NODE_4736_length_116_cov_134.034485 gi|394935450|ref|YP_005454241.1| 92.45 53 4 0 7 165 1 53 3e-28 102 NODE_4736_length_116_cov_134.034485 gi|253756608|ref|YP_003038520.1| 87.27 55 7 0 1 165 51 105 8e-27 103 NODE_4736_length_116_cov_134.034485 gi|167600356|ref|YP_001671998.1| 61.82 55 21 0 1 165 51 105 8e-15 70.5 NODE_4736_length_116_cov_134.034485 gi|253750533|ref|YP_003029846.1| 60.00 55 21 1 1 165 53 106 9e-15 70.1 NODE_4736_length_116_cov_134.034485 gi|60115393|ref|YP_209231.1| 60.00 55 21 1 1 165 53 106 7e-14 67.8 NODE_4737_length_160_cov_116.581253 gi|85718616|ref|YP_459950.1| 94.20 69 4 0 2 208 90 158 3e-41 139 NODE_4737_length_160_cov_116.581253 gi|253756596|ref|YP_003038509.1| 97.10 69 2 0 2 208 90 158 7e-41 141 NODE_4737_length_160_cov_116.581253 gi|253756583|ref|YP_003038497.1| 97.10 69 2 0 2 208 90 158 7e-41 141 NODE_4737_length_160_cov_116.581253 gi|38018024|ref|NP_937948.1| 97.10 69 2 0 2 208 90 158 9e-41 140 NODE_4737_length_160_cov_116.581253 gi|253756608|ref|YP_003038520.1| 95.65 69 3 0 2 208 90 158 1e-40 140 NODE_4737_length_160_cov_116.581253 gi|15081545|ref|NP_150075.1| 95.65 69 3 0 2 208 90 158 3e-40 139 NODE_4737_length_160_cov_116.581253 gi|167600356|ref|YP_001671998.1| 73.91 69 18 0 2 208 90 158 1e-28 109 NODE_4737_length_160_cov_116.581253 gi|60115393|ref|YP_209231.1| 55.07 69 23 2 2 208 91 151 4e-18 80.1 NODE_4737_length_160_cov_116.581253 gi|253750533|ref|YP_003029846.1| 56.52 69 22 2 2 208 91 151 1e-17 79.0 NODE_4737_length_160_cov_116.581253 gi|11192310|ref|NP_068669.1| 60.42 48 19 0 2 145 99 146 8e-16 73.9 NODE_4924_length_160_cov_76.568748 gi|38018023|ref|NP_937947.1| 100.00 69 0 0 209 3 3546 3614 8e-39 143 NODE_4924_length_160_cov_76.568748 gi|85718615|ref|YP_459949.1| 97.10 69 2 0 209 3 3546 3614 2e-37 139 NODE_4924_length_160_cov_76.568748 gi|253756594|ref|YP_003038508.1| 95.65 69 3 0 209 3 3546 3614 2e-36 136 NODE_4924_length_160_cov_76.568748 gi|253756606|ref|YP_003038519.1| 95.65 69 3 0 209 3 3546 3614 2e-36 136 NODE_4924_length_160_cov_76.568748 gi|167600355|ref|YP_001671997.1| 95.65 69 3 0 209 3 3592 3660 2e-36 136 NODE_4924_length_160_cov_76.568748 gi|15081555|ref|NP_150074.1| 95.65 69 3 0 209 3 3546 3614 2e-36 136 NODE_4924_length_160_cov_76.568748 gi|253756581|ref|YP_003038496.1| 95.65 69 3 0 209 3 3546 3614 2e-36 136 NODE_4924_length_160_cov_76.568748 gi|253756595|ref|YP_003038507.1| 95.65 69 3 0 209 3 3546 3614 2e-36 136 NODE_4924_length_160_cov_76.568748 gi|253756582|ref|YP_003038495.1| 95.65 69 3 0 209 3 3546 3614 2e-36 136 NODE_4924_length_160_cov_76.568748 gi|26008080|ref|NP_150073.2| 95.65 69 3 0 209 3 3546 3614 2e-36 136 NODE_4938_length_190_cov_99.073685 gi|253756606|ref|YP_003038519.1| 100.00 79 0 0 238 2 2505 2583 7e-45 161 NODE_4938_length_190_cov_99.073685 gi|253756607|ref|YP_003038518.1| 100.00 79 0 0 238 2 2505 2583 1e-44 160 NODE_4938_length_190_cov_99.073685 gi|85718615|ref|YP_459949.1| 100.00 79 0 0 238 2 2505 2583 1e-44 160 NODE_4938_length_190_cov_99.073685 gi|38018023|ref|NP_937947.1| 100.00 79 0 0 238 2 2505 2583 1e-44 160 NODE_4938_length_190_cov_99.073685 gi|26008083|ref|NP_742169.1| 98.73 79 1 0 238 2 1654 1732 2e-44 160 NODE_4938_length_190_cov_99.073685 gi|253756594|ref|YP_003038508.1| 98.73 79 1 0 238 2 2505 2583 2e-44 160 NODE_4938_length_190_cov_99.073685 gi|15081555|ref|NP_150074.1| 98.73 79 1 0 238 2 2505 2583 2e-44 160 NODE_4938_length_190_cov_99.073685 gi|167600355|ref|YP_001671997.1| 98.73 79 1 0 238 2 2551 2629 2e-44 160 NODE_4938_length_190_cov_99.073685 gi|253756581|ref|YP_003038496.1| 98.73 79 1 0 238 2 2505 2583 2e-44 159 NODE_4938_length_190_cov_99.073685 gi|253756595|ref|YP_003038507.1| 98.73 79 1 0 238 2 2505 2583 3e-44 159 NODE_4998_length_189_cov_4.666667 gi|6679439|ref|NP_032933.1| 82.93 41 7 0 238 116 124 164 3e-16 74.3 NODE_4998_length_189_cov_4.666667 gi|10863927|ref|NP_066953.1| 80.49 41 8 0 238 116 124 164 1e-15 72.8 NODE_4998_length_189_cov_4.666667 gi|407263453|ref|XP_001002180.3| 78.05 41 9 0 238 116 144 184 7e-14 68.2 NODE_4998_length_189_cov_4.666667 gi|407261558|ref|XP_003086687.2| 78.05 41 9 0 238 116 144 184 7e-14 68.2 NODE_4998_length_189_cov_4.666667 gi|410171187|ref|XP_003960166.1| 73.17 41 11 0 238 116 120 160 7e-13 65.5 NODE_4998_length_189_cov_4.666667 gi|410172829|ref|XP_003960579.1| 75.61 41 9 1 238 116 134 173 3e-12 63.5 NODE_4998_length_189_cov_4.666667 gi|19527310|ref|NP_598845.1| 71.43 42 12 0 238 113 165 206 7e-12 62.8 NODE_4998_length_189_cov_4.666667 gi|410173623|ref|XP_003960830.1| 70.73 41 12 0 238 116 146 186 7e-12 62.8 NODE_4998_length_189_cov_4.666667 gi|113428306|ref|XP_372741.4| 70.73 41 12 0 238 116 146 186 7e-12 62.8 NODE_4998_length_189_cov_4.666667 gi|410169990|ref|XP_001718975.4| 70.73 41 12 0 238 116 157 197 7e-12 62.8 NODE_5082_length_104_cov_2.009615 gi|488385012|ref|WP_002454397.1| 37.93 29 18 0 128 42 42 70 0.78 31.2 NODE_5082_length_104_cov_2.009615 gi|488365121|ref|WP_002434506.1| 37.93 29 18 0 128 42 42 70 0.78 31.2 NODE_5082_length_104_cov_2.009615 gi|495814946|ref|WP_008539525.1| 36.73 49 31 0 6 152 353 401 0.86 31.6 NODE_5082_length_104_cov_2.009615 gi|496436491|ref|WP_009145338.1| 36.73 49 31 0 6 152 353 401 1.4 30.8 NODE_5082_length_104_cov_2.009615 gi|110642360|ref|YP_670090.1| 40.54 37 22 0 116 6 182 218 4.5 29.3 NODE_5082_length_104_cov_2.009615 gi|209919609|ref|YP_002293693.1| 40.54 37 22 0 116 6 182 218 4.5 29.3 NODE_5082_length_104_cov_2.009615 gi|488380092|ref|WP_002449477.1| 37.93 29 18 0 128 42 42 70 4.9 28.9 NODE_5082_length_104_cov_2.009615 gi|491529818|ref|WP_005387441.1| 35.42 48 31 0 9 152 354 401 5.6 28.9 NODE_5082_length_104_cov_2.009615 gi|490832202|ref|WP_004694287.1| 35.42 48 31 0 9 152 354 401 5.6 28.9 NODE_5082_length_104_cov_2.009615 gi|493745716|ref|WP_006694755.1| 36.73 49 31 0 6 152 353 401 7.7 28.5 NODE_5204_length_218_cov_56.509174 gi|38018023|ref|NP_937947.1| 98.86 88 1 0 266 3 3682 3769 2e-39 146 NODE_5204_length_218_cov_56.509174 gi|26008085|ref|NP_742133.1| 92.05 88 7 0 266 3 133 220 7e-38 134 NODE_5204_length_218_cov_56.509174 gi|85718615|ref|YP_459949.1| 92.05 88 7 0 266 3 3682 3769 2e-36 137 NODE_5204_length_218_cov_56.509174 gi|253756595|ref|YP_003038507.1| 92.05 88 7 0 266 3 3682 3769 2e-36 137 NODE_5204_length_218_cov_56.509174 gi|253756607|ref|YP_003038518.1| 92.05 88 7 0 266 3 3682 3769 2e-36 137 NODE_5204_length_218_cov_56.509174 gi|253756582|ref|YP_003038495.1| 92.05 88 7 0 266 3 3682 3769 2e-36 137 NODE_5204_length_218_cov_56.509174 gi|26008080|ref|NP_150073.2| 92.05 88 7 0 266 3 3682 3769 2e-36 137 NODE_5204_length_218_cov_56.509174 gi|253756594|ref|YP_003038508.1| 92.05 88 7 0 266 3 3682 3769 4e-36 136 NODE_5204_length_218_cov_56.509174 gi|253756606|ref|YP_003038519.1| 92.05 88 7 0 266 3 3682 3769 5e-36 136 NODE_5204_length_218_cov_56.509174 gi|253756581|ref|YP_003038496.1| 92.05 88 7 0 266 3 3682 3769 5e-36 136 NODE_5271_length_115_cov_154.026093 gi|38018025|ref|NP_937949.1| 94.44 36 2 0 165 58 389 424 0.53 32.3 NODE_5271_length_115_cov_154.026093 gi|494932944|ref|WP_007658978.1| 42.86 28 15 1 163 83 265 292 1.3 31.2 NODE_5271_length_115_cov_154.026093 gi|253756584|ref|YP_003038498.1| 80.00 15 3 0 102 58 410 424 5.2 29.3 NODE_5271_length_115_cov_154.026093 gi|15081546|ref|NP_150076.1| 80.00 15 3 0 102 58 410 424 5.5 29.3 NODE_5271_length_115_cov_154.026093 gi|253756609|ref|YP_003038521.1| 80.00 15 3 0 102 58 410 424 5.6 28.9 NODE_5271_length_115_cov_154.026093 gi|394935453|ref|YP_005454244.1| 80.00 15 3 0 102 58 410 424 6.5 28.9 NODE_5279_length_232_cov_2.056035 gi|291575128|ref|NP_001167568.1| 90.57 53 5 0 6 164 282 334 6e-25 100 NODE_5279_length_232_cov_2.056035 gi|4557032|ref|NP_002291.1| 90.57 53 5 0 6 164 282 334 6e-25 100 NODE_5279_length_232_cov_2.056035 gi|6678674|ref|NP_032518.1| 88.68 53 6 0 6 164 282 334 1e-24 100 NODE_5279_length_232_cov_2.056035 gi|207028494|ref|NP_001128711.1| 54.90 51 23 0 6 158 223 273 2e-12 65.5 NODE_5279_length_232_cov_2.056035 gi|6754524|ref|NP_034829.1| 56.86 51 22 0 6 158 281 331 3e-12 65.9 NODE_5279_length_232_cov_2.056035 gi|257743039|ref|NP_001129541.2| 56.86 51 22 0 6 158 310 360 4e-12 65.9 NODE_5279_length_232_cov_2.056035 gi|5031857|ref|NP_005557.1| 54.90 51 23 0 6 158 281 331 4e-12 65.5 NODE_5279_length_232_cov_2.056035 gi|260099723|ref|NP_001158886.1| 54.90 51 23 0 6 158 310 360 5e-12 65.5 NODE_5279_length_232_cov_2.056035 gi|30425048|ref|NP_780558.1| 54.90 51 23 0 6 158 331 381 1e-11 64.3 NODE_5279_length_232_cov_2.056035 gi|15082234|ref|NP_149972.1| 56.86 51 22 0 6 158 330 380 2e-11 64.3 NODE_5284_length_651_cov_60.287251 gi|26008092|ref|NP_742140.1| 98.28 233 4 0 701 3 132 364 6e-168 481 NODE_5284_length_651_cov_60.287251 gi|38018023|ref|NP_937947.1| 99.57 233 1 0 701 3 6032 6264 4e-158 494 NODE_5284_length_651_cov_60.287251 gi|253756582|ref|YP_003038495.1| 98.28 233 4 0 701 3 6032 6264 3e-156 489 NODE_5284_length_651_cov_60.287251 gi|253756595|ref|YP_003038507.1| 98.28 233 4 0 701 3 6032 6264 3e-156 489 NODE_5284_length_651_cov_60.287251 gi|26008080|ref|NP_150073.2| 98.28 233 4 0 701 3 6032 6264 3e-156 489 NODE_5284_length_651_cov_60.287251 gi|253756607|ref|YP_003038518.1| 97.85 233 5 0 701 3 6032 6264 9e-155 484 NODE_5284_length_651_cov_60.287251 gi|85718615|ref|YP_459949.1| 96.57 233 8 0 701 3 6032 6264 5e-154 483 NODE_5284_length_651_cov_60.287251 gi|167600354|ref|YP_001671996.1| 88.41 233 27 0 701 3 6074 6306 8e-145 456 NODE_5284_length_651_cov_60.287251 gi|394935459|ref|YP_005454239.1| 87.98 233 28 0 701 3 6088 6320 1e-144 456 NODE_5284_length_651_cov_60.287251 gi|25121571|ref|NP_740618.1| 80.26 233 46 0 701 3 132 364 3e-141 414 NODE_5444_length_181_cov_43.127071 gi|26008084|ref|NP_742132.1| 96.10 77 3 0 231 1 140 216 6e-49 163 NODE_5444_length_181_cov_43.127071 gi|253756606|ref|YP_003038519.1| 97.40 77 2 0 231 1 3386 3462 3e-46 165 NODE_5444_length_181_cov_43.127071 gi|85718615|ref|YP_459949.1| 97.40 77 2 0 231 1 3386 3462 4e-46 164 NODE_5444_length_181_cov_43.127071 gi|253756607|ref|YP_003038518.1| 97.40 77 2 0 231 1 3386 3462 4e-46 164 NODE_5444_length_181_cov_43.127071 gi|253756594|ref|YP_003038508.1| 96.10 77 3 0 231 1 3386 3462 7e-46 164 NODE_5444_length_181_cov_43.127071 gi|253756581|ref|YP_003038496.1| 96.10 77 3 0 231 1 3386 3462 7e-46 164 NODE_5444_length_181_cov_43.127071 gi|15081555|ref|NP_150074.1| 96.10 77 3 0 231 1 3386 3462 7e-46 164 NODE_5444_length_181_cov_43.127071 gi|167600355|ref|YP_001671997.1| 96.10 77 3 0 231 1 3432 3508 7e-46 164 NODE_5444_length_181_cov_43.127071 gi|253756595|ref|YP_003038507.1| 96.10 77 3 0 231 1 3386 3462 8e-46 164 NODE_5444_length_181_cov_43.127071 gi|26008080|ref|NP_150073.2| 96.10 77 3 0 231 1 3386 3462 8e-46 164 NODE_5512_length_108_cov_3.342592 gi|493916220|ref|WP_006861438.1| 50.00 22 11 0 92 157 31 52 1.3 30.8 NODE_5512_length_108_cov_3.342592 gi|493595757|ref|WP_006548507.1| 39.29 28 17 0 62 145 286 313 1.4 30.8 NODE_5512_length_108_cov_3.342592 gi|494177392|ref|WP_007115263.1| 47.22 36 16 2 14 121 25 57 3.0 30.0 NODE_5512_length_108_cov_3.342592 gi|489075498|ref|WP_002985447.1| 42.42 33 18 1 35 130 349 381 8.6 28.5 NODE_5632_length_736_cov_58.180706 gi|38018023|ref|NP_937947.1| 100.00 261 0 0 784 2 5684 5944 1e-174 543 NODE_5632_length_736_cov_58.180706 gi|253756595|ref|YP_003038507.1| 99.62 261 1 0 784 2 5684 5944 2e-174 542 NODE_5632_length_736_cov_58.180706 gi|26008080|ref|NP_150073.2| 99.62 261 1 0 784 2 5684 5944 2e-174 542 NODE_5632_length_736_cov_58.180706 gi|253756607|ref|YP_003038518.1| 99.62 261 1 0 784 2 5684 5944 3e-174 542 NODE_5632_length_736_cov_58.180706 gi|253756582|ref|YP_003038495.1| 99.62 261 1 0 784 2 5684 5944 3e-174 542 NODE_5632_length_736_cov_58.180706 gi|85718615|ref|YP_459949.1| 99.23 260 2 0 784 5 5684 5943 2e-172 537 NODE_5632_length_736_cov_58.180706 gi|394935459|ref|YP_005454239.1| 92.34 261 16 1 784 2 5744 6000 3e-161 504 NODE_5632_length_736_cov_58.180706 gi|167600354|ref|YP_001671996.1| 91.95 261 17 1 784 2 5730 5986 8e-161 503 NODE_5632_length_736_cov_58.180706 gi|26008091|ref|NP_742139.1| 99.54 217 1 0 784 134 387 603 2e-153 449 NODE_5632_length_736_cov_58.180706 gi|253750532|ref|YP_003029844.1| 85.82 261 34 1 784 2 5765 6022 3e-150 473 NODE_5653_length_165_cov_60.066666 gi|26008091|ref|NP_742139.1| 97.18 71 2 0 213 1 283 353 2e-41 147 NODE_5653_length_165_cov_60.066666 gi|38018023|ref|NP_937947.1| 98.59 71 1 0 213 1 5580 5650 5e-41 149 NODE_5653_length_165_cov_60.066666 gi|253756595|ref|YP_003038507.1| 97.18 71 2 0 213 1 5580 5650 1e-40 148 NODE_5653_length_165_cov_60.066666 gi|253756582|ref|YP_003038495.1| 97.18 71 2 0 213 1 5580 5650 1e-40 148 NODE_5653_length_165_cov_60.066666 gi|26008080|ref|NP_150073.2| 97.18 71 2 0 213 1 5580 5650 1e-40 148 NODE_5653_length_165_cov_60.066666 gi|253756607|ref|YP_003038518.1| 97.18 71 2 0 213 1 5580 5650 1e-40 148 NODE_5653_length_165_cov_60.066666 gi|85718615|ref|YP_459949.1| 97.18 71 2 0 213 1 5580 5650 2e-40 148 NODE_5653_length_165_cov_60.066666 gi|167600354|ref|YP_001671996.1| 95.77 71 3 0 213 1 5626 5696 5e-40 147 NODE_5653_length_165_cov_60.066666 gi|25121570|ref|NP_740617.1| 92.96 71 5 0 213 1 283 353 5e-40 143 NODE_5653_length_165_cov_60.066666 gi|394935459|ref|YP_005454239.1| 94.37 71 4 0 213 1 5640 5710 1e-39 145 NODE_5774_length_149_cov_3.919463 gi|489885282|ref|WP_003788732.1| 38.30 47 26 1 27 167 845 888 2.0 30.8 NODE_5774_length_149_cov_3.919463 gi|489880355|ref|WP_003783821.1| 30.77 52 36 0 172 17 97 148 2.9 30.0 NODE_5774_length_149_cov_3.919463 gi|491565168|ref|WP_005422754.1| 46.43 28 15 0 54 137 304 331 5.4 29.3 NODE_5858_length_103_cov_1.650485 gi|493930415|ref|WP_006875012.1| 34.15 41 17 2 11 115 403 439 2.7 30.0 NODE_5858_length_103_cov_1.650485 gi|27370244|ref|NP_766418.1| 40.00 35 15 1 141 37 570 598 8.7 28.5 NODE_5932_length_129_cov_51.511627 gi|38018023|ref|NP_937947.1| 100.00 59 0 0 3 179 5537 5595 9e-34 128 NODE_5932_length_129_cov_51.511627 gi|26008091|ref|NP_742139.1| 98.31 59 1 0 3 179 240 298 1e-33 125 NODE_5932_length_129_cov_51.511627 gi|253756607|ref|YP_003038518.1| 98.31 59 1 0 3 179 5537 5595 2e-33 127 NODE_5932_length_129_cov_51.511627 gi|253756595|ref|YP_003038507.1| 98.31 59 1 0 3 179 5537 5595 2e-33 127 NODE_5932_length_129_cov_51.511627 gi|253756582|ref|YP_003038495.1| 98.31 59 1 0 3 179 5537 5595 2e-33 127 NODE_5932_length_129_cov_51.511627 gi|26008080|ref|NP_150073.2| 98.31 59 1 0 3 179 5537 5595 2e-33 127 NODE_5932_length_129_cov_51.511627 gi|85718615|ref|YP_459949.1| 98.31 59 1 0 3 179 5537 5595 3e-33 127 NODE_5932_length_129_cov_51.511627 gi|394935459|ref|YP_005454239.1| 96.61 59 2 0 3 179 5597 5655 2e-32 124 NODE_5932_length_129_cov_51.511627 gi|167600354|ref|YP_001671996.1| 94.92 59 3 0 3 179 5583 5641 1e-31 122 NODE_5932_length_129_cov_51.511627 gi|253750532|ref|YP_003029844.1| 93.22 59 4 0 3 179 5618 5676 2e-31 121 NODE_6058_length_104_cov_1.442308 gi|488501801|ref|WP_002545240.1| 31.58 38 26 0 152 39 3 40 2.5 27.7 NODE_6058_length_104_cov_1.442308 gi|295131614|ref|YP_003582277.1| 31.58 38 26 0 152 39 6 43 2.8 27.7 NODE_6058_length_104_cov_1.442308 gi|488506867|ref|WP_002550306.1| 31.58 38 26 0 152 39 6 43 3.0 27.7 NODE_6058_length_104_cov_1.442308 gi|491671053|ref|WP_005527195.1| 34.15 41 27 0 2 124 735 775 3.3 30.0 NODE_6058_length_104_cov_1.442308 gi|490982950|ref|WP_004844702.1| 45.45 22 12 0 12 77 105 126 3.6 29.3 NODE_6058_length_104_cov_1.442308 gi|448244957|ref|YP_007392677.1| 51.43 35 15 1 29 127 789 823 4.5 29.3 NODE_6058_length_104_cov_1.442308 gi|496138189|ref|WP_008862696.1| 41.67 36 15 2 32 124 72 106 6.2 28.9 NODE_6058_length_104_cov_1.442308 gi|491791853|ref|WP_005602013.1| 36.96 46 25 2 5 142 31 72 7.9 28.5 NODE_6157_length_218_cov_7.431193 gi|34538609|ref|NP_904339.1| 50.00 72 36 0 266 51 12 83 2e-16 75.5 NODE_6157_length_218_cov_7.431193 gi|251831118|ref|YP_003024037.1| 45.07 71 39 0 260 48 14 84 6e-14 68.6 NODE_6157_length_218_cov_7.431193 gi|489073598|ref|WP_002983555.1| 29.69 64 39 1 266 93 7 70 5.3 29.6 NODE_6273_length_225_cov_71.737778 gi|26008095|ref|NP_742170.1| 97.80 91 2 0 275 3 141 231 3e-57 189 NODE_6273_length_225_cov_71.737778 gi|38018023|ref|NP_937947.1| 98.90 91 1 0 275 3 2891 2981 1e-56 196 NODE_6273_length_225_cov_71.737778 gi|253756606|ref|YP_003038519.1| 97.80 91 2 0 275 3 2891 2981 3e-56 194 NODE_6273_length_225_cov_71.737778 gi|253756594|ref|YP_003038508.1| 97.80 91 2 0 275 3 2891 2981 3e-56 194 NODE_6273_length_225_cov_71.737778 gi|253756581|ref|YP_003038496.1| 97.80 91 2 0 275 3 2891 2981 3e-56 194 NODE_6273_length_225_cov_71.737778 gi|15081555|ref|NP_150074.1| 97.80 91 2 0 275 3 2891 2981 3e-56 194 NODE_6273_length_225_cov_71.737778 gi|167600355|ref|YP_001671997.1| 97.80 91 2 0 275 3 2937 3027 3e-56 194 NODE_6273_length_225_cov_71.737778 gi|253756582|ref|YP_003038495.1| 97.80 91 2 0 275 3 2891 2981 6e-56 194 NODE_6273_length_225_cov_71.737778 gi|26008080|ref|NP_150073.2| 97.80 91 2 0 275 3 2891 2981 6e-56 194 NODE_6273_length_225_cov_71.737778 gi|253756595|ref|YP_003038507.1| 97.80 91 2 0 275 3 2891 2981 6e-56 194 NODE_6358_length_763_cov_14.992136 gi|34538603|ref|NP_904333.1| 56.15 187 82 0 253 813 35 221 3e-25 105 NODE_6358_length_763_cov_14.992136 gi|251831112|ref|YP_003024031.1| 57.84 185 76 2 262 813 38 221 5e-24 102 NODE_6358_length_763_cov_14.992136 gi|494061063|ref|WP_007003145.1| 37.50 136 82 2 415 813 108 243 1e-07 56.6 NODE_6358_length_763_cov_14.992136 gi|490317897|ref|WP_004207393.1| 38.46 78 44 1 592 813 176 253 1e-04 47.0 NODE_6358_length_763_cov_14.992136 gi|298346222|ref|YP_003718909.1| 41.03 78 42 1 592 813 189 266 0.003 43.5 NODE_6358_length_763_cov_14.992136 gi|490108282|ref|WP_004009035.1| 41.03 78 42 1 592 813 189 266 0.003 43.1 NODE_6358_length_763_cov_14.992136 gi|488757798|ref|WP_002681038.1| 38.16 76 41 2 592 813 275 346 0.003 43.5 NODE_6358_length_763_cov_14.992136 gi|492833537|ref|WP_005987491.1| 34.62 78 47 1 592 813 188 265 0.008 42.0 NODE_6358_length_763_cov_14.992136 gi|493338836|ref|WP_006295782.1| 35.06 77 46 1 595 813 184 260 0.009 41.6 NODE_6358_length_763_cov_14.992136 gi|490738495|ref|WP_004600803.1| 36.36 77 46 1 592 813 179 255 0.009 41.6 NODE_6404_length_262_cov_12.572519 gi|34538601|ref|NP_904331.1| 60.00 100 39 1 302 6 6 105 3e-16 76.3 NODE_6404_length_262_cov_12.572519 gi|251831110|ref|YP_003024029.1| 61.39 101 38 1 305 6 5 105 8e-14 69.3 NODE_6528_length_178_cov_46.578651 gi|26008090|ref|NP_742138.1| 98.67 75 1 0 226 2 374 448 2e-43 155 NODE_6528_length_178_cov_46.578651 gi|38018023|ref|NP_937947.1| 100.00 75 0 0 226 2 4743 4817 4e-43 155 NODE_6528_length_178_cov_46.578651 gi|167600354|ref|YP_001671996.1| 98.67 75 1 0 226 2 4789 4863 6e-43 155 NODE_6528_length_178_cov_46.578651 gi|253756607|ref|YP_003038518.1| 98.67 75 1 0 226 2 4743 4817 6e-43 155 NODE_6528_length_178_cov_46.578651 gi|253756595|ref|YP_003038507.1| 98.67 75 1 0 226 2 4743 4817 6e-43 155 NODE_6528_length_178_cov_46.578651 gi|253756582|ref|YP_003038495.1| 98.67 75 1 0 226 2 4743 4817 6e-43 155 NODE_6528_length_178_cov_46.578651 gi|26008080|ref|NP_150073.2| 98.67 75 1 0 226 2 4743 4817 6e-43 155 NODE_6528_length_178_cov_46.578651 gi|85718615|ref|YP_459949.1| 97.33 75 2 0 226 2 4743 4817 1e-42 155 NODE_6528_length_178_cov_46.578651 gi|394935459|ref|YP_005454239.1| 96.00 75 3 0 226 2 4803 4877 6e-42 152 NODE_6528_length_178_cov_46.578651 gi|25121569|ref|NP_740616.1| 96.00 75 3 0 226 2 374 448 9e-42 150 NODE_6553_length_103_cov_3.165049 gi|407262653|ref|XP_003946441.1| 100.00 21 0 0 64 2 29 49 3e-07 48.1 NODE_6553_length_103_cov_3.165049 gi|7305443|ref|NP_038749.1| 100.00 21 0 0 64 2 29 49 1e-06 47.8 NODE_6553_length_103_cov_3.165049 gi|4506661|ref|NP_000963.1| 100.00 21 0 0 64 2 29 49 1e-06 47.8 NODE_6553_length_103_cov_3.165049 gi|407262811|ref|XP_003945666.1| 100.00 21 0 0 64 2 24 44 1e-06 47.8 NODE_6553_length_103_cov_3.165049 gi|407260908|ref|XP_003946090.1| 100.00 21 0 0 64 2 24 44 1e-06 47.8 NODE_6553_length_103_cov_3.165049 gi|407263827|ref|XP_003945548.1| 100.00 21 0 0 64 2 29 49 7e-06 45.8 NODE_6553_length_103_cov_3.165049 gi|407264240|ref|XP_003945689.1| 100.00 21 0 0 64 2 266 286 2e-05 45.4 NODE_6553_length_103_cov_3.165049 gi|493930055|ref|WP_006874666.1| 53.85 26 12 0 54 131 2 27 4.1 29.3 NODE_6553_length_103_cov_3.165049 gi|489908574|ref|WP_003811993.1| 46.15 39 18 1 27 134 1 39 4.9 29.3 NODE_6553_length_103_cov_3.165049 gi|492496619|ref|WP_005864999.1| 38.71 31 19 0 33 125 166 196 6.2 28.9 NODE_6746_length_271_cov_5.416974 gi|251831108|ref|YP_003024027.1| 45.57 79 43 0 321 85 43 121 2e-15 75.1 NODE_6746_length_271_cov_5.416974 gi|34538599|ref|NP_904329.1| 45.12 82 38 3 321 85 44 121 3e-10 60.8 NODE_6746_length_271_cov_5.416974 gi|489079060|ref|WP_002988999.1| 30.68 88 50 1 315 85 134 221 0.001 41.6 NODE_6746_length_271_cov_5.416974 gi|493308629|ref|WP_006266141.1| 31.65 79 43 1 288 85 143 221 0.002 40.8 NODE_6746_length_271_cov_5.416974 gi|493300089|ref|WP_006257704.1| 31.65 79 43 1 288 85 143 221 0.002 40.8 NODE_6746_length_271_cov_5.416974 gi|491911394|ref|WP_005666451.1| 31.82 88 48 2 312 85 162 249 0.003 40.4 NODE_6746_length_271_cov_5.416974 gi|489895417|ref|WP_003798866.1| 30.12 83 46 1 297 85 154 236 0.005 39.7 NODE_6746_length_271_cov_5.416974 gi|493250100|ref|WP_006217972.1| 31.71 82 44 1 294 85 157 238 0.007 39.3 NODE_6746_length_271_cov_5.416974 gi|492507717|ref|WP_005869747.1| 30.43 92 51 2 321 85 143 234 0.012 38.5 NODE_6746_length_271_cov_5.416974 gi|493897383|ref|WP_006843252.1| 28.89 90 51 1 315 85 138 227 0.016 38.1 NODE_6778_length_138_cov_2.217391 gi|489749629|ref|WP_003653638.1| 35.42 48 22 2 44 175 450 492 5.3 29.3 NODE_6853_length_169_cov_1.946746 gi|489017254|ref|WP_002927770.1| 53.12 32 12 1 74 169 252 280 0.44 33.1 NODE_6853_length_169_cov_1.946746 gi|489083933|ref|WP_002993846.1| 55.17 29 13 0 108 22 39 67 1.1 31.6 NODE_6853_length_169_cov_1.946746 gi|489100940|ref|WP_003010804.1| 55.17 29 13 0 108 22 39 67 1.2 31.6 NODE_6853_length_169_cov_1.946746 gi|94536848|ref|NP_060888.2| 40.00 40 19 1 179 60 335 369 1.7 31.2 NODE_6853_length_169_cov_1.946746 gi|94536850|ref|NP_001035518.1| 40.00 40 19 1 179 60 303 337 1.8 31.2 NODE_6853_length_169_cov_1.946746 gi|490462342|ref|WP_004332902.1| 38.10 42 26 0 48 173 25 66 5.3 29.3 NODE_6853_length_169_cov_1.946746 gi|146231944|ref|NP_780447.4| 38.64 44 23 1 171 52 357 400 5.8 29.6 NODE_6891_length_386_cov_3.411917 gi|493572455|ref|WP_006525678.1| 29.63 54 37 1 267 109 426 479 3.2 32.3 NODE_6891_length_386_cov_3.411917 gi|490463747|ref|WP_004334301.1| 35.85 53 31 2 276 118 137 186 8.4 31.2 NODE_6992_length_686_cov_12.574344 gi|251831113|ref|YP_003024032.1| 71.02 245 71 0 1 735 4 248 4e-103 307 NODE_6992_length_686_cov_12.574344 gi|34538604|ref|NP_904334.1| 70.61 245 72 0 1 735 4 248 1e-101 304 NODE_6992_length_686_cov_12.574344 gi|488804979|ref|WP_002717385.1| 48.43 254 120 2 7 735 9 262 2e-55 186 NODE_6992_length_686_cov_12.574344 gi|488801873|ref|WP_002714279.1| 44.94 267 123 2 7 735 9 275 6e-53 180 NODE_6992_length_686_cov_12.574344 gi|492887313|ref|WP_006022894.1| 45.32 267 122 2 7 735 9 275 6e-53 180 NODE_6992_length_686_cov_12.574344 gi|494060885|ref|WP_007002968.1| 50.20 249 120 2 1 735 16 264 8e-48 166 NODE_6992_length_686_cov_12.574344 gi|490319112|ref|WP_004208605.1| 46.43 252 127 3 1 735 5 255 7e-44 155 NODE_6992_length_686_cov_12.574344 gi|493432517|ref|WP_006388095.1| 41.78 213 99 5 169 735 69 280 2e-39 145 NODE_6992_length_686_cov_12.574344 gi|493248475|ref|WP_006216870.1| 41.78 213 99 5 169 735 69 280 3e-39 144 NODE_6992_length_686_cov_12.574344 gi|491913845|ref|WP_005668122.1| 39.62 212 104 4 169 735 69 279 7e-33 127 NODE_7001_length_124_cov_1.500000 gi|495429486|ref|WP_008154182.1| 45.45 33 17 1 2 100 87 118 1.7 30.8 NODE_7001_length_124_cov_1.500000 gi|495428155|ref|WP_008152852.1| 45.45 33 17 1 2 100 87 118 1.7 30.8 NODE_7001_length_124_cov_1.500000 gi|495298804|ref|WP_008023556.1| 42.00 50 28 1 24 173 257 305 2.0 30.4 NODE_7001_length_124_cov_1.500000 gi|495036988|ref|WP_007762511.1| 40.00 50 29 1 24 173 257 305 2.5 30.0 NODE_7001_length_124_cov_1.500000 gi|489813103|ref|WP_003716948.1| 52.00 25 12 0 24 98 10 34 3.4 29.6 NODE_7001_length_124_cov_1.500000 gi|490043695|ref|WP_003946057.1| 48.15 27 14 0 30 110 386 412 6.7 28.9 NODE_7001_length_124_cov_1.500000 gi|492341897|ref|WP_005815874.1| 34.21 38 23 1 51 158 30 67 8.5 28.1 NODE_7022_length_111_cov_1.495495 gi|489884805|ref|WP_003788255.1| 30.77 39 27 0 160 44 112 150 1.2 30.8 NODE_7036_length_103_cov_1.446602 gi|491433351|ref|WP_005291144.1| 45.83 24 13 0 35 106 347 370 5.7 28.9 NODE_7036_length_103_cov_1.446602 gi|496424684|ref|WP_009133531.1| 44.00 25 14 0 75 149 53 77 6.9 28.1 NODE_7046_length_139_cov_37.697842 gi|55956788|ref|NP_005372.2| 100.00 21 0 0 126 188 272 292 3e-04 42.4 NODE_7046_length_139_cov_37.697842 gi|84875537|ref|NP_035010.3| 85.71 21 3 0 126 188 274 294 0.031 36.2 NODE_7050_length_193_cov_1.590674 gi|304434531|ref|NP_001182122.1| 84.62 26 4 0 237 160 71 96 1e-05 47.0 NODE_7050_length_193_cov_1.590674 gi|27262628|ref|NP_002473.2| 84.62 26 4 0 237 160 135 160 1e-05 47.0 NODE_7050_length_193_cov_1.590674 gi|125490378|ref|NP_058057.3| 95.24 21 1 0 237 175 135 155 4e-04 42.7 NODE_7166_length_197_cov_5.685279 gi|34538608|ref|NP_904338.1| 68.29 82 25 1 5 247 197 278 3e-28 111 NODE_7166_length_197_cov_5.685279 gi|251831117|ref|YP_003024036.1| 68.67 83 21 3 11 247 199 280 4e-17 80.5 NODE_7166_length_197_cov_5.685279 gi|490322262|ref|WP_004211747.1| 49.37 79 40 0 8 244 210 288 2e-14 72.8 NODE_7166_length_197_cov_5.685279 gi|490654142|ref|WP_004519133.1| 47.83 69 36 0 41 247 99 167 5e-12 65.9 NODE_7166_length_197_cov_5.685279 gi|489872613|ref|WP_003776145.1| 49.21 63 32 0 59 247 235 297 5e-12 65.9 NODE_7166_length_197_cov_5.685279 gi|489846871|ref|WP_003750561.1| 49.21 63 32 0 59 247 235 297 5e-12 65.9 NODE_7166_length_197_cov_5.685279 gi|489773082|ref|WP_003676983.1| 49.21 63 32 0 59 247 235 297 5e-12 65.9 NODE_7166_length_197_cov_5.685279 gi|489804261|ref|WP_003708139.1| 49.21 63 32 0 59 247 235 297 5e-12 65.9 NODE_7166_length_197_cov_5.685279 gi|489782824|ref|WP_003686715.1| 49.21 63 32 0 59 247 235 297 5e-12 65.9 NODE_7166_length_197_cov_5.685279 gi|488144427|ref|WP_002215635.1| 49.21 63 32 0 59 247 235 297 6e-12 65.9 NODE_7371_length_145_cov_1.724138 gi|34538605|ref|NP_904335.1| 70.37 27 8 0 1 81 33 59 3e-06 45.8 NODE_7371_length_145_cov_1.724138 gi|251831114|ref|YP_003024033.1| 68.00 25 8 0 7 81 35 59 1e-05 43.9 NODE_7371_length_145_cov_1.724138 gi|491911423|ref|WP_005666469.1| 51.85 27 13 0 1 81 39 65 1e-04 40.8 NODE_7371_length_145_cov_1.724138 gi|492536241|ref|WP_005877727.1| 55.56 27 12 0 1 81 39 65 8e-04 38.9 NODE_7371_length_145_cov_1.724138 gi|493250087|ref|WP_006217959.1| 30.00 50 35 0 1 150 39 88 0.002 37.7 NODE_7371_length_145_cov_1.724138 gi|493300075|ref|WP_006257690.1| 48.00 25 13 0 7 81 43 67 0.002 37.7 NODE_7371_length_145_cov_1.724138 gi|488803215|ref|WP_002715621.1| 48.15 27 14 0 1 81 41 67 0.004 37.0 NODE_7371_length_145_cov_1.724138 gi|492880225|ref|WP_006020769.1| 48.15 27 14 0 1 81 41 67 0.004 37.0 NODE_7371_length_145_cov_1.724138 gi|488799174|ref|WP_002711580.1| 48.15 27 14 0 1 81 41 67 0.005 37.0 NODE_7371_length_145_cov_1.724138 gi|491911353|ref|WP_005666426.1| 48.15 27 14 0 1 81 39 65 0.005 37.0 NODE_7482_length_126_cov_2.198413 gi|494138448|ref|WP_007078200.1| 34.00 50 30 1 165 25 20 69 4.0 29.6 NODE_7482_length_126_cov_2.198413 gi|47716521|ref|NP_848755.1| 32.08 53 32 2 162 10 40 90 7.1 28.9 NODE_7482_length_126_cov_2.198413 gi|489627568|ref|WP_003532008.1| 39.47 38 21 1 114 1 38 73 7.9 28.1 NODE_7482_length_126_cov_2.198413 gi|491906380|ref|WP_005663965.1| 59.09 22 9 0 84 19 287 308 8.2 28.5 NODE_7495_length_113_cov_1.407080 gi|493486652|ref|WP_006441429.1| 42.86 28 13 1 84 10 172 199 3.8 29.3 NODE_7519_length_130_cov_1.538462 gi|388684894|ref|YP_006382774.1| 33.93 56 31 3 160 5 731 784 6.8 28.9 NODE_7519_length_130_cov_1.538462 gi|40796179|ref|NP_955624.1| 35.48 31 16 1 20 112 21 47 7.9 28.5 NODE_7519_length_130_cov_1.538462 gi|493397567|ref|WP_006353681.1| 46.67 30 14 1 178 89 468 495 9.2 28.5 NODE_7591_length_136_cov_1.654412 gi|490429089|ref|WP_004301231.1| 48.72 39 19 1 65 181 95 132 0.19 33.5 NODE_7591_length_136_cov_1.654412 gi|490449690|ref|WP_004320581.1| 48.72 39 19 1 65 181 93 130 0.19 33.5 NODE_7591_length_136_cov_1.654412 gi|490980850|ref|WP_004842613.1| 38.64 44 22 1 182 66 230 273 0.37 32.7 NODE_7591_length_136_cov_1.654412 gi|490040882|ref|WP_003943281.1| 34.62 52 33 1 8 160 1 52 0.85 31.6 NODE_7591_length_136_cov_1.654412 gi|489089507|ref|WP_002999406.1| 40.48 42 24 1 170 48 455 496 0.96 31.6 NODE_7591_length_136_cov_1.654412 gi|120407054|ref|NP_766309.2| 42.86 35 19 1 46 150 62 95 2.3 30.4 NODE_7591_length_136_cov_1.654412 gi|490974918|ref|WP_004836706.1| 28.00 50 36 0 17 166 777 826 6.0 29.3 NODE_7591_length_136_cov_1.654412 gi|187829745|ref|NP_001120714.1| 30.00 60 33 2 173 3 47 100 6.8 28.1 NODE_7591_length_136_cov_1.654412 gi|492512723|ref|WP_005871524.1| 44.44 36 15 1 149 57 574 609 7.9 28.9 NODE_7758_length_125_cov_2.624000 gi|45496816|ref|NP_031691.1| 62.07 58 22 0 174 1 353 410 3e-17 80.1 NODE_7758_length_125_cov_2.624000 gi|83715978|ref|NP_001032898.1| 62.07 58 22 0 174 1 354 411 3e-17 80.1 NODE_7758_length_125_cov_2.624000 gi|14589891|ref|NP_001784.2| 60.34 58 23 0 174 1 362 419 1e-16 78.2 NODE_7758_length_125_cov_2.624000 gi|4757960|ref|NP_004351.1| 56.14 57 24 1 174 4 409 464 3e-16 77.4 NODE_7758_length_125_cov_2.624000 gi|7305007|ref|NP_038533.1| 56.36 55 24 0 174 10 389 443 3e-15 74.3 NODE_7758_length_125_cov_2.624000 gi|13435364|ref|NP_077740.1| 57.14 56 24 0 174 7 389 444 4e-15 73.9 NODE_7758_length_125_cov_2.624000 gi|13435366|ref|NP_004940.1| 57.14 56 24 0 174 7 389 444 4e-15 73.9 NODE_7758_length_125_cov_2.624000 gi|133778947|ref|NP_031908.3| 58.18 55 23 0 174 10 389 443 6e-15 73.6 NODE_7758_length_125_cov_2.624000 gi|6753374|ref|NP_033994.1| 54.55 55 24 1 174 10 411 464 2e-14 72.4 NODE_7758_length_125_cov_2.624000 gi|4826702|ref|NP_004939.1| 56.36 55 24 0 171 7 389 443 9e-14 70.1 NODE_7842_length_107_cov_1.401869 gi|493962491|ref|WP_006905959.1| 44.44 27 15 0 63 143 90 116 5.2 29.3 NODE_7864_length_229_cov_2.410480 gi|490333245|ref|WP_004222667.1| 41.86 43 25 0 242 114 58 100 0.018 37.0 NODE_7864_length_229_cov_2.410480 gi|493615916|ref|WP_006568160.1| 32.73 55 35 1 278 114 48 100 0.29 33.5 NODE_7864_length_229_cov_2.410480 gi|479158967|ref|YP_007788236.1| 32.73 55 35 1 278 114 48 100 0.49 32.7 NODE_7896_length_117_cov_1.709402 gi|255918141|ref|NP_001157617.1| 50.00 54 22 1 164 18 513 566 2e-05 45.4 NODE_7896_length_117_cov_1.709402 gi|255918141|ref|NP_001157617.1| 43.10 58 27 2 167 9 446 502 0.003 39.3 NODE_7896_length_117_cov_1.709402 gi|255918139|ref|NP_001157616.1| 50.00 54 22 1 164 18 513 566 2e-05 45.4 NODE_7896_length_117_cov_1.709402 gi|255918139|ref|NP_001157616.1| 43.10 58 27 2 167 9 446 502 0.003 39.3 NODE_7896_length_117_cov_1.709402 gi|41281612|ref|NP_115812.1| 50.00 54 22 1 164 18 513 566 2e-05 45.4 NODE_7896_length_117_cov_1.709402 gi|41281612|ref|NP_115812.1| 43.10 58 27 2 167 9 446 502 0.003 39.3 NODE_7896_length_117_cov_1.709402 gi|32469497|ref|NP_862902.1| 44.44 54 25 1 164 18 503 556 0.028 36.2 NODE_7896_length_117_cov_1.709402 gi|32469497|ref|NP_862902.1| 41.94 62 24 2 167 18 466 527 0.30 33.1 NODE_7896_length_117_cov_1.709402 gi|493486496|ref|WP_006441275.1| 44.00 25 14 0 164 90 96 120 3.0 29.6 NODE_7896_length_117_cov_1.709402 gi|386316836|ref|YP_006013000.1| 27.59 58 38 1 3 164 230 287 6.3 28.9 NODE_7896_length_117_cov_1.709402 gi|491906894|ref|WP_005664284.1| 55.00 20 9 0 73 14 236 255 8.7 28.5 NODE_7896_length_117_cov_1.709402 gi|489185142|ref|WP_003094567.1| 27.59 58 38 1 3 164 230 287 9.5 28.5 NODE_7912_length_187_cov_2.770053 gi|55956788|ref|NP_005372.2| 83.33 18 3 0 183 236 272 289 1.2 31.6 NODE_7913_length_149_cov_2.288591 gi|55956788|ref|NP_005372.2| 56.92 65 28 0 198 4 318 382 2e-15 75.1 NODE_7913_length_149_cov_2.288591 gi|55956788|ref|NP_005372.2| 53.85 26 12 0 138 61 601 626 3.8 30.0 NODE_7913_length_149_cov_2.288591 gi|84875537|ref|NP_035010.3| 56.92 65 28 0 198 4 320 384 3e-15 74.7 NODE_7913_length_149_cov_2.288591 gi|84875537|ref|NP_035010.3| 53.85 26 12 0 138 61 598 623 3.4 30.0 NODE_7913_length_149_cov_2.288591 gi|23346437|ref|NP_694693.1| 41.46 41 23 1 120 1 51 91 0.15 34.3 NODE_7913_length_149_cov_2.288591 gi|5032069|ref|NP_005841.1| 41.46 41 23 1 120 1 51 91 0.15 34.3 NODE_7913_length_149_cov_2.288591 gi|25121978|ref|NP_001342.2| 32.73 55 29 2 177 37 54 108 1.3 31.2 NODE_7913_length_149_cov_2.288591 gi|299829262|ref|NP_001177740.1| 32.73 55 29 2 177 37 74 128 1.4 31.2 NODE_7913_length_149_cov_2.288591 gi|489935237|ref|WP_003838546.1| 45.16 31 16 1 157 68 459 489 1.9 30.8 NODE_7913_length_149_cov_2.288591 gi|489939962|ref|WP_003843269.1| 45.16 31 16 1 157 68 459 489 2.0 30.8 NODE_7913_length_149_cov_2.288591 gi|25470890|ref|NP_733829.1| 22.22 63 44 1 177 4 127 189 2.1 30.4 NODE_7913_length_149_cov_2.288591 gi|169790818|ref|NP_573451.2| 22.22 63 44 1 177 4 126 188 2.1 30.4 NODE_7936_length_112_cov_1.339286 gi|5031749|ref|NP_005508.1| 96.55 29 1 0 109 23 1 29 1e-10 57.4 NODE_7936_length_112_cov_1.339286 gi|10835240|ref|NP_006344.1| 93.10 29 2 0 109 23 1 29 7e-10 55.1 NODE_7936_length_112_cov_1.339286 gi|407261273|ref|XP_003946212.1| 93.55 31 2 0 109 17 1 31 8e-10 55.1 NODE_7936_length_112_cov_1.339286 gi|149263574|ref|XP_001478610.1| 93.55 31 2 0 109 17 1 31 8e-10 55.1 NODE_7936_length_112_cov_1.339286 gi|8393534|ref|NP_058653.1| 93.55 31 2 0 109 17 1 31 8e-10 55.1 NODE_7936_length_112_cov_1.339286 gi|309268322|ref|XP_003084667.1| 93.55 31 2 0 109 17 1 31 1e-09 54.3 NODE_7936_length_112_cov_1.339286 gi|149267823|ref|XP_001478444.1| 82.76 29 5 0 109 23 1 29 5e-08 50.1 NODE_7936_length_112_cov_1.339286 gi|149267483|ref|XP_001480899.1| 82.76 29 5 0 109 23 1 29 5e-08 50.1 NODE_7936_length_112_cov_1.339286 gi|407262951|ref|XP_003945399.1| 90.00 30 2 1 106 17 240 268 8e-07 48.9 NODE_7936_length_112_cov_1.339286 gi|407261051|ref|XP_003946144.1| 90.00 30 2 1 106 17 240 268 8e-07 48.9 NODE_7948_length_125_cov_2.304000 gi|481019623|ref|YP_007877974.1| 44.83 29 15 1 149 63 59 86 5.7 28.9 NODE_7948_length_125_cov_2.304000 gi|491094259|ref|WP_004955865.1| 34.29 35 23 0 137 33 661 695 7.2 28.9 NODE_7956_length_500_cov_4.390000 gi|55956788|ref|NP_005372.2| 66.84 187 52 3 2 550 429 609 7e-64 215 NODE_7956_length_500_cov_4.390000 gi|55956788|ref|NP_005372.2| 37.21 129 74 3 149 523 389 514 3e-16 82.0 NODE_7956_length_500_cov_4.390000 gi|55956788|ref|NP_005372.2| 33.33 129 81 2 2 385 523 647 4e-08 57.0 NODE_7956_length_500_cov_4.390000 gi|55956788|ref|NP_005372.2| 26.40 125 78 4 167 529 309 423 0.22 37.0 NODE_7956_length_500_cov_4.390000 gi|84875537|ref|NP_035010.3| 63.98 186 54 3 2 550 431 606 1e-59 204 NODE_7956_length_500_cov_4.390000 gi|84875537|ref|NP_035010.3| 33.59 128 77 3 152 523 392 515 3e-12 69.7 NODE_7956_length_500_cov_4.390000 gi|84875537|ref|NP_035010.3| 33.33 129 77 2 2 385 524 644 1e-07 55.5 NODE_7956_length_500_cov_4.390000 gi|84875537|ref|NP_035010.3| 29.41 119 69 5 173 529 322 425 0.029 39.3 NODE_7956_length_500_cov_4.390000 gi|9994185|ref|NP_057174.1| 37.66 77 45 1 161 382 10 86 2e-09 59.7 NODE_7956_length_500_cov_4.390000 gi|493898426|ref|WP_006844263.1| 30.77 91 57 2 167 421 3 93 1e-08 55.1 NODE_7956_length_500_cov_4.390000 gi|4504715|ref|NP_003810.1| 27.69 195 122 5 2 538 138 329 7e-08 56.2 NODE_7956_length_500_cov_4.390000 gi|23346437|ref|NP_694693.1| 32.14 140 78 6 155 550 11 141 8e-08 55.8 NODE_7956_length_500_cov_4.390000 gi|5032069|ref|NP_005841.1| 32.14 140 78 6 155 550 11 141 8e-08 55.8 NODE_7956_length_500_cov_4.390000 gi|208431836|ref|NP_001129126.1| 27.69 195 122 5 2 538 138 329 8e-08 55.8 NODE_7956_length_500_cov_4.390000 gi|496427194|ref|WP_009136041.1| 29.59 98 63 3 164 439 2 99 1e-07 52.4 NODE_7956_length_500_cov_4.390000 gi|208431833|ref|NP_001129125.1| 27.69 195 122 5 2 538 138 329 1e-07 55.5 NODE_8086_length_177_cov_1.694915 gi|493172907|ref|WP_006174984.1| 37.50 56 27 2 1 168 407 454 0.30 33.5 NODE_8086_length_177_cov_1.694915 gi|489954241|ref|WP_003857548.1| 35.71 56 28 2 1 168 407 454 0.54 32.7 NODE_8086_length_177_cov_1.694915 gi|493873627|ref|WP_006820074.1| 33.93 56 29 2 1 168 407 454 2.4 30.8 NODE_8086_length_177_cov_1.694915 gi|491361664|ref|WP_005219582.1| 34.15 41 24 1 31 153 24 61 7.2 29.3 NODE_8086_length_177_cov_1.694915 gi|497217900|ref|WP_009532162.1| 28.89 45 27 1 106 225 292 336 8.3 29.3 NODE_8086_length_177_cov_1.694915 gi|493735427|ref|WP_006684642.1| 30.36 56 31 2 1 168 407 454 9.3 28.9 NODE_8166_length_106_cov_3.820755 gi|494750693|ref|WP_007486101.1| 63.64 22 7 1 80 15 58 78 8.9 28.1 NODE_8166_length_106_cov_3.820755 gi|493930786|ref|WP_006875378.1| 40.00 30 18 0 51 140 35 64 9.1 26.6 NODE_8170_length_107_cov_1.467290 gi|491917641|ref|WP_005670950.1| 38.00 50 31 0 157 8 336 385 9e-05 43.5 NODE_8170_length_107_cov_1.467290 gi|46401749|ref|YP_006840.1| 34.48 29 19 0 121 35 22 50 1.2 29.3 NODE_8170_length_107_cov_1.467290 gi|490319206|ref|WP_004208699.1| 35.00 40 23 1 121 2 120 156 1.5 30.4 NODE_8170_length_107_cov_1.467290 gi|490375595|ref|WP_004255196.1| 30.77 39 27 0 133 17 174 212 3.0 29.6 NODE_8170_length_107_cov_1.467290 gi|493754408|ref|WP_006703291.1| 39.02 41 20 2 121 2 120 156 5.4 28.9 NODE_8196_length_109_cov_1.825688 gi|493895109|ref|WP_006841037.1| 41.67 36 21 0 10 117 22 57 1.4 30.4 NODE_8196_length_109_cov_1.825688 gi|488971639|ref|WP_002882570.1| 48.65 37 16 1 159 49 45 78 3.5 29.6 NODE_8196_length_109_cov_1.825688 gi|493135698|ref|WP_006154282.1| 44.74 38 18 1 159 46 45 79 6.6 28.1 NODE_8196_length_109_cov_1.825688 gi|446773341|ref|WP_000850597.1| 45.95 37 17 1 159 49 45 78 7.0 28.5 NODE_8196_length_109_cov_1.825688 gi|331266607|ref|YP_004326237.1| 45.95 37 17 1 159 49 45 78 7.0 28.5 NODE_8196_length_109_cov_1.825688 gi|446773313|ref|WP_000850569.1| 45.95 37 17 1 159 49 45 78 7.0 28.5 NODE_8196_length_109_cov_1.825688 gi|446773340|ref|WP_000850596.1| 45.95 37 17 1 159 49 45 78 7.4 28.5 NODE_8196_length_109_cov_1.825688 gi|446773314|ref|WP_000850570.1| 45.95 37 17 1 159 49 45 78 7.4 28.5 NODE_8196_length_109_cov_1.825688 gi|446714424|ref|WP_000791755.1| 45.95 37 17 1 159 49 45 78 7.4 28.5 NODE_8196_length_109_cov_1.825688 gi|446773343|ref|WP_000850599.1| 45.95 37 17 1 159 49 45 78 7.5 28.5 NODE_8312_length_134_cov_2.686567 gi|495113824|ref|WP_007838643.1| 34.69 49 30 1 15 155 133 181 0.49 32.3 NODE_8312_length_134_cov_2.686567 gi|492328979|ref|WP_005811289.1| 39.47 38 19 1 183 70 207 240 1.5 30.8 NODE_8375_length_623_cov_5.855538 gi|251831117|ref|YP_003024036.1| 67.66 167 54 0 603 103 287 453 1e-58 201 NODE_8375_length_623_cov_5.855538 gi|34538608|ref|NP_904338.1| 64.21 190 68 0 672 103 264 453 4e-55 192 NODE_8375_length_623_cov_5.855538 gi|494060703|ref|WP_007002786.1| 52.25 111 53 0 603 271 293 403 8e-35 135 NODE_8375_length_623_cov_5.855538 gi|489880098|ref|WP_003783566.1| 52.73 110 52 0 579 250 309 418 2e-31 126 NODE_8375_length_623_cov_5.855538 gi|488718785|ref|WP_002642661.1| 52.78 108 51 0 579 256 309 416 7e-31 125 NODE_8375_length_623_cov_5.855538 gi|489884516|ref|WP_003787966.1| 52.78 108 51 0 579 256 309 416 8e-31 125 NODE_8375_length_623_cov_5.855538 gi|489919575|ref|WP_003822936.1| 51.85 108 52 0 579 256 309 416 2e-30 124 NODE_8375_length_623_cov_5.855538 gi|490654142|ref|WP_004519133.1| 50.00 116 58 0 603 256 176 291 3e-30 122 NODE_8375_length_623_cov_5.855538 gi|489895414|ref|WP_003798863.1| 48.31 118 61 0 603 250 301 418 3e-30 123 NODE_8375_length_623_cov_5.855538 gi|493897385|ref|WP_006843254.1| 54.55 110 50 0 603 274 291 400 6e-30 122 NODE_8433_length_196_cov_2.795918 gi|433652797|ref|YP_007296651.1| 60.00 20 8 0 137 78 241 260 7.4 29.3 NODE_8534_length_387_cov_3.046512 gi|410172476|ref|XP_003960507.1| 80.65 31 6 0 78 170 1 31 0.50 33.5 NODE_8534_length_387_cov_3.046512 gi|113420837|ref|XP_001126659.1| 80.65 31 6 0 78 170 1 31 0.50 33.5 NODE_8534_length_387_cov_3.046512 gi|7110705|ref|NP_032998.1| 83.87 31 5 0 78 170 1 31 3.1 31.6 NODE_8534_length_387_cov_3.046512 gi|151101407|ref|NP_001092755.1| 83.87 31 5 0 78 170 1 31 3.7 31.2 NODE_8534_length_387_cov_3.046512 gi|151101404|ref|NP_002814.3| 83.87 31 5 0 78 170 1 31 3.9 31.2 NODE_8644_length_271_cov_2.169742 gi|124487199|ref|NP_001074632.1| 32.73 55 36 1 188 24 24 77 5.2 30.8 NODE_8644_length_271_cov_2.169742 gi|491920844|ref|WP_005673165.1| 45.00 40 20 1 113 232 35 72 8.5 30.0 NODE_8839_length_109_cov_10.449541 gi|304361742|ref|NP_899228.4| 98.00 50 1 0 3 152 869 918 1.5 30.8 NODE_8839_length_109_cov_10.449541 gi|304361742|ref|NP_899228.4| 92.31 13 1 0 119 157 815 827 3.1 30.0 NODE_8839_length_109_cov_10.449541 gi|157266285|ref|NP_001096133.1| 92.31 13 1 0 119 157 490 502 3.2 30.0 NODE_8839_length_109_cov_10.449541 gi|282721104|ref|NP_001164226.1| 92.31 13 1 0 119 157 490 502 3.2 29.6 NODE_8839_length_109_cov_10.449541 gi|282721102|ref|NP_775909.2| 92.31 13 1 0 119 157 490 502 3.2 29.6 NODE_8839_length_109_cov_10.449541 gi|92110019|ref|NP_060410.2| 92.31 13 1 0 119 157 1032 1044 3.2 30.0 NODE_8839_length_109_cov_10.449541 gi|92110019|ref|NP_060410.2| 70.00 50 14 1 2 148 1087 1136 5.0 29.3 NODE_8839_length_109_cov_10.449541 gi|14149997|ref|NP_115640.1| 92.31 13 1 0 119 157 471 483 3.6 29.6 NODE_8839_length_109_cov_10.449541 gi|374088176|ref|NP_001243346.1| 92.31 13 1 0 119 157 401 413 3.8 29.6 NODE_8839_length_109_cov_10.449541 gi|374088174|ref|NP_001243345.1| 92.31 13 1 0 119 157 459 471 4.1 29.6 NODE_8839_length_109_cov_10.449541 gi|221218991|ref|NP_001137461.1| 84.62 13 2 0 119 157 410 422 8.0 28.5 NODE_8839_length_109_cov_10.449541 gi|221136848|ref|NP_001137460.1| 84.62 13 2 0 119 157 410 422 8.3 28.5 NODE_8909_length_237_cov_2.299578 gi|488755457|ref|WP_002678722.1| 77.78 18 3 1 235 285 38 55 5.0 30.0 NODE_8909_length_237_cov_2.299578 gi|490452970|ref|WP_004323817.1| 52.00 25 12 0 190 264 785 809 9.6 29.6 NODE_8938_length_126_cov_2.841270 gi|490416432|ref|WP_004288922.1| 41.03 39 19 2 167 63 396 434 3.8 29.6 NODE_8938_length_126_cov_2.841270 gi|494109638|ref|WP_007050422.1| 30.56 36 25 0 49 156 337 372 9.9 28.5 NODE_8981_length_113_cov_1.796460 gi|6753374|ref|NP_033994.1| 90.48 21 2 0 57 119 864 884 1e-06 49.3 NODE_8981_length_113_cov_1.796460 gi|4757960|ref|NP_004351.1| 90.48 21 2 0 57 119 862 882 1e-06 49.3 NODE_8981_length_113_cov_1.796460 gi|14589891|ref|NP_001784.2| 85.71 21 3 0 57 119 809 829 8e-06 47.0 NODE_8981_length_113_cov_1.796460 gi|83715978|ref|NP_001032898.1| 85.71 21 3 0 57 119 802 822 9e-06 46.6 NODE_8981_length_113_cov_1.796460 gi|45496816|ref|NP_031691.1| 85.71 21 3 0 57 119 801 821 9e-06 46.6 NODE_8981_length_113_cov_1.796460 gi|356640224|ref|NP_001239268.1| 76.19 21 5 0 57 119 822 842 1e-04 43.5 NODE_8981_length_113_cov_1.796460 gi|356640221|ref|NP_001239267.1| 76.19 21 5 0 57 119 859 879 1e-04 43.5 NODE_8981_length_113_cov_1.796460 gi|14589893|ref|NP_001785.2| 76.19 21 5 0 57 119 896 916 1e-04 43.5 NODE_8981_length_113_cov_1.796460 gi|6753376|ref|NP_033997.1| 76.19 21 5 0 57 119 893 913 1e-04 43.5 NODE_8981_length_113_cov_1.796460 gi|161760627|ref|NP_031690.3| 75.00 20 5 0 57 116 887 906 6e-04 41.2 NODE_9050_length_309_cov_9.757281 gi|34538601|ref|NP_904331.1| 66.67 114 38 0 354 13 107 220 2e-54 176 NODE_9050_length_309_cov_9.757281 gi|251831110|ref|YP_003024029.1| 68.42 114 36 0 354 13 107 220 9e-51 167 NODE_9050_length_309_cov_9.757281 gi|494060890|ref|WP_007002973.1| 48.25 114 59 0 351 10 152 265 2e-30 116 NODE_9050_length_309_cov_9.757281 gi|490319117|ref|WP_004208610.1| 48.25 114 58 1 351 13 192 305 1e-29 115 NODE_9050_length_309_cov_9.757281 gi|488801868|ref|WP_002714274.1| 49.06 106 49 2 354 37 148 248 9e-29 111 NODE_9050_length_309_cov_9.757281 gi|492887322|ref|WP_006022899.1| 48.11 106 50 2 354 37 148 248 2e-28 110 NODE_9050_length_309_cov_9.757281 gi|493248465|ref|WP_006216866.1| 44.64 112 55 3 351 37 129 240 4e-25 102 NODE_9050_length_309_cov_9.757281 gi|493432514|ref|WP_006388092.1| 48.78 82 42 0 282 37 171 252 1e-24 101 NODE_9050_length_309_cov_9.757281 gi|488804984|ref|WP_002717390.1| 45.61 114 57 2 354 13 147 255 1e-22 95.1 NODE_9050_length_309_cov_9.757281 gi|491913834|ref|WP_005668116.1| 45.45 77 42 0 270 40 186 262 2e-19 87.0 NODE_9116_length_132_cov_3.045455 gi|157277969|ref|NP_444493.1| 88.24 17 2 0 131 181 2 18 0.010 37.4 NODE_9116_length_132_cov_3.045455 gi|34740329|ref|NP_919223.1| 93.33 15 1 0 137 181 26 40 0.095 34.7 NODE_9116_length_132_cov_3.045455 gi|37674277|ref|NP_932758.1| 93.33 15 1 0 137 181 26 40 0.095 34.7 NODE_9116_length_132_cov_3.045455 gi|31559916|ref|NP_666242.2| 93.33 15 1 0 137 181 26 40 0.095 34.7 NODE_9116_length_132_cov_3.045455 gi|260304980|ref|NP_001159443.1| 77.78 18 4 0 128 181 2 19 0.53 32.3 NODE_9116_length_132_cov_3.045455 gi|14043070|ref|NP_112420.1| 77.78 18 4 0 128 181 2 19 0.63 32.0 NODE_9116_length_132_cov_3.045455 gi|85060507|ref|NP_001034218.1| 77.78 18 4 0 128 181 2 19 0.63 32.0 NODE_9116_length_132_cov_3.045455 gi|6754220|ref|NP_034577.1| 77.78 18 4 0 128 181 2 19 0.63 32.0 NODE_9116_length_132_cov_3.045455 gi|4504445|ref|NP_002127.1| 77.78 18 4 0 128 181 2 19 0.63 32.0 NODE_9116_length_132_cov_3.045455 gi|58761498|ref|NP_001011725.1| 77.78 18 4 0 128 181 2 19 0.69 32.0 NODE_9133_length_153_cov_1.150327 gi|5454088|ref|NP_006392.1| 67.31 52 17 0 44 199 1 52 7e-17 76.6 NODE_9133_length_153_cov_1.150327 gi|40254600|ref|NP_033802.2| 67.31 52 17 0 44 199 1 52 7e-15 70.9 NODE_9133_length_153_cov_1.150327 gi|18700032|ref|NP_570959.1| 63.46 52 19 0 44 199 1 52 8e-15 70.9 NODE_9133_length_153_cov_1.150327 gi|5453880|ref|NP_006296.1| 63.46 52 19 0 44 199 1 52 7e-14 68.2 NODE_9133_length_153_cov_1.150327 gi|210147569|ref|NP_001129950.1| 63.46 52 19 0 44 199 1 52 2e-12 63.9 NODE_9133_length_153_cov_1.150327 gi|13569879|ref|NP_112182.1| 63.46 52 19 0 44 199 1 52 3e-12 63.9 NODE_9133_length_153_cov_1.150327 gi|359279956|ref|NP_001240686.1| 59.62 52 21 0 44 199 1 52 2e-11 61.6 NODE_9133_length_153_cov_1.150327 gi|254587996|ref|NP_075699.3| 59.62 52 21 0 44 199 1 52 2e-11 61.6 NODE_9133_length_153_cov_1.150327 gi|6912604|ref|NP_036535.1| 56.86 51 22 0 44 196 1 51 5e-11 60.1 NODE_9133_length_153_cov_1.150327 gi|21071028|ref|NP_036536.2| 53.85 52 24 0 44 199 1 52 1e-10 58.5 NODE_9165_length_116_cov_1.715517 gi|145046220|ref|NP_647466.2| 50.98 51 21 2 160 8 384 430 2e-05 45.8 NODE_9165_length_116_cov_1.715517 gi|169636420|ref|NP_001207.2| 45.10 51 22 2 160 8 408 452 0.006 38.1 NODE_9165_length_116_cov_1.715517 gi|493593396|ref|WP_006546195.1| 50.00 26 13 0 123 46 486 511 1.5 30.8 NODE_9165_length_116_cov_1.715517 gi|488752328|ref|WP_002675610.1| 44.00 25 14 0 164 90 273 297 1.5 30.8 NODE_9165_length_116_cov_1.715517 gi|488744766|ref|WP_002668107.1| 44.00 25 14 0 164 90 273 297 1.5 30.8 NODE_9165_length_116_cov_1.715517 gi|7304955|ref|NP_038517.1| 43.14 51 23 2 163 26 212 261 1.6 30.8 NODE_9165_length_116_cov_1.715517 gi|498383651|ref|WP_010697807.1| 44.00 25 14 0 164 90 273 297 1.6 30.8 NODE_9165_length_116_cov_1.715517 gi|488778528|ref|WP_002690935.1| 44.00 25 14 0 164 90 273 297 1.6 30.8 NODE_9165_length_116_cov_1.715517 gi|42527670|ref|NP_972768.1| 44.00 25 14 0 164 90 273 297 1.6 30.8 NODE_9165_length_116_cov_1.715517 gi|498381448|ref|WP_010695604.1| 44.00 25 14 0 164 90 273 297 1.8 30.8 NODE_9198_length_510_cov_4.376471 gi|320461711|ref|NP_001189360.1| 89.29 140 15 0 2 421 60 199 5e-90 269 NODE_9198_length_510_cov_4.376471 gi|32455266|ref|NP_859048.1| 89.29 140 15 0 2 421 60 199 5e-90 269 NODE_9198_length_510_cov_4.376471 gi|32455264|ref|NP_859047.1| 89.29 140 15 0 2 421 60 199 5e-90 269 NODE_9198_length_510_cov_4.376471 gi|4505591|ref|NP_002565.1| 89.29 140 15 0 2 421 60 199 5e-90 269 NODE_9198_length_510_cov_4.376471 gi|6754976|ref|NP_035164.1| 88.57 140 16 0 2 421 60 199 9e-89 266 NODE_9198_length_510_cov_4.376471 gi|377835575|ref|XP_003688912.1| 87.14 140 18 0 2 421 60 199 1e-86 261 NODE_9198_length_510_cov_4.376471 gi|377834422|ref|XP_003689480.1| 87.14 140 18 0 2 421 60 199 1e-86 261 NODE_9198_length_510_cov_4.376471 gi|32189392|ref|NP_005800.3| 74.29 140 36 0 2 421 59 198 2e-75 233 NODE_9198_length_510_cov_4.376471 gi|148747558|ref|NP_035693.3| 72.86 140 38 0 2 421 59 198 6e-75 231 NODE_9198_length_510_cov_4.376471 gi|7948999|ref|NP_058044.1| 70.80 137 40 0 5 415 136 272 2e-65 209 NODE_9356_length_159_cov_1.257862 gi|493248865|ref|WP_006217062.1| 91.30 23 2 0 208 140 272 294 1e-05 45.8 NODE_9356_length_159_cov_1.257862 gi|491906484|ref|WP_005664033.1| 91.30 23 2 0 208 140 262 284 3e-05 44.7 NODE_9356_length_159_cov_1.257862 gi|493431167|ref|WP_006386767.1| 86.96 23 3 0 208 140 272 294 4e-05 44.7 NODE_9356_length_159_cov_1.257862 gi|491911804|ref|WP_005666697.1| 91.30 23 2 0 208 140 260 282 5e-05 44.3 NODE_9356_length_159_cov_1.257862 gi|492548958|ref|WP_005882265.1| 91.30 23 2 0 208 140 260 282 6e-05 43.9 NODE_9356_length_159_cov_1.257862 gi|495815720|ref|WP_008540299.1| 82.61 23 4 0 208 140 264 286 1e-04 43.5 NODE_9356_length_159_cov_1.257862 gi|492539463|ref|WP_005878499.1| 82.61 23 4 0 208 140 237 259 3e-04 42.0 NODE_9356_length_159_cov_1.257862 gi|489879301|ref|WP_003782774.1| 82.61 23 4 0 208 140 261 283 6e-04 41.2 NODE_9356_length_159_cov_1.257862 gi|490654012|ref|WP_004519003.1| 82.61 23 4 0 208 140 262 284 6e-04 41.2 NODE_9356_length_159_cov_1.257862 gi|489847300|ref|WP_003750989.1| 82.61 23 4 0 208 140 262 284 6e-04 41.2 NODE_9391_length_274_cov_3.521898 gi|489885574|ref|WP_003789024.1| 33.33 51 32 2 14 163 209 258 0.72 33.1 NODE_9391_length_274_cov_3.521898 gi|494130065|ref|WP_007069832.1| 37.04 54 31 2 20 175 26 78 2.2 32.0 NODE_9391_length_274_cov_3.521898 gi|46397375|ref|NP_060620.2| 38.10 42 25 1 284 162 82 123 2.7 31.6 NODE_9391_length_274_cov_3.521898 gi|37059808|ref|NP_080015.3| 38.10 42 25 1 284 162 82 123 2.7 31.6 NODE_9391_length_274_cov_3.521898 gi|491653759|ref|WP_005510479.1| 36.73 49 27 1 83 229 100 144 3.5 31.2 NODE_9391_length_274_cov_3.521898 gi|491653759|ref|WP_005510479.1| 33.33 60 27 3 29 169 93 152 5.6 30.8 NODE_9391_length_274_cov_3.521898 gi|490362255|ref|WP_004242018.1| 31.67 60 35 2 17 178 1145 1204 3.7 31.2 NODE_9391_length_274_cov_3.521898 gi|493579915|ref|WP_006532998.1| 33.90 59 27 2 230 54 33 79 5.0 30.8 NODE_9391_length_274_cov_3.521898 gi|472339611|ref|YP_007673145.1| 29.03 62 42 1 317 132 112 171 5.5 30.8 NODE_9391_length_274_cov_3.521898 gi|491540951|ref|WP_005398570.1| 43.24 37 21 0 143 33 34 70 7.6 30.4 NODE_9391_length_274_cov_3.521898 gi|494181537|ref|WP_007116906.1| 46.43 28 15 0 218 135 192 219 9.4 30.0 NODE_9428_length_103_cov_1.194175 gi|126032348|ref|NP_004658.3| 45.45 22 12 0 26 91 4770 4791 8.9 28.5 NODE_9428_length_103_cov_1.194175 gi|134288898|ref|NP_034548.2| 45.45 22 12 0 26 91 4772 4793 8.9 28.5 NODE_9428_length_103_cov_1.194175 gi|489099774|ref|WP_003009643.1| 42.86 28 16 0 123 40 196 223 9.6 28.1 NODE_9428_length_103_cov_1.194175 gi|489088586|ref|WP_002998487.1| 42.86 28 16 0 123 40 196 223 9.6 28.1 NODE_9523_length_160_cov_2.100000 gi|491490995|ref|WP_005348729.1| 57.89 19 8 0 108 164 50 68 1.3 30.4 NODE_9523_length_160_cov_2.100000 gi|150004710|ref|YP_001299454.1| 32.43 37 25 0 203 93 470 506 1.9 30.8 NODE_9523_length_160_cov_2.100000 gi|9626876|ref|NP_041146.1| 29.82 57 38 1 205 41 149 205 4.3 29.6 NODE_9523_length_160_cov_2.100000 gi|489517744|ref|WP_003422556.1| 61.11 18 7 0 153 206 162 179 5.9 29.3 NODE_9523_length_160_cov_2.100000 gi|116284394|ref|NP_079005.3| 46.15 39 18 2 84 191 826 864 7.7 29.3 NODE_9523_length_160_cov_2.100000 gi|116284396|ref|NP_001070654.1| 46.15 39 18 2 84 191 834 872 7.7 29.3 NODE_9523_length_160_cov_2.100000 gi|224831241|ref|NP_001139281.1| 46.15 39 18 2 84 191 867 905 7.7 29.3 NODE_9523_length_160_cov_2.100000 gi|26248871|ref|NP_754911.1| 33.33 45 29 1 203 72 596 640 7.8 29.3 NODE_9523_length_160_cov_2.100000 gi|488947213|ref|WP_002858288.1| 38.78 49 25 1 167 36 223 271 9.2 28.9 NODE_9523_length_160_cov_2.100000 gi|489066779|ref|WP_002976774.1| 44.00 25 14 0 85 11 146 170 9.7 28.5 NODE_9533_length_115_cov_1.739130 gi|161621271|ref|NP_001104548.1| 41.67 36 14 1 29 115 290 325 1.7 30.8 NODE_9533_length_115_cov_1.739130 gi|161621269|ref|NP_035061.3| 41.67 36 14 1 29 115 290 325 1.7 30.8 NODE_9533_length_115_cov_1.739130 gi|491471372|ref|WP_005329126.1| 48.15 27 14 0 2 82 5 31 5.9 28.9 NODE_9533_length_115_cov_1.739130 gi|491466013|ref|WP_005323776.1| 48.15 27 14 0 2 82 18 44 6.3 28.9 NODE_9533_length_115_cov_1.739130 gi|491650733|ref|WP_005507455.1| 45.83 24 13 0 8 79 288 311 7.3 28.9 NODE_9533_length_115_cov_1.739130 gi|491871039|ref|WP_005644219.1| 44.44 27 14 1 156 76 217 242 8.9 28.5 NODE_9533_length_115_cov_1.739130 gi|21389473|ref|NP_653239.1| 38.89 36 20 1 2 109 12 45 9.3 28.1 NODE_9533_length_115_cov_1.739130 gi|491648115|ref|WP_005505641.1| 45.83 24 13 0 8 79 287 310 9.4 28.5 NODE_9571_length_191_cov_2.418848 gi|492247394|ref|WP_005789090.1| 24.68 77 57 1 8 238 28 103 0.97 31.6 NODE_9571_length_191_cov_2.418848 gi|492259722|ref|WP_005792610.1| 24.68 77 57 1 8 238 30 105 1.1 31.6 NODE_9571_length_191_cov_2.418848 gi|494177798|ref|WP_007115528.1| 45.45 33 17 1 29 124 267 299 1.1 32.0 NODE_9571_length_191_cov_2.418848 gi|490747450|ref|WP_004609758.1| 33.33 39 26 0 50 166 22 60 2.1 31.2 NODE_9571_length_191_cov_2.418848 gi|491061077|ref|WP_004922711.1| 42.42 33 19 0 142 240 3 35 2.8 30.4 NODE_9571_length_191_cov_2.418848 gi|490502877|ref|WP_004368968.1| 51.85 27 13 0 26 106 442 468 3.4 30.4 NODE_9571_length_191_cov_2.418848 gi|493963437|ref|WP_006906891.1| 36.96 46 25 2 107 238 116 159 3.9 30.0 NODE_9571_length_191_cov_2.418848 gi|49237332|ref|YP_031613.1| 42.86 42 20 1 5 118 22 63 4.7 29.6 NODE_9571_length_191_cov_2.418848 gi|491057703|ref|WP_004919340.1| 34.04 47 30 1 50 190 378 423 6.1 29.6 NODE_9571_length_191_cov_2.418848 gi|488982132|ref|WP_002892951.1| 38.89 36 20 2 95 199 95 129 7.5 28.9 metaMix/inst/extdata/dat1/names_example.dmp.bck0000644000176200001440000034423113403500106021173 0ustar liggesusers72 72 | "Caryophanon muelleri" (Schmid 1922) Peshkoff 1948 | | authority | 72 72 | ATCC 29453 | | type material | 72 72 | CCUG 30554 | | type material | 72 72 | CIP 103436 | | type material | 72 72 | Caryophanon muelleri | | synonym | 72 72 | DSM 2579 | | type material | 72 72 | LMG 7828 | | type material | 72 72 | Scheibenbakterien | | common name | 72 72 | Scheibenbakterien Muller 1911 | | common name | 72 72 | Simonsiella muelleri | | scientific name | 72 72 | Simonsiella muelleri Schmid 1922 | | authority | 158 158 | "Spirillum dentium" (Miller 1889) Sternberg 1892 | | authority | 158 158 | "Spirochaeta ambigua" Seguin and Vinzent 1936 | | authority | 158 158 | "Spirochaeta comandonii" Seguin and Vinzent 1936 | | authority | 158 158 | "Spirochaeta dentium" (Miller 1889) Migula 1895 | | authority | 158 158 | "Spirochaeta microdentium" (Noguchi 1912) Heim 1922 | | authority | 158 158 | "Spirochaeta orthodonta" Hoffmann 1920 | | authority | 158 158 | "Spirochaete denticola" Flugge 1886 | | authority | 158 158 | "Spirochaete dentium" Miller 1889 | | authority | 158 158 | "Spironema dentium" (Miller 1889) Gross 1912 | | authority | 158 158 | "Treponema ambiguum" (Seguin and Vinzent 1936) Prevot 1940 | | authority | 158 158 | "Treponema comandonii" (Seguin and Vinzent 1936) Prevot 1940 | | authority | 158 158 | "Treponema dentium" (Miller 1889) Dobell 1912 | | authority | 158 158 | "Treponema dentium-stenogyratum" Pettit 1928 | | authority | 158 158 | "Treponema microdentium" Noguchi 1912 | | authority | 158 158 | "Treponema orthodontum" (Hoffmann 1920) Noguchi 1928 | | authority | 158 158 | ATCC 35405 | | type material | 158 158 | CIP 103919 | | type material | 158 158 | DSM 14222 | | type material | 158 158 | JCM 8153 | | type material | 158 158 | Spirillum dentium | | synonym | 158 158 | Spirochaeta ambigua | | synonym | 158 158 | Spirochaeta comandonii | | synonym | 158 158 | Spirochaeta dentium | | synonym | 158 158 | Spirochaeta microdentium | | synonym | 158 158 | Spirochaeta orthodonta | | synonym | 158 158 | Spirochaete denticola | | synonym | 158 158 | Spirochaete dentium | | synonym | 158 158 | Spironema dentium | | synonym | 158 158 | Treponema ambiguum | | synonym | 158 158 | Treponema comandonii | | synonym | 158 158 | Treponema denticola | | scientific name | 158 158 | Treponema denticola (ex Brumpt 1925) Chan et al. 1993 | | authority | 158 158 | Treponema denticola (ex Flugge 1886) Chan et al. 1993 | | authority | 158 158 | Treponema dentium | | synonym | 158 158 | Treponema dentium-stenogyratum | | synonym | 158 158 | Treponema microdentium | | synonym | 158 158 | Treponema orthodontum | | synonym | 204 204 | ATCC 51146 | | type material | 204 204 | CCUG 30254 | | type material | 204 204 | CIP 103970 | | type material | 204 204 | Campylobacter showae | | scientific name | 204 204 | Campylobacter showae Etoh et al. 1993 | | authority | 204 204 | JCM 12989 | | type material | 204 204 | LMG 12635 | | type material | 204 204 | strain SU A4 | | type material | 222 222 | Achromobacter | | scientific name | 222 222 | Achromobacter Yabuuchi and Yano 1981 emend. Yabuuchi et al. 1998 | | authority | 250 250 | ATCC 35910 | | type material | 250 250 | CCUG 14555 | | type material | 250 250 | CIP 103039 | | type material | 250 250 | Chryseobacterium gleum | | scientific name | 250 250 | Chryseobacterium gleum (Holmes et al. 1984) Vandamme et al. 1994 | | authority | 250 250 | DSM 16776 | | type material | 250 250 | Flavobacterium gleum | | synonym | 250 250 | Flavobacterium gleum Holmes et al. 1984 | | authority | 250 250 | IFO 15054 | | type material | 250 250 | JCM 2410 | | type material | 250 250 | LMG 8334 | | type material | 250 250 | NBRC 15054 | | type material | 250 250 | NCTC 11432 | | type material | 250 250 | strain F93 | | type material | 258 258 | ATCC 33861 | | type material | 258 258 | CCUG 13224 | | type material | 258 258 | CDC E7288 | | type material | 258 258 | CIP 100542 | | type material | 258 258 | DSM 11722 | | type material | 258 258 | Flavibacterium yabuuchiae | | synonym | 258 258 | Flavobacterium spiritivorum | | synonym | 258 258 | Flavobacterium spiritivorum Holmes et al. 1982 | | authority | 258 258 | Flavobacterium yabuuchiae | | synonym | 258 258 | Flavobacterium yabuuchiae Holmes et al. 1988 | | authority | 258 258 | GIFU 3101 | | type material | 258 258 | IFO 14948 | | type material | 258 258 | JCM 1277 | | type material | 258 258 | JCM 6897 | | type material | 258 258 | LMG 8347 | | type material | 258 258 | NBRC 14948 | | type material | 258 258 | NCTC 11386 | | type material | 258 258 | Sphingobacter spiritivorum | | misspelling | 258 258 | Sphingobacterium spiritivorum | | scientific name | 258 258 | Sphingobacterium spiritivorum (Holmes et al. 1982) Yabuuchi et al. 1983 | | authority | 258 258 | strain E7288 | | type material | 469 469 | Acinetobacter | | scientific name | 469 469 | Acinetobacter Brisou and Prevot 1954 | | authority | 471 471 | "Micrococcus calco-aceticus" Beijerinck 1911 | | authority | 471 471 | ATCC 23055 | | type material | 471 471 | Acinetobacter calcoaceticus | | scientific name | 471 471 | Acinetobacter calcoaceticus (Beijerinck 1911) Baumann et al. 1968 (Approved Lists 1980) emend. Bouvet and Grimont 1986 | | authority | 471 471 | Acinetobacter genomosp. 1 | | synonym | 471 471 | Acinetobacter genomospecies 1 | | synonym | 471 471 | Acinetobacter sp. AV6 | | includes | 471 471 | Acinetobacter sp. HNR | | includes | 471 471 | Acinetobacter sp. STB1 | | includes | 471 471 | CAIM 17 | | type material | 471 471 | CCUG 12804 | | type material | 471 471 | CIP 81.8 | | type material | 471 471 | DSM 30006 | | type material | 471 471 | JCM 6842 | | type material | 471 471 | LMG 1046 | | type material | 471 471 | Micrococcus calcoaceticus | | synonym | 471 471 | Moraxella calcoacetica | | synonym | 471 471 | NCCB 22016 | | type material | 471 471 | NCTC 12983 | | type material | 471 471 | Neisseria winogradskyi | | synonym | 482 482 | "Gonococcus" Lindau 1898 | | synonym | 482 482 | "Merismopedia" Zopf 1885 | | synonym | 482 482 | Gonococcus | | synonym | 482 482 | Neisseria | | scientific name | 482 482 | Neisseria Trevisan 1885 | | synonym | 482 482 | Nesseira | | misspelling | 483 483 | "Micrococcus cinereus" von Lingelsheim 1906 | | authority | 483 483 | ATCC 14685 | | type material | 483 483 | CCUG 2156 | | type material | 483 483 | CCUG 346 | | type material | 483 483 | CIP 73.16 | | type material | 483 483 | DSM 4630 | | type material | 483 483 | LMG 8380 | | type material | 483 483 | Micrococcus cinereus | | synonym | 483 483 | NCTC 10294 | | type material | 483 483 | Neisseria cinerea | | scientific name | 483 483 | Neisseria cinerea (von Lingelsheim 1906) Murray 1939 | | authority | 484 484 | ATCC 13120 | | type material | 484 484 | CCUG 17913 | | type material | 484 484 | CCUG 345 | | type material | 484 484 | CIP 73.15 | | type material | 484 484 | DSM 17633 | | type material | 484 484 | LMG 5297 | | type material | 484 484 | NCTC 8263 | | type material | 484 484 | Neisseria flavescens | | scientific name | 484 484 | Neisseria flavescens Branham 1930 | | authority | 486 486 | "Neisseria lactamicus" (sic) Hollis et al. 1969 | | authority | 486 486 | ATCC 23970 | | type material | 486 486 | CCUG 5853 | | type material | 486 486 | CIP 72.17 | | type material | 486 486 | DSM 4691 | | type material | 486 486 | NCTC 10617 | | type material | 486 486 | Neisseria lactamica | | scientific name | 486 486 | Neisseria lactamica Hollis et al. 1969 | | authority | 486 486 | Neisseria lactamicus | | synonym | 487 487 | "Diplokokkus intracellularis meningitidis" (sic) Weichselbaum 1887 | | authority | 487 487 | "Micrococcus intracellularis" (Jaeger) Migula 1900 | | authority | 487 487 | "Micrococcus meningitidis cerebrospinalis" Albrecht and Ghon 1901 | | authority | 487 487 | "Micrococcus meningitidis" Albrecht and Ghon 1903 | | authority | 487 487 | "Neisseria weichselbaumii" Trevisan 1889 | | authority | 487 487 | ATCC 13077 | | type material | 487 487 | CCUG 3269 | | type material | 487 487 | CIP 73.10 | | type material | 487 487 | DSM 10036 | | type material | 487 487 | Diplokokkus intracellularis meningitidis | | synonym | 487 487 | Micrococcus intracellularis | | synonym | 487 487 | Micrococcus meningitidis | | synonym | 487 487 | Micrococcus meningitidis cerebrospinalis | | synonym | 487 487 | NCTC 10025 | | type material | 487 487 | Neisseria meningitidis | | scientific name | 487 487 | Neisseria meningitidis (Albrecht and Ghon 1901) Murray 1929 | | authority | 487 487 | Neisseria meningitidis. | | misspelling | 487 487 | Neisseria weichselbaumii | | synonym | 487 487 | strain Sara E. Branham M1027 | | type material | 488 488 | "Diplococcus mucosus" von Lingelsheim 1906 | | authority | 488 488 | ATCC 19696 | | type material | 488 488 | CCUG 26877 | | type material | 488 488 | CIP 59.51 | | type material | 488 488 | DSM 17611 | | type material | 488 488 | Diplococcus mucosus | | synonym | 488 488 | JCM 12992 | | type material | 488 488 | NCTC 12978 | | type material | 488 488 | Neisseria mucosa | | scientific name | 488 488 | Neisseria mucosa (von Lingelsheim 1906) Veron et al. 1959 | | authority | 488 488 | Neisseria mucosa Veron et al. 1959 (sic) | | authority | 489 489 | "Neisseria polysacchareae" Riou et al. 1983 | | authority | 489 489 | ATCC 43768 | | type material | 489 489 | CCUG 18030 | | type material | 489 489 | CIP 100113 | | type material | 489 489 | NCTC 11858 | | type material | 489 489 | Neisseria polysaccharea | | scientific name | 489 489 | Neisseria polysaccharea Riou and Guibourdenche 1987 | | authority | 489 489 | Neisseria polysacchareae | | synonym | 496 496 | ATCC 33926 | | type material | 496 496 | CIP 103346 | | type material | 496 496 | Neisseria macaca | | misspelling | 496 496 | Neisseria macacae | | scientific name | 496 496 | Neisseria macacae Vedros et al. 1983 | | authority | 496 496 | strain M-740 | | type material | 502 502 | ATCC 33394 | | type material | 502 502 | CCUG 6516 | | type material | 502 502 | CCUG 9125 | | type material | 502 502 | CIP 103473 | | type material | 502 502 | DSM 10202 | | type material | 502 502 | Kingella denitrificans | | scientific name | 502 502 | Kingella denitrificans Snell and Lapage 1976 | | authority | 502 502 | NCTC 10995 | | type material | 504 504 | "Moraxella kingae" Bovre et al. 1974 | | authority | 504 504 | "Moraxella kingii" (sic) Henriksen and Bovre 1968 | | authority | 504 504 | ATCC 23330 | | type material | 504 504 | CCUG 352 | | type material | 504 504 | CIP 80.16 | | type material | 504 504 | DSM 7536 | | type material | 504 504 | Kingella kingae | | scientific name | 504 504 | Kingella kingae (Henriksen and Bovre 1968) Henriksen and Bovre 1976 | | authority | 504 504 | Kingella kingii | | equivalent name | 504 504 | Moraxella kingae | | synonym | 504 504 | Moraxella kingii | | synonym | 504 504 | NCTC 10529 | | type material | 505 505 | ATCC 51147 | | type material | 505 505 | CCUG 30450 | | type material | 505 505 | CIP 103803 | | type material | 505 505 | DSM 18271 | | type material | 505 505 | Kingella orale | | synonym | 505 505 | Kingella oralis | | scientific name | 505 505 | Kingella oralis corrig. Dewhirst et al. 1993 | | authority | 505 505 | strain UB-38 | | type material | 539 539 | "Bacteroides corrodens" Eiken 1958 (in part) | | synonym | 539 539 | "Ristella corrodens" (Eiken 1958) Prevot 1966 | | synonym | 539 539 | ATCC 23834 | | type material | 539 539 | Bacteroides corrodens | Bacteroides corrodens | synonym | 539 539 | CCUG 2138 | | type material | 539 539 | CIP 70.75 | | type material | 539 539 | DSM 8340 | | type material | 539 539 | Eikenella corrodens | | scientific name | 539 539 | Eikenella corrodens (Eiken 1958) Jackson and Goodman 1972 | | synonym | 539 539 | JCM 12952 | | type material | 539 539 | LMG 15557 | | type material | 539 539 | NCTC 10596 | | type material | 539 539 | Ristella corrodens | | synonym | 587 587 | "Bacterium rettgeri" Hadley 1918 | | authority | 587 587 | "Shigella rettgeri" (Hadley et al. 1918) Weldin 1927 | | authority | 587 587 | ATCC 29944 | | type material | 587 587 | Bacterium rettgeri | | synonym | 587 587 | CCUG 14804 | | type material | 587 587 | CIP 103182 | | type material | 587 587 | DSM 4542 | | type material | 587 587 | JCM 1675 | | type material | 587 587 | LMG 3259 | | type material | 587 587 | NCTC 11801 | | type material | 587 587 | Proteus rettgeri | | synonym | 587 587 | Proteus rettgeri (Hadley et al. 1918) Rustigian and Stuart 1943 (Approved Lists 1980) | | authority | 587 587 | Providencia rettgeri | | scientific name | 587 587 | Providencia rettgeri (Hadley 1918) Brenner et al. 1978 | | authority | 587 587 | Shigella rettgeri | | synonym | 588 588 | "Proteus stuartii" Buttiaux et al. 1954 | | authority | 588 588 | ATCC 29914 | | type material | 588 588 | CCUG 14805 | | type material | 588 588 | CIP 104687 | | type material | 588 588 | DSM 4539 | | type material | 588 588 | LMG 3260 | | type material | 588 588 | NCTC 11800 | | type material | 588 588 | Proteus stuartii | | synonym | 588 588 | Providencia stuartii | | scientific name | 588 588 | Providencia stuartii (Buttiaux et al. 1954) Ewing 1962 | | authority | 618 618 | ATCC 33077 | | type material | 618 618 | CCUG 14508 | | type material | 618 618 | CDC 1979-77 | | type material | 618 618 | CIP 79.1 | | type material | 618 618 | DSM 4582 | | type material | 618 618 | JCM 1243 | | type material | 618 618 | NBRC 102598 | | type material | 618 618 | NCTC 11214 | | type material | 618 618 | Serratia odorifera | | scientific name | 618 618 | Serratia odorifera Grimont et al. 1978 | | authority | 618 618 | Serratia odorifora | | misspelling | 636 636 | "Paracolobactrum anguillimortiferum" Hoshina 1962 | | authority | 636 636 | ATCC 15947 | | type material | 636 636 | CCUG 1638 | | type material | 636 636 | CIP 78.61 | | type material | 636 636 | DSM 30052 | | type material | 636 636 | Edwardsiella anguillimortifera | | synonym | 636 636 | Edwardsiella anguillimortifera (Hoshina 1962) Sakazaki and Tamura 1975 | | authority | 636 636 | Edwardsiella tarda | | scientific name | 636 636 | Edwardsiella tarda Ewing and McWhorter 1965 | | authority | 636 636 | JCM 1656 | | type material | 636 636 | LMG 2793 | | type material | 636 636 | NCCB 73021 | | type material | 636 636 | NCTC 10396 | | type material | 636 636 | Paracolobactrum anguillimortiferum | | synonym | 816 816 | "Ristella" Prevot 1938 | | authority | 816 816 | Bacteroides | Bacteroides | scientific name | 816 816 | Bacteroides Castellani and Chalmers 1919 (Approved Lists 1980) emend. Shah and Collins 1989 | | authority | 816 816 | Capsularis | | synonym | 816 816 | Capsularis Prevot 1938 (Approved Lists 1980) | | authority | 816 816 | Ristella | Ristella | synonym | 817 817 | "Bacteroides inaequalis" Eggerth and Gagnon 1933 | | authority | 817 817 | "Bacteroides incommunis" Eggerth and Gagnon 1933 | | authority | 817 817 | "Bacteroides uncatus" Eggerth and Gagnon 1933 | | authority | 817 817 | "Fusiformis fragilis" Topley and Wilson 1929 | | authority | 817 817 | "Pseudobacterium fragilis" Krasil'nikov 1949 | | authority | 817 817 | "Pseudobacterium inaequalis" (Eggerth and Gagnon 1933) Krasil'nikov 1949 | | authority | 817 817 | "Pseudobacterium incommunis" (Eggerth and Gagnon 1933) Krasil'nikov 1949 | | authority | 817 817 | "Pseudobacterium uncatum" (Eggerth and Gagnon 1933) Krasil'nikov 1949 | | authority | 817 817 | "Ristella fragilis" Prevot 1938 | | authority | 817 817 | "Ristella incommunis" (Eggerth and Gagnon 1933) Prevot 1938 | | authority | 817 817 | "Ristella uncata" (Eggerth and Gagnon 1933) Prevot 1938 | | authority | 817 817 | "Sphaerophorus inaequalis" (Eggerth and Gagnon 1933) Prevot 1938 | | authority | 817 817 | "Sphaerophorus intermedius" Bergan and Hovig 1968 | | authority | 817 817 | ATCC 25285 | | type material | 817 817 | Bacillus fragilis | | synonym | 817 817 | Bacillus fragilis Veillon and Zuber 1898 | | authority | 817 817 | Bacteroides fragili | | misspelling | 817 817 | Bacteroides fragilis | | scientific name | 817 817 | Bacteroides fragilis (Veillon and Zuber 1898) Castellani and Chalmers 1919 | | authority | 817 817 | Bacteroides inaequalis | | synonym | 817 817 | Bacteroides incommunis | | synonym | 817 817 | Bacteroides uncatus | | synonym | 817 817 | CCUG 4856 | | type material | 817 817 | CIP 77.16 | | type material | 817 817 | DSM 2151 | | type material | 817 817 | Fusiformis fragilis | | synonym | 817 817 | JCM 11019 | | type material | 817 817 | LMG 10263 | | type material | 817 817 | NCTC 9343 | | type material | 817 817 | Pseudobacterium fragilis | | synonym | 817 817 | Pseudobacterium inaequalis | | synonym | 817 817 | Pseudobacterium incommunis | | synonym | 817 817 | Pseudobacterium uncatum | | synonym | 817 817 | Ristella fragilis | | synonym | 817 817 | Ristella incommunis | | synonym | 817 817 | Ristella uncata | | synonym | 817 817 | Sphaerophorus inaequalis | | synonym | 817 817 | Sphaerophorus intermedius | | synonym | 823 823 | "Bacteroides fragilis subsp. distasonis" (Eggerth and Gagnon 1933) Holdeman and Moore 1970 | | authority | 823 823 | "Pseudobacterium distasonis" (Eggerth and Gagnon 1933) Krasil'nikov 1949 | | authority | 823 823 | "Ristella distasonis" (Eggerth and Gagnon 1933) Prevot 1938 | | authority | 823 823 | ATCC 8503 | | type material | 823 823 | Bacteroides distasonis | | synonym | 823 823 | Bacteroides distasonis Eggerth and Gagnon 1933 (Approved Lists 1980) | | authority | 823 823 | Bacteroides fragilis subsp. distasoni | | synonym | 823 823 | CCUG 4941 | | type material | 823 823 | CIP 104284 | | type material | 823 823 | DSM 20701 | | type material | 823 823 | JCM 5825 | | type material | 823 823 | NCTC 11152 | | type material | 823 823 | Parabacteroides distasonis | | scientific name | 823 823 | Parabacteroides distasonis (Eggerth and Gagnon 1933) Sakamoto and Benno 2006 | | authority | 823 823 | Pseudobacterium distasonis | | synonym | 823 823 | Ristella distasonis | | synonym | 824 824 | ATCC 33236 | | type material | 824 824 | Bacteroides gracilis | | synonym | 824 824 | Bacteroides gracilis Tanner et al. 1981 | | synonym | 824 824 | CCUG 27720 | | type material | 824 824 | Campylobacter gracilis | | scientific name | 824 824 | Campylobacter gracilis (Tanner et al. 1981) Vandamme et al. 1995 | | synonym | 824 824 | DSM 19528 | | type material | 824 824 | FDC 1084 | | type material | 824 824 | JCM 8538 | | type material | 824 824 | NCTC 12738 | | type material | 847 847 | ATCC 35274 | | type material | 847 847 | CIP 106513 | | type material | 847 847 | Oxalobacter formigenes | | scientific name | 847 847 | Oxalobacter formigenes Allison et al. 1985 | | authority | 847 847 | strain OxB | | type material | 1017 1017 | ATCC 33624 | | type material | 1017 1017 | CCUG 9715 | | type material | 1017 1017 | CIP 102945 | | type material | 1017 1017 | Capnocytophaga gingivalis | | scientific name | 1017 1017 | Capnocytophaga gingivalis Leadbetter et al. 1982 emend. London et al. 1985 | | authority | 1017 1017 | DSM 3290 | | type material | 1017 1017 | JCM 12953 | | type material | 1017 1017 | LMG 11514 | | type material | 1017 1017 | NCTC 12372 | | type material | 1017 1017 | strain 27 | strain 27 | type material | 1019 1019 | ATCC 33612 | | type material | 1019 1019 | CCUG 9714 | | type material | 1019 1019 | CIP 104301 | | type material | 1019 1019 | Capnocytophaga sputigena | | scientific name | 1019 1019 | Capnocytophaga sputigena Leadbetter et al. 1982 | | authority | 1019 1019 | DSM 3292 | | type material | 1019 1019 | DSM 7273 | | type material | 1019 1019 | JCM 12967 | | type material | 1019 1019 | LMG 11518 | | type material | 1019 1019 | NCTC 11653 | | type material | 1019 1019 | strain 4 | | type material | 1033 1033 | Afipia | | scientific name | 1033 1033 | Afipia Brenner et al. 1992 emend. La Scola et al. 2002 | | authority | 1034 1034 | ATCC 49720 | | type material | 1034 1034 | Afipia clevelandensis | | scientific name | 1034 1034 | Afipia clevelandensis Brenner et al. 1992 | | authority | 1034 1034 | CCUG 30457 | | type material | 1034 1034 | CIP 103516 | | type material | 1034 1034 | DSM 7315 | | type material | 1034 1034 | NCTC 12721 | | type material | 1034 1034 | strain B-91-007353 | | type material | 1035 1035 | AFIP strain BV | | type material | 1035 1035 | ATCC 53690 | | type material | 1035 1035 | Afipia felis | | scientific name | 1035 1035 | Afipia felis Brenner et al. 1992 | | authority | 1035 1035 | CCUG 30456 | | type material | 1035 1035 | CIP 103515 | | type material | 1035 1035 | DSM 7326 | | type material | 1035 1035 | NCTC 12499 | | type material | 1035 1035 | cat scratch disease bacillus | | genbank common name | 1035 1035 | strain B-91-007352 | | type material | 1260 1260 | "Diplococcus magnus" Prevot 1933 | | authority | 1260 1260 | ATCC 15794 | | type material | 1260 1260 | CCUG 17636 | | type material | 1260 1260 | DSM 20470 | | type material | 1260 1260 | Finegoldia magna | | scientific name | 1260 1260 | Finegoldia magna (Prevot 1933) Murdoch and Shah 2000 | | authority | 1260 1260 | GIFU 7629 | | type material | 1260 1260 | JCM 1766 | | type material | 1260 1260 | NCTC 11804 | | type material | 1260 1260 | Peptococcus magnus | | synonym | 1260 1260 | Peptococcus magnus (Prevot 1933) Holdeman and Moore 1972 (Approved Lists 1980) | | authority | 1260 1260 | Peptostreptococcus magnus | | synonym | 1260 1260 | Peptostreptococcus magnus (Prevot 1933) Ezaki et al. 1983 | | authority | 1270 1270 | "Bacteridium luteum" Schroeter 1872 | | authority | 1270 1270 | "Micrococcus flavus" Trevisan | | authority | 1270 1270 | "Micrococcus lysodeikticus" Fleming 1933 | | authority | 1270 1270 | "Sarcina lutea" (Schroeter 1872) Schroeter 1886 | | authority | 1270 1270 | ATCC 4698 | | type material | 1270 1270 | Bacteridium luteum | | synonym | 1270 1270 | CCM 169 | | type material | 1270 1270 | CCUG 5858 | | type material | 1270 1270 | CIP A270 | | type material | 1270 1270 | DSM 20030 | | type material | 1270 1270 | HAMBI 1399 | | type material | 1270 1270 | HAMBI 26 | | type material | 1270 1270 | IEGM 391 | | type material | 1270 1270 | IFO 3333 | | type material | 1270 1270 | JCM 1464 | | type material | 1270 1270 | LMG 4050 | | type material | 1270 1270 | Micrococcus luteus | | scientific name | 1270 1270 | Micrococcus luteus (Schroeter 1872) Cohn 1872 (Approved Lists 1980) emend. Wieser et al. 2002 | | authority | 1270 1270 | Micrococcus lysodeikticus | | synonym | 1270 1270 | NBRC 3333 | | type material | 1270 1270 | NCCB 78001 | | type material | 1270 1270 | NCTC 2665 | | type material | 1270 1270 | NRRL B-287 | | type material | 1270 1270 | Sarcina lutea | | synonym | 1270 1270 | VKM B-1314 | | type material | 1270 1270 | not "Micrococcus luteus" Lehmann and Neumann 1896 | | authority | 1279 1279 | "Aurococcus" Winslow and Rogers 1906 | | authority | 1279 1279 | Aurococcus | | synonym | 1279 1279 | Staphylococcus | | scientific name | 1279 1279 | Staphylococcus Rosenbach 1884 | | authority | 1301 1301 | Streptococcus | | scientific name | 1301 1301 | Streptococcus Rosenbach 1884 | | authority | 1303 1303 | ATCC 35037 | | type material | 1303 1303 | CCUG 13229 | | type material | 1303 1303 | CCUG 24891 | | type material | 1303 1303 | CIP 102922 | | type material | 1303 1303 | DSM 20627 | | type material | 1303 1303 | JCM 12997 | | type material | 1303 1303 | LMG 14532 | | type material | 1303 1303 | NCTC 11427 | | type material | 1303 1303 | Streptococcus oralis | | scientific name | 1303 1303 | Streptococcus oralis Bridge and Sneath 1982 emend. Kilian et al. 1989 | | authority | 1303 1303 | Streptococcus oralis Bridge and Sneath 1982 emend. Kilpper-Balz et al. 1985 | | authority | 1303 1303 | strain LVG 1 | | type material | 1303 1303 | strain PB 182 | | type material | 1303 1303 | strain SK23 | | type material | 1305 1305 | ATCC 10556 | | type material | 1305 1305 | CCUG 17826 | | type material | 1305 1305 | CCUG 35770 | | type material | 1305 1305 | CIP 55.128 | | type material | 1305 1305 | DSM 20567 | | type material | 1305 1305 | JCM 5708 | | type material | 1305 1305 | LMG 14702 | | type material | 1305 1305 | NCTC 7863 | | type material | 1305 1305 | Streptococcus sanguinis | | scientific name | 1305 1305 | Streptococcus sanguinis corrig. White and Niven 1946 (Approved Lists 1980) emend. Kilian et al. 1989 | | authority | 1305 1305 | Streptococcus sanguis | | misspelling | 1305 1305 | strain SK1 | strain SK1 | type material | 1317 1317 | ATCC 33748 | | type material | 1317 1317 | CCUG 24890 | | type material | 1317 1317 | CIP 103222 | | type material | 1317 1317 | DSM 5635 | | type material | 1317 1317 | LMG 14514 | | type material | 1317 1317 | NCTC 11391 | | type material | 1317 1317 | Streptococcus downei | | scientific name | 1317 1317 | Streptococcus downei Whiley et al. 1988 | | authority | 1317 1317 | Streptococcus downensis | | equivalent name | 1317 1317 | strain MFe28 | | type material | 1322 1322 | ATCC 27752 | | type material | 1322 1322 | Blautia hansenii | | scientific name | 1322 1322 | Blautia hansenii (Holdeman and Moore 1974) Liu et al. 2008 | | authority | 1322 1322 | CIP 104219 | | type material | 1322 1322 | DSM 20583 | | type material | 1322 1322 | JCM 14655 | | type material | 1322 1322 | Ruminococcus hansenii | | synonym | 1322 1322 | Ruminococcus hansenii (Holdeman and Moore 1974) Ezaki et al. 1994 | | authority | 1322 1322 | Streptococcus hansenii | | synonym | 1322 1322 | Streptococcus hansenii Holdeman and Moore 1974 (Approved Lists 1980) | | authority | 1343 1343 | ATCC 49124 | | type material | 1343 1343 | CCUG 24893 | | type material | 1343 1343 | CIP 103363 | | type material | 1343 1343 | DSM 5636 | | type material | 1343 1343 | LMG 13516 | | type material | 1343 1343 | NCTC 12166 | | type material | 1343 1343 | Streptococcus vestibularis | | scientific name | 1343 1343 | Streptococcus vestibularis Whiley and Hardie 1988 | | authority | 1343 1343 | strain MM1 | strain MM1 | type material | 1352 1352 | ATCC 19434 | | type material | 1352 1352 | CCUG 542 | | type material | 1352 1352 | CFBP 4248 | | type material | 1352 1352 | CIP 103014 | | type material | 1352 1352 | DSM 20477 | | type material | 1352 1352 | Enterococcus faecium | | scientific name | 1352 1352 | Enterococcus faecium (Orla-Jensen 1919) Schleifer and Kilpper-Balz 1984 | | authority | 1352 1352 | HAMBI 1710 | | type material | 1352 1352 | JCM 5804 | | type material | 1352 1352 | JCM 8727 | | type material | 1352 1352 | LMG 11423 | | type material | 1352 1352 | NBRC 100485 | | type material | 1352 1352 | NBRC 100486 | | type material | 1352 1352 | NCDO 942 | | type material | 1352 1352 | NCIMB 11508 | | type material | 1352 1352 | NCTC 7171 | | type material | 1352 1352 | Streptococcus faecium | | synonym | 1352 1352 | Streptococcus faecium Orla-Jensen 1919 (Approved Lists 1980) | | authority | 1383 1383 | ATCC 49626 | | type material | 1383 1383 | Atopobium rimae | | scientific name | 1383 1383 | Atopobium rimae (Olsen et al. 1991) Collins and Wallbanks 1993 | | synonym | 1383 1383 | CCUG 31168 | | type material | 1383 1383 | DSM 7090 | | type material | 1383 1383 | IFO 15546 | | type material | 1383 1383 | JCM 10299 | | type material | 1383 1383 | LMG 11476 | | type material | 1383 1383 | Lactobacillus rimae | | synonym | 1383 1383 | Lactobacillus rimae Olsen et al. 1991 | | synonym | 1383 1383 | NBRC 15546 | | type material | 1383 1383 | VPI D140H-11A | | type material | 1496 1496 | "Bacillus difficilis" Hall and O'Toole 1935 | | authority | 1496 1496 | AS 1.2184 | | type material | 1496 1496 | ATCC 9689 | | type material | 1496 1496 | BCRC 10642 | | type material | 1496 1496 | Bacillus difficilis | | synonym | 1496 1496 | CCRC 10642 | | type material | 1496 1496 | CCUG 4938 | | type material | 1496 1496 | CIP 104282 | | type material | 1496 1496 | Clostridium difficile | | equivalent name | 1496 1496 | Clostridium difficile (Hall and O'Toole 1935) Prevot 1938 | | authority | 1496 1496 | DSM 1296 | | type material | 1496 1496 | JCM 1296 | | type material | 1496 1496 | LMG 15861 | | type material | 1496 1496 | NCIMB 10666 | | type material | 1496 1496 | NCTC 11209 | | type material | 1496 1496 | [Clostridium] difficile | | scientific name | 1509 1509 | "Bacillus sporogenes var. A" Metchnikoff 1908 | | authority | 1509 1509 | "Clostridium sporogenes var. A" (Metchnikoff 1908) Prevot 1938 | | authority | 1509 1509 | "Clostridium sporogenes" (Heller 1922) Bergey et al. 1923 | | authority | 1509 1509 | "Metchnikovillus sporogenes" (sic) Heller 1922 | | authority | 1509 1509 | ATCC 3584 | | type material | 1509 1509 | BCRC 11259 | | type material | 1509 1509 | Bacillus sporogenes var. A | | synonym | 1509 1509 | CCRC 11259 | | type material | 1509 1509 | CCUG 15941 | | type material | 1509 1509 | CIP 106155 | | type material | 1509 1509 | Clostridium sporogenes | | scientific name | 1509 1509 | Clostridium sporogenes (Metchnikoff 1908) Bergey et al. 1923 | | authority | 1509 1509 | Clostridium sporogenes var. A | | synonym | 1509 1509 | DSM 795 | | type material | 1509 1509 | JCM 1416 | | type material | 1509 1509 | LMG 8421 | | type material | 1509 1509 | Metchnikovillus sporogenes | | synonym | 1509 1509 | NCIMB 10696 | | type material | 1509 1509 | NCTC 13020 | | type material | 1535 1535 | ATCC 29065 | | type material | 1535 1535 | CCUG 48287 | | type material | 1535 1535 | Clostridium leptum | | scientific name | 1535 1535 | Clostridium leptum Moore et al. 1976 | | authority | 1535 1535 | DSM 753 | | type material | 1535 1535 | [Clostridium] leptum | | equivalent name | 1623 1623 | ATCC 27780 | | type material | 1623 1623 | CCUG 39465 | | type material | 1623 1623 | CIP 103153 | | type material | 1623 1623 | DSM 20403 | | type material | 1623 1623 | JCM 1152 | | type material | 1623 1623 | LMG 10756 | | type material | 1623 1623 | Lactobacillus ruminis | | scientific name | 1623 1623 | Lactobacillus ruminis Sharpe et al. 1973 | | authority | 1623 1623 | NBRC 102161 | | type material | 1623 1623 | NRRL B-14853 | | type material | 1633 1633 | ATCC 49540 | | type material | 1633 1633 | CCUG 31452 | | type material | 1633 1633 | CIP 105932 | | type material | 1633 1633 | DSM 5837 | | type material | 1633 1633 | JCM 9505 | | type material | 1633 1633 | LMG 12891 | | type material | 1633 1633 | Lactobacillus vaginalis | | scientific name | 1633 1633 | Lactobacillus vaginalis Embley et al. 1989 | | synonym | 1633 1633 | NCTC 12197 | | type material | 1656 1656 | "Odontomyces viscosus" Howell et al. 1965 | | synonym | 1656 1656 | ATCC 15987 | | type material | 1656 1656 | Actinomyces viscosus | | scientific name | 1656 1656 | Actinomyces viscosus (Howell et al. 1965) Georg et al. 1969 | | synonym | 1656 1656 | CCUG 14476 | | type material | 1656 1656 | CIP 103147 | | type material | 1656 1656 | DSM 43327 | | type material | 1656 1656 | JCM 8353 | | type material | 1656 1656 | NCTC 10951 | | type material | 1656 1656 | Odontomyces viscosus | | synonym | 1660 1660 | ATCC 17929 | | type material | 1660 1660 | Actinomyces odontolyticus | | scientific name | 1660 1660 | Actinomyces odontolyticus Batty 1958 | | synonym | 1660 1660 | CCUG 20536 | | type material | 1660 1660 | CIP 101124 | | type material | 1660 1660 | DSM 19120 | | type material | 1660 1660 | DSM 43760 | | type material | 1660 1660 | JCM 14871 | | type material | 1660 1660 | LMG 18080 | | type material | 1660 1660 | NCTC 9935 | | type material | 1681 1681 | "Actinobacterium bifidum" (Tissier 1900) Puntoni 1937 | | authority | 1681 1681 | "Actinomyces bifidus" (Tissier 1900) Nannizzi 1934 | | authority | 1681 1681 | "Actinomyces parabifidus" (Weiss and Rettger 1938) Pine and Georg 1965 | | authority | 1681 1681 | "Bacillus bifidus communis" Tissier 1900 | | authority | 1681 1681 | "Bacillus bifidus" Tissier 1900 | | authority | 1681 1681 | "Bacterium bifidum" (Tissier 1900) Lehmann and Neumann 1927 | | authority | 1681 1681 | "Bacteroides bifidus" (Tissier 1900) Castellani and Chalmers 1919 | | authority | 1681 1681 | "Bifidibacterium bifidum" (Tissier 1900) Prevot 1938 | | authority | 1681 1681 | "Cohnistreptothrix bifidus" (Tissier 1900) Negroni and Fischer 1944 | | authority | 1681 1681 | "Lactobacillus bifidus type II" Weiss and Rettger 1938 | | authority | 1681 1681 | "Lactobacillus parabifidus" Weiss and Rettger 1938 | | authority | 1681 1681 | "Nocardia bifida" (Tissier 1900) Vuillemin 1931 | | authority | 1681 1681 | "Tissieria bifida" (Tissier 1900) Pribram 1929 | | authority | 1681 1681 | AS 1.2212 | | type material | 1681 1681 | ATCC 29521 | | type material | 1681 1681 | Actinobacterium bifidum | | synonym | 1681 1681 | Actinomyces bifidus | | synonym | 1681 1681 | Actinomyces parabifidus | | synonym | 1681 1681 | BCRC 14615 | | type material | 1681 1681 | Bacillus bifidus | | synonym | 1681 1681 | Bacillus bifidus communis | | synonym | 1681 1681 | Bacterium bifidum | | synonym | 1681 1681 | Bacteroides bifidus | | synonym | 1681 1681 | Bifidibacterium bifidum | | synonym | 1681 1681 | Bifidobacterium bifidum | | scientific name | 1681 1681 | Bifidobacterium bifidum (Tissier 1900) Orla-Jensen 1924 | | authority | 1681 1681 | CCRC 14615 | | type material | 1681 1681 | CCUG 18364 | | type material | 1681 1681 | CCUG 45217 | | type material | 1681 1681 | CIP 56.7 | | type material | 1681 1681 | Cohnistreptothrix bifidus | | synonym | 1681 1681 | DSM 20456 | | type material | 1681 1681 | HAMBI 1380 | | type material | 1681 1681 | IFO 14252 | | type material | 1681 1681 | JCM 1255 | | type material | 1681 1681 | KCTC 3202 | | type material | 1681 1681 | LMG 11041 | | type material | 1681 1681 | LMG 8810 | | type material | 1681 1681 | Lactobacillus bifidus type II | | synonym | 1681 1681 | Lactobacillus parabifidus | | synonym | 1681 1681 | NBRC 100015 | | type material | 1681 1681 | NBRC 14252 | | type material | 1681 1681 | NCFB 2715 | | type material | 1681 1681 | NCIMB 702715 | | type material | 1681 1681 | NCTC 13001 | | type material | 1681 1681 | Nocardia bifida | | synonym | 1681 1681 | Tissieria bifida | | synonym | 1681 1681 | strain Ti | | type material | 1689 1689 | AS 1.2188 | | type material | 1689 1689 | ATCC 27534 | | type material | 1689 1689 | Actinomyces eriksonii | | synonym | 1689 1689 | BCRC 14662 | | type material | 1689 1689 | Bifidobacterium dentium | | scientific name | 1689 1689 | Bifidobacterium dentium Scardovi and Crociani 1974 | | authority | 1689 1689 | CCRC 14662 | | type material | 1689 1689 | CCUG 18367 | | type material | 1689 1689 | CIP 104176 | | type material | 1689 1689 | DSM 20436 | | type material | 1689 1689 | HAMBI 556 | | type material | 1689 1689 | JCM 1195 | | type material | 1689 1689 | LMG 10506 | | type material | 1689 1689 | LMG 11045 | | type material | 1689 1689 | NCFB 2243 | | type material | 1689 1689 | NCIMB 702243 | | type material | 1689 1689 | NCTC 11816 | | type material | 1747 1747 | "Bacillus acnes" Gilchrist 1900 | | authority | 1747 1747 | "Corynebacterium acnes" (Gilchrist 1900) Eberson 1918 | | authority | 1747 1747 | ATCC 6919 | | type material | 1747 1747 | Bacillus acnes | | synonym | 1747 1747 | CCUG 1794 | | type material | 1747 1747 | CIP 53.117 | | type material | 1747 1747 | Corynebacterium acnes | | synonym | 1747 1747 | DSM 1897 | | type material | 1747 1747 | JCM 6425 | | type material | 1747 1747 | LMG 16711 | | type material | 1747 1747 | NCTC 737 | | type material | 1747 1747 | NRRL B-4224 | | type material | 1747 1747 | Propionibacterium acnes | | scientific name | 1747 1747 | Propionibacterium acnes (sic) (Gilchrist 1900) Douglas and Gunter 1946 | | authority | 1747 1747 | Propionicibacterium acnes | | equivalent name | 1747 1747 | VKM Ac-1450 | | type material | 1827 1827 | Rhodococcus | | scientific name | 1827 1827 | Rhodococcus Zopf 1891 | | authority | 2051 2051 | ATCC 35241 | | type material | 2051 2051 | ATCC 43063 [[Falcivibrio vaginalis]] | | type material | 2051 2051 | CCUG 21018 | | type material | 2051 2051 | CCUG 24716 [[Falcivibrio vaginalis]] | | type material | 2051 2051 | DSM 23059 | | type material | 2051 2051 | DSM 2711 [[Falcivibrio vaginalis]] | | type material | 2051 2051 | Falcivibrio vaginalis | | synonym | 2051 2051 | Falcivibrio vaginalis Hammann et al. 1984 | | authority | 2051 2051 | LMG 7856 [[Falcivibrio vaginalis]] | | type material | 2051 2051 | Mobiluncus curtisii | | scientific name | 2051 2051 | Mobiluncus curtisii Spiegel and Roberts 1984 emend. Hoyles et al. 2004 | | authority | 2051 2051 | NCTC 11656 | | type material | 2051 2051 | NCTC 11820 [[Falcivibrio vaginalis]] | | type material | 2051 2051 | strain BV345-16 | | type material | 2051 2051 | strain V125 [[Falcivibrio vaginalis]] | | type material | 2173 2173 | ATCC 35061 | | type material | 2173 2173 | DSM 861 | | type material | 2173 2173 | Methanobrevibacter smithii | | scientific name | 2173 2173 | Methanobrevibacter smithii Balch and Wolfe 1981 | | authority | 2173 2173 | OCM 144 | | type material | 2173 2173 | strain PS | | type material | 9606 9606 | Homo sapiens | | scientific name | 9606 9606 | Homo sapiens Linnaeus, 1758 | | authority | 9606 9606 | human | | genbank common name | 9606 9606 | man | | common name | 10090 10090 | LK3 transgenic mice | | includes | 10090 10090 | Mus muscaris | | misnomer | 10090 10090 | Mus musculus | | scientific name | 10090 10090 | Mus musculus Linnaeus, 1758 | | authority | 10090 10090 | Mus sp. 129SV | | includes | 10090 10090 | house mouse | | genbank common name | 10090 10090 | mice C57BL/6xCBA/CaJ hybrid | | misspelling | 10090 10090 | mouse | | common name | 10090 10090 | nude mice | | includes | 10090 10090 | transgenic mice | | includes | 10401 10401 | Channel catfish virus | | genbank common name | 10401 10401 | IcHV-1 | | genbank acronym | 10401 10401 | Ictalurid herpesvirus 1 | | scientific name | 10401 10401 | channel catfish virus CCV | | synonym | 10493 10493 | FV3 | | acronym | 10493 10493 | Frog virus 3 | | scientific name | 10493 10493 | Frog virus 3 iridovirus | | synonym | 10493 10493 | frog virus 3 FV3 | | synonym | 10493 10493 | frog virus 3, FV3 | | synonym | 10506 10506 | Chlorella PBCV-1 virus | | synonym | 10506 10506 | Chlorella virus PBCV-1 | | synonym | 10506 10506 | PBCV-1 | | acronym | 10506 10506 | Paramecium bursaria Chlorella virus 1 | | scientific name | 10506 10506 | Paramecium bursaria Chlorella virus 1, PBCV-1 | | synonym | 10506 10506 | Paramecium bursaria Chlorella virus PBCV-1 | | synonym | 10726 10726 | Bacteriophage T5 | | synonym | 10726 10726 | Enterobacteria phage T5 | | scientific name | 10726 10726 | phage T5 | | synonym | 11128 11128 | BCV | | acronym | 11128 11128 | BECV | | acronym | 11128 11128 | Bovine coronavirus | | scientific name | 11128 11128 | Bovine enteritic coronavirus | | synonym | 11128 11128 | Bovine enteritic coronavirus BECV | | synonym | 11128 11128 | bovine coronavirus BCV | | synonym | 11128 11128 | bovine enteric coronavirus | | synonym | 11128 11128 | calf diarrheal coronavirus | | synonym | 11128 11128 | neonatal calf diarrhea virus | | synonym | 11142 11142 | Murine coronavirus mhv (STRAIN A59) | | synonym | 11142 11142 | Murine hepatitis virus (strain A59) | | synonym | 11142 11142 | Murine hepatitis virus strain A59 | | scientific name | 11144 11144 | Murine coronavirus mhv (STRAIN JHM) | | synonym | 11144 11144 | Murine hepatitis virus (strain JHM) | | synonym | 11144 11144 | Murine hepatitis virus strain JHM | | scientific name | 13690 13690 | ATCC 51230 | | type material | 13690 13690 | Beijerinckia B1 | | includes | 13690 13690 | Beijerinckia sp. B1 | | includes | 13690 13690 | CCUG 28380 | | type material | 13690 13690 | CCUG 31205 | | type material | 13690 13690 | CIP 106726 | | type material | 13690 13690 | DSM 7462 | | type material | 13690 13690 | GIFU 9882 | | type material | 13690 13690 | HAMBI 1842 | | type material | 13690 13690 | IFO 15102 | | type material | 13690 13690 | JCM 7371 | | type material | 13690 13690 | LMG 11252 | | type material | 13690 13690 | NBRC 15102 | | type material | 13690 13690 | Sphingobium yanoikuyae | | scientific name | 13690 13690 | Sphingobium yanoikuyae (Yabuuchi et al. 1990) Takeuchi et al. 2001 | | synonym | 13690 13690 | Sphingomonas yanoikuyae | | genbank synonym | 13690 13690 | Sphingomonas yanoikuyae Yabuuchi et al. 1990 | | synonym | 28037 28037 | ATCC 49456 | ATCC 49456 | type material | 28037 28037 | CCUG 31611 | CCUG 31611 | type material | 28037 28037 | CCUG 35790 | CCUG 35790 | type material | 28037 28037 | CIP 103335 | CIP 103335 | type material | 28037 28037 | DSM 12643 | DSM 12643 | type material | 28037 28037 | JCM 12971 | JCM 12971 | type material | 28037 28037 | LMG 14557 | LMG 14557 | type material | 28037 28037 | NCTC 12261 | NCTC 12261 | type material | 28037 28037 | Streptococcus mitis | | scientific name | 28037 28037 | Streptococcus mitis Andrewes and Horder 1906 (Approved Lists 1980) emend. Kilian et al. 1989 | | authority | 28037 28037 | Streptococcus mitis Andrewes and Horder 1906 emend. Judicial Commission 1993 | | authority | 28037 28037 | strain NS 51 | strain NS 51 | type material | 28080 28080 | ATCC 43954 | | type material | 28080 28080 | CCUG 14913 | | type material | 28080 28080 | CIP 103681 | | type material | 28080 28080 | CNW group | | synonym | 28080 28080 | Campylobacter upsaliensis | | scientific name | 28080 28080 | Campylobacter upsaliensis Sandstedt and Ursing 1991 | | authority | 28080 28080 | DSM 5365 | | type material | 28080 28080 | NCTC 11541 | | type material | 28080 28080 | catalase-negative or weak group of campylobacteria | | synonym | 28111 28111 | ATCC 27754 | | type material | 28111 28111 | Bacteroides eggerthii | | scientific name | 28111 28111 | Bacteroides eggerthii Holdeman and Moore 1974 | | authority | 28111 28111 | CCUG 9559 | | type material | 28111 28111 | CIP 104285 | | type material | 28111 28111 | DSM 20697 | | type material | 28111 28111 | JCM 12986 | | type material | 28111 28111 | NCTC 11155 | | type material | 28116 28116 | "Bacteroides fragilis subsp. ovatus" (Eggerth and Gagnon 1933) Holdeman and Moore 1970 | | authority | 28116 28116 | "Pasteurella ovata" (Eggerth and Gagnon 1933) Prevot 1938 | | authority | 28116 28116 | "Pseudobacterium ovatum" (Eggerth and Gagnon 1933) Krasil'nikov 1949 | | authority | 28116 28116 | ATCC 8483 | | type material | 28116 28116 | BCRC 10623 | | type material | 28116 28116 | Bacteroides fragilis subsp. ovatus | | synonym | 28116 28116 | Bacteroides ovatus | | scientific name | 28116 28116 | Bacteroides ovatus Eggerth and Gagnon 1933 | | authority | 28116 28116 | CCRC 10623 | | type material | 28116 28116 | CCUG 4943 | | type material | 28116 28116 | CIP 103756 | | type material | 28116 28116 | DSM 1896 | | type material | 28116 28116 | JCM 5824 | | type material | 28116 28116 | NCTC 11153 | | type material | 28116 28116 | Pasteurella ovata | | synonym | 28116 28116 | Pseudobacterium ovatum | | synonym | 28117 28117 | "Bacillus putredinis" Weinberg et al. 1937 | | authority | 28117 28117 | "Pseudobacterium putredinis" (Weinberg et al. 1937) Krasil'nikov 1949 | | authority | 28117 28117 | "Ristella putredinis" (Weinberg et al. 1937) Prevot 1938 | | authority | 28117 28117 | ATCC 29800 | | type material | 28117 28117 | Alistipes putredinis | | scientific name | 28117 28117 | Alistipes putredinis (Weinberg et al. 1937) Rautio et al. 2003 | | authority | 28117 28117 | Bacillus putredinis | | synonym | 28117 28117 | Bacteroides putredenis | | misspelling | 28117 28117 | Bacteroides putredinis | | synonym | 28117 28117 | Bacteroides putredinis (Weinberg et al. 1937) Kelly 1957 (Approved Lists 1980) | | authority | 28117 28117 | CCUG 45780 | | type material | 28117 28117 | CIP 104286 | | type material | 28117 28117 | DSM 17216 | | type material | 28117 28117 | JCM 16772 | | type material | 28117 28117 | Pseudobacterium putredinis | | synonym | 28117 28117 | Ristella putredinis | | synonym | 28124 28124 | ATCC 35406 | | type material | 28124 28124 | Bacteroides endodontalis | | synonym | 28124 28124 | Bacteroides endodontalis van Steenbergen et al. 1984 | | authority | 28124 28124 | DSM 24491 | | type material | 28124 28124 | JCM 8526 | | type material | 28124 28124 | NCTC 13058 | | type material | 28124 28124 | Porphyromonas endodontalis | | scientific name | 28124 28124 | Porphyromonas endodontalis (van Steenbergen et al. 1984) Shah and Collins 1988 | | authority | 28124 28124 | strain HG370 | | type material | 28127 28127 | ATCC 35310 | | type material | 28127 28127 | Bacteroides buccalis | | synonym | 28127 28127 | Bacteroides buccalis Shah and Collins 1982 | | synonym | 28127 28127 | CCUG 15557 | | type material | 28127 28127 | DSM 20616 | | type material | 28127 28127 | JCM 12246 | | type material | 28127 28127 | NCDO 2354 | | type material | 28127 28127 | NCTC 13064 | | type material | 28127 28127 | Prevotella buccalis | | scientific name | 28127 28127 | Prevotella buccalis (Shah and Collins 1982) Shah and Collins 1990 | | synonym | 28133 28133 | ATCC 33563 | | type material | 28133 28133 | CCUG 9560 | | type material | 28133 28133 | CIP 105552 | | type material | 28133 28133 | DSM 13386 | | type material | 28133 28133 | JCM 12250 | | type material | 28133 28133 | JCM 6322 | | type material | 28133 28133 | NCTC 9336 | | type material | 28133 28133 | Prevotella nigrescens | | scientific name | 28133 28133 | Prevotella nigrescens Shah and Gharbia 1992 | | authority | 28133 28133 | VPI 8944 | | type material | 28133 28133 | strain Lambe 729-74 | | type material | 28134 28134 | "Ristella oralis" (Loesche et al. 1964) Prevot et al. 1967 | | authority | 28134 28134 | ATCC 33269 | | type material | 28134 28134 | Bacteroides oralis | | synonym | 28134 28134 | Bacteroides oralis Loesche et al. 1964 (Approved Lists 1980) | | authority | 28134 28134 | CCUG 15408 | | type material | 28134 28134 | DSM 20702 | | type material | 28134 28134 | JCM 12251 | | type material | 28134 28134 | NCTC 11459 | | type material | 28134 28134 | Prevotella oralis | | scientific name | 28134 28134 | Prevotella oralis (Loesche et al. 1964) Shah and Collins 1990 | | authority | 28134 28134 | Ristella oralis | | synonym | 28134 28134 | VPI D27B-24 | | type material | 28135 28135 | ATCC 33573 | | type material | 28135 28135 | Bacteroides oris | | synonym | 28135 28135 | Bacteroides oris Holdeman et al. 1982 | | authority | 28135 28135 | CCUG 15405 | | type material | 28135 28135 | CIP 104480 | | type material | 28135 28135 | DSM 18711 | | type material | 28135 28135 | JCM 12252 | | type material | 28135 28135 | JCM 8540 | | type material | 28135 28135 | NCTC 13071 | | type material | 28135 28135 | Prevotella oris | | scientific name | 28135 28135 | Prevotella oris (Holdeman et al. 1982) Shah and Collins 1990 | | authority | 28135 28135 | VPI D1A-1A | | type material | 28137 28137 | ATCC 33779 | | type material | 28137 28137 | Bacteroides veroralis | | synonym | 28137 28137 | Bacteroides veroralis Watabe et al. 1983 | | authority | 28137 28137 | CCUG 15422 | | type material | 28137 28137 | JCM 6290 | | type material | 28137 28137 | Prevotella veroralis | | scientific name | 28137 28137 | Prevotella veroralis (Watabe et al. 1983) Shah and Collins 1990 emend. Wu et al. 1992 | | authority | 28137 28137 | VPI D22A-7 | | type material | 28197 28197 | ATCC 49616 | | type material | 28197 28197 | Arcibacter butzleri | | equivalent name | 28197 28197 | Arcobacter butzleri | | scientific name | 28197 28197 | Arcobacter butzleri (Kiehlbauch et al. 1991) Vandamme et al. 1992 | | authority | 28197 28197 | Arcobacter butzlerii | | misspelling | 28197 28197 | Arquibacter butzleri | | equivalent name | 28197 28197 | CCUG 30485 | | type material | 28197 28197 | CDC D2686 | | type material | 28197 28197 | CIP 103493 | | type material | 28197 28197 | CIP 103537 | | type material | 28197 28197 | Campylobacter butzleri | | synonym | 28197 28197 | Campylobacter butzleri Kiehlbauch et al. 1991 | | authority | 28197 28197 | DSM 8739 | | type material | 28197 28197 | LMG 10828 | | type material | 28197 28197 | NCTC 12481 | | type material | 28197 28197 | strain D2686 | | type material | 28211 28211 | "Alphabacteria" Cavalier-Smith 1992 | | authority | 28211 28211 | Alphabacteria | | synonym | 28211 28211 | Alphabacteria Cavalier-Smith 2002 | | authority | 28211 28211 | Alphaproteobacteria | | scientific name | 28211 28211 | Alphaproteobacteria Garrity et al. 2006 | | authority | 28211 28211 | Proteobacteria alpha subdivision | | synonym | 28211 28211 | Purple bacteria, alpha subdivision | | synonym | 28211 28211 | a-proteobacteria | alpha proteos | blast name | 28211 28211 | alpha proteobacteria | | synonym | 28211 28211 | alpha subdivision | | synonym | 28211 28211 | alpha subgroup | | synonym | 28449 28449 | "Micrococcus subflavus" Flugge 1886 | | authority | 28449 28449 | ATCC 49275 | | type material | 28449 28449 | CCUG 23930 | | type material | 28449 28449 | CIP 103343 | | type material | 28449 28449 | DSM 17610 | | type material | 28449 28449 | LMG 5313 | | type material | 28449 28449 | Micrococcus subflavus | | synonym | 28449 28449 | NRL 30,017 | | type material | 28449 28449 | Neisseria subflava | | scientific name | 28449 28449 | Neisseria subflava (Flugge 1886) Trevisan 1889 | | authority | 28449 28449 | strain U37 | | type material | 29321 29321 | ATCC 51513 | | type material | 29321 29321 | CCUG 32254 | | type material | 29321 29321 | CDC coryneform group ANF-1 like | | synonym | 29321 29321 | CIP 104075 | | type material | 29321 29321 | Corynebacterium otitidis | | synonym | 29321 29321 | DSM 8821 | | type material | 29321 29321 | JCM 12146 | | type material | 29321 29321 | LMG 19071 | | type material | 29321 29321 | Turicella otitidis | | scientific name | 29321 29321 | Turicella otitidis Funke et al. 1994 | | authority | 29321 29321 | strain 234/92 | | type material | 29347 29347 | ATCC 35704 | | type material | 29347 29347 | CIP 106687 | | type material | 29347 29347 | Clostridium scindens | | scientific name | 29347 29347 | Clostridium scindens Morris et al. 1985 | | authority | 29347 29347 | DSM 5676 | | type material | 29347 29347 | Eubacterium VPI-12708 | | includes | 29347 29347 | Eubacterium sp. (strain VPI 12708) | | includes | 29347 29347 | Eubacterium sp. VPI 12708 | | includes | 29347 29347 | Eubacterium sp. VPI-12708 | | includes | 29347 29347 | JCM 6567 | | type material | 29347 29347 | [Clostridium] scindens | | equivalent name | 29347 29347 | strain Bokkenheuser 19 | | type material | 29348 29348 | ATCC 29900 | | type material | 29348 29348 | CCUG 46510 | | type material | 29348 29348 | CIP 106966 | | type material | 29348 29348 | Clostridium spiroforme | | equivalent name | 29348 29348 | Clostridium spiroforme Kaneuchi et al. 1979 | | authority | 29348 29348 | DSM 1552 | | type material | 29348 29348 | JCM 1432 | | type material | 29348 29348 | NCTC 11211 | | type material | 29348 29348 | VPI C28-23-1A | | type material | 29348 29348 | [Clostridium] spiroforme | | scientific name | 29361 29361 | ATCC 27757 | | type material | 29361 29361 | Clostridium nexile | | scientific name | 29361 29361 | Clostridium nexile Holdeman and Moore 1974 | | authority | 29361 29361 | DSM 1787 | | type material | 29361 29361 | [Clostridium] nexile | | equivalent name | 29380 29380 | ATCC 35538 | | type material | 29380 29380 | CCM 3573 | | type material | 29380 29380 | CCUG 15604 | | type material | 29380 29380 | CIP 104000 | | type material | 29380 29380 | DSM 20608 | | type material | 29380 29380 | NCTC 12196 | | type material | 29380 29380 | NRRL B-14757 | | type material | 29380 29380 | Staphylococcus caprae | | scientific name | 29380 29380 | Staphylococcus caprae Devriese et al. 1983 emend. Kawamura et al. 1998 | | synonym | 29380 29380 | strain 143.22 | | type material | 29388 29388 | ATCC 27840 | | type material | 29388 29388 | CCM 2734 | | type material | 29388 29388 | CCUG 7326 | | type material | 29388 29388 | CIP 81.53 | | type material | 29388 29388 | DSM 20326 | | type material | 29388 29388 | JCM 2420 | | type material | 29388 29388 | LMG 13353 | | type material | 29388 29388 | NCTC 11045 | | type material | 29388 29388 | NRRL B-14752 | | type material | 29388 29388 | Staphylococcus capiti | | misspelling | 29388 29388 | Staphylococcus capitis | | scientific name | 29388 29388 | Staphylococcus capitis Kloos and Schleifer 1975 | | synonym | 29466 29466 | "Micrococcus gazogenes alcalescens anaerobius" Lewkowicz 1901 | | authority | 29466 29466 | "Micrococcus gazogenes" Hall and Howitt 1925 | | authority | 29466 29466 | "Micrococcus lactilyticus" Foubert and Douglas 1948 | | authority | 29466 29466 | "Staphylococcus parvulus" Veillon and Zuber 1898 | | authority | 29466 29466 | "Veillonella gazogenes" (Hall and Howitt 1925) Murray 1939 | | authority | 29466 29466 | ATCC 10790 | | type material | 29466 29466 | CCUG 5123 | | type material | 29466 29466 | DSM 2008 | | type material | 29466 29466 | JCM 12972 | | type material | 29466 29466 | Micrococcus gazogenes | | synonym | 29466 29466 | Micrococcus gazogenes alcalescens anaerobius | | synonym | 29466 29466 | Micrococcus lactilyticus | | synonym | 29466 29466 | NCTC 11810 | | type material | 29466 29466 | Staphylococcus parvulus | | synonym | 29466 29466 | Veillonella alcalescens | | synonym | 29466 29466 | Veillonella alcalescens Prevot 1933 | | authority | 29466 29466 | Veillonella gazogenes | | synonym | 29466 29466 | Veillonella parvula | | scientific name | 29466 29466 | Veillonella parvula (Veillon and Zuber 1898) Prevot 1933 (AL 1980) emend. Mays et al. 1982 | | authority | 29466 29466 | not "Micrococcus gazogenes" Choukevitch 1911 | | authority | 31631 31631 | HCoV-OC43 | | genbank acronym | 31631 31631 | Human coronavirus (strain OC43) | | synonym | 31631 31631 | Human coronavirus OC43 | | scientific name | 31631 31631 | Human coronavirus strain OC43 | | synonym | 31732 31732 | PWV | | acronym | 31732 31732 | Passion fruit woodiness potyvirus | | synonym | 31732 31732 | Passion fruit woodiness virus | | scientific name | 31732 31732 | Passionfruit woodiness virus | | synonym | 33030 33030 | "Micrococcus indolicus" Christiansen 1934 | | authority | 33030 33030 | "Schleiferella indolica" Rajendram et al. 2001 | | authority | 33030 33030 | ATCC 29427 | | type material | 33030 33030 | CCUG 17639 | | type material | 33030 33030 | CCUG 46591 | | type material | 33030 33030 | DSM 20464 | | type material | 33030 33030 | Micrococcus indolicus | | synonym | 33030 33030 | NCTC 11088 | | type material | 33030 33030 | Peptococcus indolicus | | synonym | 33030 33030 | Peptococcus indolicus (Christiansen 1934) Sorensen 1975 (Approved Lists 1980) | | authority | 33030 33030 | Peptoniphilus indolicus | | scientific name | 33030 33030 | Peptoniphilus indolicus (Christiansen 1934) Ezaki et al. 2001 | | authority | 33030 33030 | Peptostreptococcus indolicus | | synonym | 33030 33030 | Peptostreptococcus indolicus (Christiansen 1934) Ezaki et al. 1983 | | authority | 33030 33030 | Schleiferella indolica | | synonym | 33032 33032 | ATCC 51172 | | type material | 33032 33032 | Anaerococcus lactolyticus | | scientific name | 33032 33032 | Anaerococcus lactolyticus (Li et al. 1992) Ezaki et al. 2001 | | authority | 33032 33032 | CCUG 31351 | | type material | 33032 33032 | CIP 103725 | | type material | 33032 33032 | DSM 7456 | | type material | 33032 33032 | GIFU 8586 | | type material | 33032 33032 | JCM 8140 | | type material | 33032 33032 | Peptostreptococcus lactolyticus | | synonym | 33032 33032 | Peptostreptococcus lactolyticus Li et al. 1992 | | authority | 33033 33033 | "Streptococcus anaerobius micros" Lewkowicz 1901 | | authority | 33033 33033 | "Streptococcus micros" Prevot 1933 | | authority | 33033 33033 | 'Diplococcus glycinophilus' | | synonym | 33033 33033 | ATCC 33270 | | type material | 33033 33033 | CCUG 17638 | | type material | 33033 33033 | CCUG 17638 A | | type material | 33033 33033 | CCUG 46357 | | type material | 33033 33033 | CIP 105294 | | type material | 33033 33033 | DSM 20468 | | type material | 33033 33033 | Diplococcus glycinophilus | | synonym | 33033 33033 | JCM 12970 | | type material | 33033 33033 | KCTC 5196 | | type material | 33033 33033 | Micromonas micros | | misnomer | 33033 33033 | Micromonas micros (Prevot 1933) Murdoch and Shah 2000 | | authority | 33033 33033 | NCTC 11808 | | type material | 33033 33033 | Parvimonas micra | | scientific name | 33033 33033 | Parvimonas micra (Prevot 1933) Tindall and Euzeby 2006 | | authority | 33033 33033 | Peptococcus glycinophilus | | synonym | 33033 33033 | Peptostreptococcus micros | | synonym | 33033 33033 | Peptostreptococcus micros (Prevot 1933) Smith 1957 (Approved Lists 1980) | | authority | 33033 33033 | Streptococcus anaerobius micros | | synonym | 33033 33033 | Streptococcus micros | | synonym | 33033 33033 | strain 3119B | | type material | 33036 33036 | "Gaffkya anaerobius" (sic) (Choukevitch 1911) Prevot 1933 | | authority | 33036 33036 | "Tetracoccus anaerobius" Choukevitch 1911 | | authority | 33036 33036 | ATCC 35098 | | type material | 33036 33036 | Anaerococcus tetradius | | scientific name | 33036 33036 | Anaerococcus tetradius (Ezaki et al. 1983) Ezaki et al. 2001 | | authority | 33036 33036 | CCM 3634 | | type material | 33036 33036 | CCUG 17637 | | type material | 33036 33036 | CCUG 46590 | | type material | 33036 33036 | CIP 103927 | | type material | 33036 33036 | DSM 2951 | | type material | 33036 33036 | GIFU 7672 | | type material | 33036 33036 | Gaffkya anaerobius | | synonym | 33036 33036 | JCM 1964 | | type material | 33036 33036 | LMG 14264 | | type material | 33036 33036 | Peptostreptococcus tetradius | | synonym | 33036 33036 | Peptostreptococcus tetradius (ex Choukevitch 1911) Ezaki et al. 1983 | | authority | 33036 33036 | Tetracoccus anaerobius | | synonym | 33038 33038 | ATCC 29149 | | type material | 33038 33038 | Ruminococcus gnavus | | equivalent name | 33038 33038 | Ruminococcus gnavus Moore et al. 1976 | | authority | 33038 33038 | Ruminococcus gravus | | misspelling | 33038 33038 | VPI C7-9 | | type material | 33038 33038 | [Ruminococcus] gnavus | | scientific name | 33043 33043 | ATCC 27759 | | type material | 33043 33043 | Coprococcus eutactus | | scientific name | 33043 33043 | Coprococcus eutactus Holdeman and Moore 1974 | | synonym | 37372 37372 | ATCC 51630 | | type material | 37372 37372 | CCUG 38995 B | | type material | 37372 37372 | CIP 104752 | | type material | 37372 37372 | Flexispira rappini species 8 | | includes | 37372 37372 | Flexispira taxon 9 | | includes | 37372 37372 | Helicobacter bilis | | scientific name | 37372 37372 | Helicobacter bilis Fox et al. 1997 | | authority | 37372 37372 | Helicobacter sp. 'Flexispira taxon 2' | | includes | 37372 37372 | Helicobacter sp. 'Flexispira taxon 3' | | includes | 37372 37372 | Helicobacter sp. 'Flexispira taxon 8' | | includes | 37372 37372 | Helicobacter sp. 'Flexispira taxon 9' | | includes | 37372 37372 | Helicobacter sp. ATCC 43879 | | includes | 37372 37372 | Helicobacter sp. ATCC 49314 | | includes | 37372 37372 | Helicobacter sp. ATCC 49317 | | includes | 37372 37372 | Helicobacter sp. ATCC 49320 | | includes | 37372 37372 | strain Hb1 | strain Hb1 | type material | 38303 38303 | "Corynebacterium pseudogenitalium" Furness et al. 1979 | | synonym | 38303 38303 | Corynebacterium pseudogenitalium | | scientific name | 38304 38304 | "Corynebacterium tuberculostearicum" Brown et al. 1984 | | synonym | 38304 38304 | ATCC 35692 | | type material | 38304 38304 | CCUG 45418 | | type material | 38304 38304 | CIP 107291 | | type material | 38304 38304 | Corynebacterium sp. CIP101775 | | includes | 38304 38304 | Corynebacterium sp. CIP102076 | | includes | 38304 38304 | Corynebacterium sp. CIP102124 | | includes | 38304 38304 | Corynebacterium sp. CIP102211 | | includes | 38304 38304 | Corynebacterium sp. CIP102346 | | includes | 38304 38304 | Corynebacterium sp. CIP102590 | | includes | 38304 38304 | Corynebacterium sp. CIP102622 | | includes | 38304 38304 | Corynebacterium sp. CIP102645 | | includes | 38304 38304 | Corynebacterium sp. CIP102857 | | includes | 38304 38304 | Corynebacterium sp. CIP107067 | | includes | 38304 38304 | Corynebacterium sp. CIP107291 | | includes | 38304 38304 | Corynebacterium tuberculostearicum | | scientific name | 38304 38304 | Corynebacterium tuberculostearicum Feurer et al. 2004 | | synonym | 38304 38304 | DSM 44922 | | type material | 38304 38304 | JCM 13389 | | type material | 38304 38304 | strain LDC-20 | | type material | 38304 38304 | strain Medalle X | | type material | 39488 39488 | ATCC 27751 | | type material | 39488 39488 | DSM 3353 | | type material | 39488 39488 | Eubacterium halii | | misspelling | 39488 39488 | Eubacterium hallii | | scientific name | 39488 39488 | Eubacterium hallii Holdeman and Moore 1974 | | authority | 39488 39488 | VPI B4-27 | | type material | 39488 39488 | [Eubacterium] hallii | | equivalent name | 39496 39496 | "Bacillus ventriosus" Tissier 1908 | | authority | 39496 39496 | "Bacteroides ventriosus" (Tissier 1908) Eggerth 1935 | | authority | 39496 39496 | "Pseudobacterium ventriosum" (Tissier 1908) Krasil'nikov 1949 | | authority | 39496 39496 | ATCC 27560 | | type material | 39496 39496 | Bacillus ventriosus | | synonym | 39496 39496 | Bacteroides ventriosus | | synonym | 39496 39496 | DSM 3988 | | type material | 39496 39496 | Eubacterium ventriosum | | scientific name | 39496 39496 | Eubacterium ventriosum (Tissier 1908) Prevot 1938 | | authority | 39496 39496 | Pseudobacterium ventriosum | | synonym | 39496 39496 | [Eubacterium] ventriosum | | equivalent name | 39778 39778 | ATCC 17748 | | type material | 39778 39778 | DSM 20735 | | type material | 39778 39778 | NCTC 11831 | | type material | 39778 39778 | Veillonella alcalescens subsp. dispar | | synonym | 39778 39778 | Veillonella dispar | | scientific name | 39778 39778 | Veillonella dispar (Rogosa 1965) Mays et al. 1982 | | synonym | 40091 40091 | ATCC 51366 | | type material | 40091 40091 | CCUG 32213 | | type material | 40091 40091 | CIP 103932 | | type material | 40091 40091 | DSM 10548 | | type material | 40091 40091 | Helcococcus kunzii | | scientific name | 40091 40091 | Helcococcus kunzii Collins et al. 1993 | | authority | 40091 40091 | Helococcus kunzii | | misspelling | 40091 40091 | IFO 15552 | | type material | 40091 40091 | LMG 15123 | | type material | 40091 40091 | NBRC 15552 | | type material | 40091 40091 | NCFB 2900 | | type material | 40091 40091 | NCIMB 702900 | | type material | 40091 40091 | strain n. 22 | | type material | 40215 40215 | ATCC 17908 | | type material | 40215 40215 | Acinetobacter genomosp. 5 | | synonym | 40215 40215 | Acinetobacter genomospecies 5 | | synonym | 40215 40215 | Acinetobacter grimontii | | genbank synonym | 40215 40215 | Acinetobacter grimontii Carr et al. 2003 | | authority | 40215 40215 | Acinetobacter junii | | scientific name | 40215 40215 | Acinetobacter junii Bouvet and Grimont 1986 | | authority | 40215 40215 | CCUG 889 | | type material | 40215 40215 | CIP 64.5 | | type material | 40215 40215 | DSM 6964 | | type material | 40215 40215 | LMG 998 | | type material | 40215 40215 | NCTC 12153 | | type material | 40215 40215 | strain Mannheim 2723/59 | | type material | 40216 40216 | ATCC 43998 | | type material | 40216 40216 | Acinetobacter genomosp. 12 | | synonym | 40216 40216 | Acinetobacter genomospecies 12 | | synonym | 40216 40216 | Acinetobacter radiiresistens | | misspelling | 40216 40216 | Acinetobacter radioresistens | | scientific name | 40216 40216 | Acinetobacter radioresistens Nishimura et al. 1988 | | authority | 40216 40216 | CIP 103788 | | type material | 40216 40216 | DSM 6976 | | type material | 40216 40216 | IAM 13186 | | type material | 40216 40216 | JCM 9326 | | type material | 40216 40216 | LMG 10613 | | type material | 40216 40216 | NBRC 102413 | | type material | 40216 40216 | strain FO-1 | | type material | 40520 40520 | ATCC 29174 | | type material | 40520 40520 | DSM 25238 | | type material | 40520 40520 | Eubacterium obeum | | misspelling | 40520 40520 | Ruminococcus obeum | | equivalent name | 40520 40520 | Ruminococcus obeum Moore et al. 1976 | | authority | 40520 40520 | [Ruminococcus] obeum | | scientific name | 41294 41294 | 'Bradyrhizobiaceae' | | synonym | 41294 41294 | BANA domain | | synonym | 41294 41294 | Bradyrhizobiaceae | | scientific name | 41294 41294 | Bradyrhizobium group | | synonym | 41294 41294 | Nitrobacteraceae | | includes | 41294 41294 | Nitrobacteraceae Buchanan 1917 | | includes | 41294 41294 | Nitrobacteriaceae | | misspelling | 41294 41294 | alpha-2 proteobacteria | alpha-2 proteobacteria <2> | in-part | 42005 42005 | HEV | HEV <#2> | acronym | 42005 42005 | Hemagglutinating encephalomyelitis virus | | synonym | 42005 42005 | PHEV | | acronym | 42005 42005 | Porcine hemagglutinating encephalomyelitis coronavirus | | synonym | 42005 42005 | Porcine hemagglutinating encephalomyelitis virus | | scientific name | 42005 42005 | porcine hemagglutinating encephalomyelitis virus HEV | | misspelling | 42475 42475 | RRSV | | acronym | 42475 42475 | Rice ragged stunt virus | | scientific name | 42475 42475 | rice ragged stunt oryzavirus | | synonym | 43675 43675 | "Micrococcus mucilaginosus" Migula 1900 | | authority | 43675 43675 | ATCC 25296 | | type material | 43675 43675 | CCM 2417 | | type material | 43675 43675 | CCUG 20962 | | type material | 43675 43675 | CIP 71.14 | | type material | 43675 43675 | DSM 20746 | | type material | 43675 43675 | IFO 15673 | | type material | 43675 43675 | JCM 10910 | | type material | 43675 43675 | Micrococcus mucilaginosus | | synonym | 43675 43675 | NBRC 15673 | | type material | 43675 43675 | NCTC 10663 | | type material | 43675 43675 | Rothia mucilaginosa | | scientific name | 43675 43675 | Rothia mucilaginosa (Bergan and Kocur 1982) Collins et al. 2000 | | authority | 43675 43675 | Stomatococcus mucilaginosus | | synonym | 43675 43675 | Stomatococcus mucilaginosus (ex Migula 1900) Bergan and Kocur 1982 | | authority | 43765 43765 | 'Corynebacterium asperum' | | synonym | 43765 43765 | ATCC 49368 | | type material | 43765 43765 | CCUG 35685 | | type material | 43765 43765 | CDC coryneform group F-2 | | includes | 43765 43765 | CDC coryneform group I-2 | | includes | 43765 43765 | CIP 103452 | | type material | 43765 43765 | Corynebacterium amycolatum | | scientific name | 43765 43765 | Corynebacterium amycolatum Collins et al. 1988 | | synonym | 43765 43765 | Corynebacterium asperum | | synonym | 43765 43765 | DSM 6922 | | type material | 43765 43765 | IFO 15207 | | type material | 43765 43765 | JCM 7447 | | type material | 43765 43765 | NBRC 15207 | | type material | 43765 43765 | NCFB 2768 | | type material | 43765 43765 | NCIMB 13130 | | type material | 43765 43765 | strain S160 | | type material | 43768 43768 | "Actinomyces matruchoti" (Mendel 1919) Nannizzi 1934 | | synonym | 43768 43768 | "Cladothrix matruchoti" (sic) Mendel 1919 | | synonym | 43768 43768 | "Oospora matruchoti" (Mendel 1919) Sartory 1930 | | synonym | 43768 43768 | ATCC 14266 | | type material | 43768 43768 | Actinomyces matruchoti | | synonym | 43768 43768 | Bacterionema matruchotii | | synonym | 43768 43768 | Bacterionema matruchotii (Mendel 1919) Gilmour et al. 1961 (Approved Lists 1980) | | synonym | 43768 43768 | CCUG 27545 | | type material | 43768 43768 | CCUG 46620 | | type material | 43768 43768 | CIP 81.82 | | type material | 43768 43768 | Cladothrix matruchoti | | synonym | 43768 43768 | Corynebacterium matruchotii | | scientific name | 43768 43768 | Corynebacterium matruchotii (Mendel 1919) Collins 1983 | | synonym | 43768 43768 | DSM 20635 | | type material | 43768 43768 | IFO 15360 | | type material | 43768 43768 | JCM 9386 | | type material | 43768 43768 | NBRC 15360 | | type material | 43768 43768 | NCTC 10254 | | type material | 43768 43768 | Oospora matruchoti | | synonym | 43770 43770 | "Bacterium striatum" Chester 1901 | | synonym | 43770 43770 | ATCC 6940 | | type material | 43770 43770 | Bacterium striatum | | synonym | 43770 43770 | CCUG 27949 | | type material | 43770 43770 | CIP 81.15 | | type material | 43770 43770 | Corynebacterium striatum | | scientific name | 43770 43770 | Corynebacterium striatum (Chester 1901) Eberson 1918 | | synonym | 43770 43770 | DSM 20668 | | type material | 43770 43770 | IFO 15291 | | type material | 43770 43770 | JCM 9390 | | type material | 43770 43770 | NBRC 15291 | | type material | 43770 43770 | NCTC 764 | | type material | 44088 44088 | Avipoxvirus clade B1 | | synonym | 44088 44088 | Canarypox virus | | scientific name | 45851 45851 | ATCC 29175 | | type material | 45851 45851 | Butyrivibrio crossotus | | scientific name | 45851 45851 | Butyrivibrio crossotus Moore et al. 1976 | | synonym | 45851 45851 | DSM 2876 | | type material | 45851 45851 | VPI T9-40A | | type material | 46015 46015 | AcMNPV | | acronym | 46015 46015 | Autographa californica multicapsid nuclear polyhedrosis virus | | synonym | 46015 46015 | Autographa californica multicapsid nuclear polyhedrosis virus AcMNPV | | synonym | 46015 46015 | Autographa californica nuclear polyhedrosis virus | | synonym | 46015 46015 | Autographa californica nuclear polyhedrosis virus AcMNPV | | synonym | 46015 46015 | Autographa californica nuclear polyhedrosis virus AcNPV | | synonym | 46015 46015 | Autographa californica nuclear polyhedrosis virus, AcMNPV | | synonym | 46015 46015 | Autographa californica nucleopolyhedrovirus | | scientific name | 46503 46503 | ATCC 43184 | | type material | 46503 46503 | Bacteroides merdae | | synonym | 46503 46503 | Bacteroides merdae Johnson et al. 1986 | | authority | 46503 46503 | CCUG 38734 | | type material | 46503 46503 | CIP 104202 | | type material | 46503 46503 | JCM 9497 | | type material | 46503 46503 | NCTC 13052 | | type material | 46503 46503 | Parabacteroides merdae | | scientific name | 46503 46503 | Parabacteroides merdae (Johnson et al. 1986) Sakamoto and Benno 2006 | | authority | 46503 46503 | VPI T4-1 | | type material | 47229 47229 | CCUG 45783 | | type material | 47229 47229 | CIP 105350 | | type material | 47229 47229 | Janthinobacterium sp. R2-11 | | includes | 47229 47229 | Massilia timonae | | scientific name | 47229 47229 | Massilia timonae La Scola et al. 2000 emend. Lindquist et al. 2003 | | authority | 47229 47229 | Timone isolate | | synonym | 47229 47229 | strain UR/MT95 | | type material | 47671 47671 | ATCC 51599 | | type material | 47671 47671 | CCUG 34794 | | type material | 47671 47671 | CIP 106317 | | type material | 47671 47671 | DSM 11362 | | type material | 47671 47671 | Lautropia mirabilis | | scientific name | 47671 47671 | Lautropia mirabilis Gerner-Smidt et al. 1995 | | authority | 47671 47671 | NCTC 12852 | | type material | 47671 47671 | strain AB2188 | | type material | 47678 47678 | ATCC 43185 | | type material | 47678 47678 | Bacteroides caccae | | scientific name | 47678 47678 | Bacteroides caccae Johnson et al. 1986 | | authority | 47678 47678 | CCUG 38735 | | type material | 47678 47678 | CIP 104201 | | type material | 47678 47678 | DSM 19024 | | type material | 47678 47678 | JCM 9498 | | type material | 47678 47678 | NCTC 13051 | | type material | 47678 47678 | VPI 3452A | | type material | 49338 49338 | DSM 10664 | | type material | 49338 49338 | Desulfitobacterium frappieri | | synonym | 49338 49338 | Desulfitobacterium frappieri Bouchard et al. 1996 | | authority | 49338 49338 | Desulfitobacterium hafniense | | scientific name | 49338 49338 | Desulfitobacterium hafniense Christiansen and Ahring 1996 emend. Niggemyer et al. 2001 | | authority | 49338 49338 | anaerobic eubacterium PCP-1 | | includes | 49338 49338 | strain DCB-2 | | type material | 52226 52226 | ATCC 27723 | | type material | 52226 52226 | Bacteroides multiacidus Mitsuoka et al. 1974 (Approved Lists 1980) | | synonym | 52226 52226 | CCUG 21055 | | type material | 52226 52226 | CIP 107116 | | type material | 52226 52226 | DSM 20544 | | type material | 52226 52226 | JCM 2054 | | type material | 52226 52226 | Mitsuokella multacida | | scientific name | 52226 52226 | Mitsuokella multacida corrig. (Mitsuoka et al. 1974) Shah and Collins 1983 | | synonym | 52226 52226 | Mitsuokella multiacidus | | synonym | 52226 52226 | NCTC 10934 | | type material | 53443 53443 | Blautia hydrogenotrophica | | scientific name | 53443 53443 | Blautia hydrogenotrophica (Bernalier et al. 1997) Liu et al. 2008 | | authority | 53443 53443 | DSM 10507 | | type material | 53443 53443 | JCM 14656 | | type material | 53443 53443 | Ruminococcus hydrogenotrophicus | | synonym | 53443 53443 | Ruminococcus hydrogenotrophicus Bernalier et al. 1997 | | authority | 53443 53443 | strain S5a33 | | type material | 55565 55565 | Actinomyces graevenitzii | | scientific name | 55565 55565 | Actinomyces graevenitzii Pascual Ramos et al. 1997 | | authority | 55565 55565 | CCUG 27294 | | type material | 55565 55565 | CIP 105737 | | type material | 55565 55565 | DSM 15540 | | type material | 56774 56774 | Eubacterium infirmum | | equivalent name | 56774 56774 | Eubacterium infirmum Cheeseman et al. 1996 | | authority | 56774 56774 | Eubacterium sp. (strain W 1417) | | includes | 56774 56774 | NCTC 12940 | | type material | 56774 56774 | [Eubacterium] infirmum | | scientific name | 56946 56946 | ATCC 49717 | | type material | 56946 56946 | Afipia broomae | | misspelling | 56946 56946 | Afipia broomeae | | scientific name | 56946 56946 | Afipia broomeae Brenner et al. 1992 | | authority | 56946 56946 | CCUG 30458 | | type material | 56946 56946 | CIP 103517 | | type material | 56946 56946 | DSM 7327 | | type material | 56946 56946 | NCTC 12720 | | type material | 56946 56946 | strain B-91-007286 | | type material | 60133 60133 | AHN 10371 | | type material | 60133 60133 | ATCC 700821 | | type material | 60133 60133 | CCUG 39484 | | type material | 60133 60133 | CIP 105551 | | type material | 60133 60133 | DSM 18710 | | type material | 60133 60133 | JCM 11140 | | type material | 60133 60133 | NCTC 13042 | | type material | 60133 60133 | Prevotella intermedia / Prevotella nigrescens-like organism (PINLO) | | synonym | 60133 60133 | Prevotella pallens | | scientific name | 60133 60133 | Prevotella pallens Kononen et al. 1998 | | authority | 61171 61171 | ATCC 51649 | | type material | 61171 61171 | DSM 12042 | | type material | 61171 61171 | Eubacterium-like group S14 | | synonym | 61171 61171 | Holdemania filiformis | | scientific name | 61171 61171 | Holdemania filiformis Willems et al. 1997 | | synonym | 61171 61171 | strain J1-31B-1 | | type material | 68892 68892 | ATCC 700779 | | type material | 68892 68892 | CCUG 39817 | | type material | 68892 68892 | CIP 105949 | | type material | 68892 68892 | DSM 12492 | | type material | 68892 68892 | GTC 849 | | type material | 68892 68892 | JCM 10157 | | type material | 68892 68892 | LMG 18720 | | type material | 68892 68892 | Streptococcus infantis | | scientific name | 68892 68892 | Streptococcus infantis Kawamura et al. 1998 | | authority | 68892 68892 | strain O-122 | | type material | 69218 69218 | ATCC 33241 | | type material | 69218 69218 | CCUG 25231 | | type material | 69218 69218 | CDC Enteric Group 19 | | synonym | 69218 69218 | CFBP 4167 | | type material | 69218 69218 | CIP 103787 | | type material | 69218 69218 | DSM 17580 | | type material | 69218 69218 | Enterobacter cancerogenus | | scientific name | 69218 69218 | Enterobacter cancerogenus (Urosevic 1966) Dickey and Zumoff 1988 | | authority | 69218 69218 | Enterobacter taylorae | | synonym | 69218 69218 | Enterobacter taylorae Farmer et al. 1985 | | authority | 69218 69218 | Erwinia cancerogena | | synonym | 69218 69218 | Erwinia cancerogena Urosevic 1966 (Approved Lists 1980) | | authority | 69218 69218 | ICMP 5706 | | type material | 69218 69218 | LMG 2693 | | type material | 69218 69218 | NCPPB 2176 | | type material | 69823 69823 | "Spirillum sputigenum" Flugge 1886 | | authority | 69823 69823 | "Vibrio sputigenus" Prevot 1940 | | authority | 69823 69823 | ATCC 35185 | ATCC 35185 | type material | 69823 69823 | CCUG 44933 | CCUG 44933 | type material | 69823 69823 | DSM 20758 | DSM 20758 | type material | 69823 69823 | Selenomonas sputigena | | scientific name | 69823 69823 | Selenomonas sputigena (Flugge 1886) Boskamp 1922 (Approved Lists 1980) emend. Judicial Commission 1992 | | authority | 69823 69823 | Spirillum sputigenum | | synonym | 69823 69823 | VPI D 19B-28 | VPI D 19B-28 | type material | 69823 69823 | Vibrio sputigenus | | synonym | 72556 72556 | ATCC 43552 | | type material | 72556 72556 | Achromobacter piechaudii | | scientific name | 72556 72556 | Achromobacter piechaudii (Kiredjian et al. 1986) Yabuuchi et al. 1998 | | authority | 72556 72556 | Alcaligenes piechaudii | | synonym | 72556 72556 | Alcaligenes piechaudii Kiredjian et al. 1986 | | authority | 72556 72556 | CCUG 724 | | type material | 72556 72556 | CIP 60.75 | | type material | 72556 72556 | DSM 10342 | | type material | 72556 72556 | IAM 12591 | | type material | 72556 72556 | JCM 20668 | | type material | 72556 72556 | LMG 1873 | | type material | 72556 72556 | NBRC 102461 | | type material | 72556 72556 | NCTC 11970 | | type material | 72556 72556 | strain Hugh 366-5 | | type material | 74426 74426 | "Bacteroides aerofaciens" Eggerth 1935 | | synonym | 74426 74426 | "Pseudobacterium aerofaciens" (Eggerth 1935) Krasil'nikov 1949 | | synonym | 74426 74426 | ATCC 25986 | | type material | 74426 74426 | Bacteroides aerofaciens | | synonym | 74426 74426 | CCUG 28087 | | type material | 74426 74426 | Collinsella aerofaciens | | scientific name | 74426 74426 | Collinsella aerofaciens (Eggerth 1935) Kageyama et al. 1999 | | synonym | 74426 74426 | DSM 3979 | | type material | 74426 74426 | Eubacterium aerofaciens | | synonym | 74426 74426 | Eubacterium aerofaciens (Eggerth 1935) Prevot 1938 (Approved Lists 1980) | | synonym | 74426 74426 | JCM 10188 | | type material | 74426 74426 | NCTC 11838 | | type material | 74426 74426 | Pseudobacterium aerofaciens | | synonym | 74426 74426 | VPI 1003 | | type material | 76831 76831 | Myroides | | scientific name | 76831 76831 | Myroides Vancanneyt et al. 1996 emend. Yan et al. 2012 | | authority | 76832 76832 | CCUG 39352 | | type material | 76832 76832 | CIP 105170 | | type material | 76832 76832 | JCM 7460 | | type material | 76832 76832 | LMG 4029 | | type material | 76832 76832 | Myroides odoratimimus | | scientific name | 76832 76832 | Myroides odoratimimus Vancanneyt et al. 1996 | | authority | 76832 76832 | NCTC 11180 | | type material | 78342 78342 | AS 1.2274 | | type material | 78342 78342 | ATCC 49850 | | type material | 78342 78342 | Bifidobacterium gallicum | | scientific name | 78342 78342 | Bifidobacterium gallicum Lauer 1990 | | synonym | 78342 78342 | CCUG 34979 | | type material | 78342 78342 | CIP 103417 | | type material | 78342 78342 | DSM 20093 | | type material | 78342 78342 | JCM 8224 | | type material | 78342 78342 | LMG 11596 | | type material | 80366 80366 | NOT Rachiplusia nu MNPV | | equivalent name | 80366 80366 | Rachiplusia ou MNPV | | scientific name | 80366 80366 | Rachiplusia ou multiple nucleopolyhedrovirus | | synonym | 80366 80366 | Rachiplusia ou nuclear polyhedrosis virus | | synonym | 82135 82135 | ATCC BAA-55 | | type material | 82135 82135 | Atopobium vaginae | | scientific name | 82135 82135 | Atopobium vaginae Rodriguez Jovita et al. 1999 | | authority | 82135 82135 | CCUG 38953 | | type material | 82135 82135 | CIP 106431 | | type material | 82135 82135 | DSM 15829 | | type material | 84026 84026 | ATCC 43829 | | type material | 84026 84026 | Clostridium methylpentosum | | scientific name | 84026 84026 | Clostridium methylpentosum Himelbloom and Canale-Parola 1989 | | authority | 84026 84026 | DSM 5476 | | type material | 84026 84026 | [Clostridium] methylpentosum | | equivalent name | 84026 84026 | strain R2 | strain R2 | type material | 85698 85698 | "Achromobacter xylosoxidans" Yabuuchi and Ohyama 1971 | | authority | 85698 85698 | ATCC 27061 | | type material | 85698 85698 | Achromobacter xylosoxidans | | scientific name | 85698 85698 | Achromobacter xylosoxidans (ex Yabuuchi and Ohyama 1971) Yabuuchi and Yano 1981 | | authority | 85698 85698 | Achromobacter xylosoxidans KF701 | | includes | 85698 85698 | Achromobacter xylosoxidans subsp. xylosoxidans | | includes | 85698 85698 | Achromobacter xylosoxidans subsp. xylosoxidans (ex Yabuuchi & Ohyama 1971) Yabuuchi & Yano 1981 | | authority | 85698 85698 | Achromobacter xylosoxydans | | equivalent name | 85698 85698 | Alcaligenes denitrificans subsp. xylosoxydans | | includes | 85698 85698 | Alcaligenes denitrificans subsp. xylosoxydans (Yabuuchi and Yano 1981) Kersters and De Ley 1984 | | authority | 85698 85698 | Alcaligenes denitrificans xylosoxydans | | includes | 85698 85698 | Alcaligenes xylosoxidans | | synonym | 85698 85698 | Alcaligenes xylosoxidans (Yabuuchi and Yano 1981) Kiredjian et al. 1986 | | authority | 85698 85698 | Alcaligenes xylosoxidans subsp. xylosoxidans | | includes | 85698 85698 | Alcaligenes xylosoxidans subsp. xylosoxidans (Yabuuchi and Yano 1981) Kiredjian et al. 1986 | | authority | 85698 85698 | Alcaligenes xylosoxydans | | equivalent name | 85698 85698 | Alcaligenes xylosoxydans xylosoxydans | | includes | 85698 85698 | CCUG 12689 | | type material | 85698 85698 | CIP 71.32 | | type material | 85698 85698 | DSM 10346 | | type material | 85698 85698 | DSM 2402 | | type material | 85698 85698 | Flavobacterium sp. 650 | | includes | 85698 85698 | IFO 15126 | | type material | 85698 85698 | JCM 9659 | | type material | 85698 85698 | LMG 1863 | | type material | 85698 85698 | NBRC 15126 | | type material | 85698 85698 | NCTC 10807 | | type material | 85698 85698 | NRRL B-4082 | | type material | 85698 85698 | strain Hugh 2838 | | type material | 85698 85698 | strain KM 543 | | type material | 85698 85698 | strain Yabuuchi KM 543 | | type material | 89153 89153 | CIP 106689 | | type material | 89153 89153 | Clostridium hylemonae | | scientific name | 89153 89153 | Clostridium hylemonae Kitahara et al. 2000 | | authority | 89153 89153 | DSM 15053 | | type material | 89153 89153 | JCM 10539 | | type material | 89153 89153 | [Clostridium] hylemonae | | equivalent name | 89153 89153 | strain TN-271 | | type material | 91753 91753 | CABYV | | acronym | 91753 91753 | Cucurbit aphid borne yellowing virus | | misnomer | 91753 91753 | Cucurbit aphid-borne yellows virus | | scientific name | 101850 101850 | Thysanoplusia orichalcea MNPV | | synonym | 101850 101850 | Thysanoplusia orichalcea NPV | | synonym | 101850 101850 | Thysanoplusia orichalcea multicapsid nucleopolyhedrovirus | | synonym | 101850 101850 | Thysanoplusia orichalcea multiple nucleopolyhedrovirus | | synonym | 101850 101850 | Thysanoplusia orichalcea nucleopolyhedrovirus | | scientific name | 102148 102148 | Bulleidia moorei | | misspelling | 102148 102148 | CIP 106864 | | type material | 102148 102148 | JCM 10645 | | type material | 102148 102148 | Solobacterium moorei | | scientific name | 102148 102148 | Solobacterium moorei Kageyama and Benno 2000 | | authority | 102148 102148 | strain RCA59-74 | | type material | 102148 102148 | unclassified Clostridium group RCA59 | | synonym | 102862 102862 | ATCC 33519 | | type material | 102862 102862 | CCUG 15722 | | type material | 102862 102862 | CDC 1808-73 | | type material | 102862 102862 | CIP 103030 | | type material | 102862 102862 | DSM 4544 | | type material | 102862 102862 | JCM 3948 | | type material | 102862 102862 | NCTC 12737 | | type material | 102862 102862 | Proteus genomosp. 1 | | synonym | 102862 102862 | Proteus genomospecies 1 | | synonym | 102862 102862 | Proteus penneri | | scientific name | 102862 102862 | Proteus penneri Hickman et al. 1983 | | synonym | 102862 102862 | Proteus vulgaris biogroup 1 | | synonym | 102862 102862 | Proteus vulgaris indole negative | | synonym | 103618 103618 | Actinomyces coleocanis | | scientific name | 103618 103618 | Actinomyces coleocanis Hoyles et al. 2002 | | authority | 103618 103618 | Actinomyces sp. CCUG 41708 | | includes | 103618 103618 | CCUG 41708 | | type material | 103618 103618 | CIP 106873 | | type material | 103618 103618 | DSM 15436 | | type material | 103618 103618 | strain M343/98/2 | | type material | 103621 103621 | Actinomyces sp. CCUG 28744 | | includes | 103621 103621 | Actinomyces sp. CCUG 42029 | | equivalent name | 103621 103621 | Actinomyces urogenitalis | | scientific name | 103621 103621 | Actinomyces urogenitalis Nikolaitchouk et al. 2000 | | synonym | 103621 103621 | CCUG 38702 | | type material | 103621 103621 | CIP 106421 | | type material | 103621 103621 | DSM 15434 | | type material | 106588 106588 | "Bacillus capillosus" Tissier 1908 | | authority | 106588 106588 | "Pseudobacterium capillosum" (Tissier 1908) Krasil'nikov 1949 | | authority | 106588 106588 | "Ristella capillosa" (Tissier 1908) Prevot 1938 | | authority | 106588 106588 | ATCC 29799 | | type material | 106588 106588 | Bacillus capillosus | | synonym | 106588 106588 | Bacteroides capillosus | | synonym | 106588 106588 | Bacteroides capillosus (Tissier 1908) Kelly 1957 | | authority | 106588 106588 | CCUG 15402 A | | type material | 106588 106588 | DSM 23940 | | type material | 106588 106588 | Pseudobacterium capillosum | | synonym | 106588 106588 | Pseudoflavonifractor capillosus | | scientific name | 106588 106588 | Pseudoflavonifractor capillosus (Tissier 1908) Carlier et al. 2010 | | authority | 106588 106588 | Ristella capillosa | | synonym | 106588 106588 | VPI R2-29-1 | | type material | 112023 112023 | Streptococcus phage 7201 | | scientific name | 112023 112023 | Streptococcus thermophilus bacteriophage 7201 | | synonym | 113287 113287 | "Ramibacterium alactolyticum" Prevot and Taffanel 1942 | | authority | 113287 113287 | "Ramibacterium dentium" Vinzent and Reynes 1947 | | authority | 113287 113287 | "Ramibacterium pleuriticum" Prevot et al. 1947 | | authority | 113287 113287 | ATCC 23263 | | type material | 113287 113287 | CIP 106365 | | type material | 113287 113287 | DSM 3980 | | type material | 113287 113287 | Eubacterium alactolyticum | | synonym | 113287 113287 | Eubacterium alactolyticum (Prevot and Taffanel 1942) Holdeman and Moore 1970 (Approved Lists 1980) | | authority | 113287 113287 | JCM 6480 | | type material | 113287 113287 | Pseudoramibacter alactolyticus | | scientific name | 113287 113287 | Pseudoramibacter alactolyticus (Prevot and Taffanel 1942) Willems and Collins 1996 | | authority | 113287 113287 | Ramibacterium alactolyticum | | synonym | 113287 113287 | Ramibacterium dentium | | synonym | 113287 113287 | Ramibacterium pleuriticum | | synonym | 118748 118748 | ATCC BAA-170 | | type material | 118748 118748 | Bulleidia extructa | | scientific name | 118748 118748 | Bulleidia extructa Downes et al. 2000 | | synonym | 118748 118748 | DSM 13220 | | type material | 118748 118748 | strain W 1219 | | type material | 133448 133448 | ATCC 29935 | | type material | 133448 133448 | CCUG 30791 | | type material | 133448 133448 | CDC 460-61 | | type material | 133448 133448 | CIP 105016 | | type material | 133448 133448 | Citrobacter genomospecies 5 | | synonym | 133448 133448 | Citrobacter youngae | | scientific name | 133448 133448 | Citrobacter youngae Brenner et al. 1993 | | authority | 133448 133448 | DSM 17578 | | type material | 133448 133448 | GTC 1314 | | type material | 135083 135083 | ATCC 43541 | | type material | 135083 135083 | DSM 19578 | | type material | 135083 135083 | JCM 8546 | | type material | 135083 135083 | Selenomonas noxia | | scientific name | 135083 135083 | Selenomonas noxia Moore et al. 1987 | | authority | 135083 135083 | VPI D9B-5 | | type material | 136187 136187 | Equine coronavirus | | scientific name | 137732 137732 | ATCC 700633 | | type material | 137732 137732 | Abiotrophia elegans | | synonym | 137732 137732 | Abiotrophia elegans Roggenkamp et al. 1999 | | authority | 137732 137732 | Abiotrophia sp. B1333 | | includes | 137732 137732 | CCUG 38949 | | type material | 137732 137732 | CIP 105513 | | type material | 137732 137732 | DSM 11693 | | type material | 137732 137732 | Granulicatella elegans | | scientific name | 137732 137732 | Granulicatella elegans (Roggenkamp et al. 1999) Collins and Lawson 2000 | | authority | 137732 137732 | strain B1333 | | type material | 138119 138119 | Desulfitobacterium hafniense Y51 | | scientific name | 138119 138119 | Desulfitobacterium hafniense str. Y51 | | equivalent name | 138119 138119 | Desulfitobacterium hafniense strain Y51 | | equivalent name | 138119 138119 | Desulfitobacterium sp. Y51 | | equivalent name | 147207 147207 | CCUG 45296 | | type material | 147207 147207 | CIP 106914 | | type material | 147207 147207 | Collinsella group 2 | | synonym | 147207 147207 | Collinsella intestinalis | | scientific name | 147207 147207 | Collinsella intestinalis Kageyama and Benno 2000 | | synonym | 147207 147207 | Collinsella sp. RCA56-68 | | includes | 147207 147207 | Collinsella sp. RCA56-80 | | includes | 147207 147207 | DSM 13280 | | type material | 147207 147207 | JCM 10643 | | type material | 147207 147207 | strain RCA56-68 | | type material | 154046 154046 | CCUG 43506 | | type material | 154046 154046 | Clostridium hathewayi | | scientific name | 154046 154046 | Clostridium hathewayi Steer et al. 2002 | | authority | 154046 154046 | Clostridium sp. DSM 13479 | | includes | 154046 154046 | DSM 13479 | | type material | 154046 154046 | [Clostridium] hathewayi | | equivalent name | 154046 154046 | strain 1313 | | type material | 158877 158877 | ATCC 49455 | | type material | 158877 158877 | BCRC 12225 | | type material | 158877 158877 | CCRC 12225 | | type material | 158877 158877 | CIP 105435 | | type material | 158877 158877 | Enteric Group 45 | | synonym | 158877 158877 | JCM 2403 | | type material | 158877 158877 | Koserella trabulsii | | synonym | 158877 158877 | Koserella trabulsii Hickman-Brenner et al. 1985 | | authority | 158877 158877 | NBRC 102600 | | type material | 158877 158877 | NCTC 11966 | | type material | 158877 158877 | NIH 725-83 | | type material | 158877 158877 | Yokenella regensburgei | | scientific name | 158877 158877 | Yokenella regensburgei Kosako et al. 1985 | | authority | 161889 161889 | ATCC 700352 | | type material | 161889 161889 | CCUG 37336 | | type material | 161889 161889 | CIP 105127 | | type material | 161889 161889 | Corynebacterium lipophiloflavum | | scientific name | 161889 161889 | Corynebacterium lipophiloflavum Funke et al. 1997 | | synonym | 161889 161889 | Corynebacterium sp. 1944 | | includes | 161889 161889 | DMMZ 1944 | | type material | 161889 161889 | DSM 44291 | | type material | 161889 161889 | JCM 10383 | | type material | 163665 163665 | CCUG 43457 | | type material | 163665 163665 | CDC F9489 | | type material | 163665 163665 | CIP 107079 | | type material | 163665 163665 | Dysgonomonas mossii | | scientific name | 163665 163665 | Dysgonomonas mossii Lawson et al. 2002 | | authority | 163665 163665 | Dysgonomonas shahii | | misspelling | 163665 163665 | JCM 16699 | | type material | 168384 168384 | Bryantella formatexigens | | synonym | 168384 168384 | Bryantella formatexigens Wolin et al. 2004 | | authority | 168384 168384 | CCUG 46960 | | type material | 168384 168384 | DSM 14469 | | type material | 168384 168384 | Marvinbryantia formatexigens | | scientific name | 168384 168384 | Marvinbryantia formatexigens (Wolin et al. 2004) Wolin et al. 2008 | | authority | 168384 168384 | strain I-52 | | type material | 169435 169435 | Anaerotruncus colihominis | | scientific name | 169435 169435 | Anaerotruncus colihominis Lawson et al. 2004 | | synonym | 169435 169435 | CCUG 45055 | | type material | 169435 169435 | CIP 107754 | | type material | 169435 169435 | DSM 17241 | | type material | 169435 169435 | JCM 15631 | | type material | 169435 169435 | Ruminococcus sp. 14565 | | includes | 169435 169435 | WAL 14565 | | type material | 171549 171549 | "Bacteroidales" Krieg 2011 | | authority | 171549 171549 | Bacteroidales | | scientific name | 177972 177972 | CCUG 45864 | | type material | 177972 177972 | DSM 14600 | | type material | 177972 177972 | Shuttleworthia satelles | | scientific name | 177972 177972 | Shuttleworthia satelles Downes et al. 2002 | | authority | 177972 177972 | VPI D143K-13 | | type material | 181082 181082 | EhV-86 | | acronym | 181082 181082 | Emiliana huxleyi virus 86 | | misspelling | 181082 181082 | Emiliania huxleyi virus 86 | | scientific name | 186802 186802 | Clostridiales | | scientific name | 186802 186802 | Clostridiales Prevot 1953 | | authority | 186803 186803 | Lachnospiraceae | | scientific name | 186803 186803 | Lachnospiraceae Rainey 2010 | | authority | 189723 189723 | CCUG 56105 | | type material | 189723 189723 | DSM 21469 | | type material | 189723 189723 | JCM 16134 | | type material | 189723 189723 | Prevotella genomosp. E3 | | synonym | 189723 189723 | Prevotella genomospecies E3 | | synonym | 189723 189723 | Prevotella micans | | scientific name | 189723 189723 | Prevotella micans Downes et al. 2009 | | authority | 189723 189723 | Prevotella sp. E7.56 | | includes | 189723 189723 | Prevotella sp. E7_56 | | misspelling | 189723 189723 | strain E7.56 | | type material | 195099 195099 | Campylobacter jejuni RM1221 | | scientific name | 195099 195099 | Campylobacter jejuni str. RM1221 | | equivalent name | 195099 195099 | Campylobacter jejuni strain RM1221 | | equivalent name | 199310 199310 | Escherichia coli CFT073 | | scientific name | 199310 199310 | Escherichia coli str. CFT073 | | equivalent name | 199310 199310 | Escherichia coli strain CFT073 | | equivalent name | 204525 204525 | ATCC 49957 | | type material | 204525 204525 | CIP 104027 | | type material | 204525 204525 | Roseomonas cervicalis | | scientific name | 204525 204525 | Roseomonas cervicalis Rihs et al. 1998 | | synonym | 204525 204525 | strain E7107 | | type material | 207244 207244 | Anaerostipes | | scientific name | 207244 207244 | Anaerostipes Schwiertz et al. 2002 emend. Eeckhaut et al. 2010 | | authority | 211110 211110 | Streptococcus agalactiae NEM316 | | scientific name | 211110 211110 | Streptococcus agalactiae str. NEM316 | | synonym | 214853 214853 | ATCC BAA-858 | | type material | 214853 214853 | Anaerofustis stercorihominis | | scientific name | 214853 214853 | Anaerofustis stercorihominis Finegold et al 2004 | | synonym | 214853 214853 | CCUG 47767 | | type material | 214853 214853 | DSM 17244 | | type material | 214853 214853 | Pseudoramibacter sp. wal 14563 | | includes | 214853 214853 | WAL 14563 | | type material | 218538 218538 | CCUG 47026 | | type material | 218538 218538 | DSM 15470 | | type material | 218538 218538 | Dialister invisus | | scientific name | 218538 218538 | Dialister invisus Downes et al. 2003 | | authority | 218538 218538 | JCM 17566 | | type material | 218538 218538 | strain E7.25 | | type material | 219314 219314 | Aeromicrobium marinum | | scientific name | 219314 219314 | Aeromicrobium marinum Bruns et al. 2003 | | authority | 219314 219314 | DSM 15272 | | type material | 219314 219314 | JCM 13314 | | type material | 219314 219314 | LMG 21768 | | type material | 225324 225324 | ATCC 27094 | | type material | 225324 225324 | Enhydrobacter aerosaccus | | scientific name | 225324 225324 | Enhydrobacter aerosaccus Staley et al. 1987 | | synonym | 225324 225324 | LMG 21877 | | type material | 228604 228604 | DSM 15606 | | type material | 228604 228604 | JCM 12084 | | type material | 228604 228604 | Prevotella salivae | | scientific name | 228604 228604 | Prevotella salivae Sakamoto et al. 2004 | | authority | 228604 228604 | strain EPSA11 | | type material | 243275 243275 | Treponema denticola ATCC 35405 | | scientific name | 243275 243275 | Treponema denticola str. ATCC 35405 | | equivalent name | 245018 245018 | Clostridiales bacterium SSC/2 | | synonym | 245018 245018 | Clostridiales sp. SSC/2 | | misspelling | 245018 245018 | butyrate-producing bacterium SSC/2 | | scientific name | 262177 262177 | OpMNPV | | acronym | 262177 262177 | Orgya pseudotsugata MNPV | | misspelling | 262177 262177 | Orgya pseudotsugata nucleopolyhedrovirus | | synonym | 262177 262177 | Orgyia pseudotsugata MNPV | | synonym | 262177 262177 | Orgyia pseudotsugata multicapsid nuclear polyhedrosis virus | | synonym | 262177 262177 | Orgyia pseudotsugata multicapsid nuclear polyhedrosis virus OpMNPV | | synonym | 262177 262177 | Orgyia pseudotsugata multicapsid nucleopolyhedrovirus | | synonym | 262177 262177 | Orgyia pseudotsugata multicapsid polyhedrosis virus | | synonym | 262177 262177 | Orgyia pseudotsugata multinucleocapsid nuclear polyhedrosis virus | | synonym | 262177 262177 | Orgyia pseudotsugata multiple nucleopolyhedrovirus | | scientific name | 282402 282402 | DSM 16608 | | type material | 282402 282402 | JCM 12541 | | type material | 282402 282402 | Prevotella multiformis | | scientific name | 282402 282402 | Prevotella multiformis Sakamoto et al. 2005 | | authority | 282402 282402 | strain PPPA21 | | type material | 290028 290028 | CoV-HKU1 | | synonym | 290028 290028 | HCoV-HKU1 | | genbank acronym | 290028 290028 | Human CoV/HKU1 | | synonym | 290028 290028 | Human coronavirus HKU1 | | scientific name | 291644 291644 | ATCC BAA-997 | | type material | 291644 291644 | Bacteroides salyersae | | synonym | 291644 291644 | Bacteroides salyersiae | | scientific name | 291644 291644 | Bacteroides salyersiae corrig. Song et al. 2005 | | authority | 291644 291644 | Bacteroides sp. WAL 10018 | | includes | 291644 291644 | CCUG 48945 | | type material | 291644 291644 | DSM 18765 | | type material | 291644 291644 | JCM 12988 | | type material | 291644 291644 | WAL 10018 | | type material | 291645 291645 | ATCC BAA-998 | | type material | 291645 291645 | Bacteroides nordii | | scientific name | 291645 291645 | Bacteroides nordii Song et al. 2005 | | authority | 291645 291645 | Bacteroides sp. WAL 11050 | | includes | 291645 291645 | CCUG 48943 | | type material | 291645 291645 | JCM 12987 | | type material | 291645 291645 | WAL 11050 | | type material | 292800 292800 | "Bacille de Plaut, Kritchevsky and Seguin 1921" | | authority | 292800 292800 | "Bacillus plauti" (sic) Seguin 1928 | | authority | 292800 292800 | "Fusocillus plauti" (sic) (Seguin 1928) Prevot 1938 | | authority | 292800 292800 | "Zuberella plauti" (sic) (Seguin 1928) Sebald 1962 | | authority | 292800 292800 | ATCC 29863 | | type material | 292800 292800 | ATCC 49531 [[Clostridium orbiscindens]] | | type material | 292800 292800 | Bacillus plauti | | synonym | 292800 292800 | CCUG 28093 | | type material | 292800 292800 | Clostridium orbiscindens | | synonym | 292800 292800 | Clostridium orbiscindens Winter et al. 1991 | | authority | 292800 292800 | DSM 4000 | | type material | 292800 292800 | DSM 6740 [[Clostridium orbiscindens]] | | type material | 292800 292800 | DSM 6749 [[Clostridium orbiscindens]] | | type material | 292800 292800 | Eubacterium plautii | | synonym | 292800 292800 | Eubacterium plautii (Seguin 1928) Hofstad and Aasjord 1982 | | authority | 292800 292800 | Flavonifractor plautii | | scientific name | 292800 292800 | Flavonifractor plautii (Seguin 1928) Carlier et al. 2010 | | authority | 292800 292800 | Fusobacterium plautii | | synonym | 292800 292800 | Fusobacterium plautii corrig. Seguin 1928 (Approved Lists 1980) | | authority | 292800 292800 | Fusocillus plauti | | synonym | 292800 292800 | Zuberella plauti | | synonym | 293178 293178 | Enterobacteria phage JS98 | | scientific name | 295405 295405 | Bacteroides fragilis YCH46 | | scientific name | 295405 295405 | Bacteroides fragilis str. YCH46 | | equivalent name | 295405 295405 | Bacteroides fragilis strain YCH46 | | equivalent name | 310297 310297 | Bacteroides plebeius | | scientific name | 310297 310297 | Bacteroides plebeius Kitahara et al. 2005 | | authority | 310297 310297 | DSM 17135 | | type material | 310297 310297 | JCM 12973 | | type material | 310297 310297 | strain M12 | strain M12 | type material | 312008 312008 | Citrus sudden death marafivirus | | synonym | 312008 312008 | Citrus sudden death-associated virus | | scientific name | 328812 328812 | ATCC BAA-1180 | | type material | 328812 328812 | Bacteroides goldsteinii | | synonym | 328812 328812 | Bacteroides goldsteinii Song et al. 2006 | | authority | 328812 328812 | Bacteroides sp. WAL 12034 | | includes | 328812 328812 | CCUG 48944 | | type material | 328812 328812 | DSM 19448 | | type material | 328812 328812 | JCM 13446 | | type material | 328812 328812 | Parabacteroides goldsteinii | | scientific name | 328812 328812 | Parabacteroides goldsteinii (Song et al. 2006) Sakamoto and Benno 2006 | | authority | 328812 328812 | WAL 12034 | | type material | 331278 331278 | Bacteriophage phiR1-37 | | synonym | 331278 331278 | Yersinia phage phiR1-37 | | scientific name | 331278 331278 | Yersiniophage phiR1-37 | | synonym | 334390 334390 | Lactobacillus fermentum IFO 3956 | | scientific name | 334390 334390 | Lactobacillus fermentum IFO3956 | | misspelling | 334390 334390 | Lactobacillus fermentum NBRC 3956 | | synonym | 334390 334390 | Lactobacillus fermentum str. IFO 3956 | | equivalent name | 334390 334390 | Lactobacillus fermentum strain IFO 3956 | | equivalent name | 338188 338188 | Bacteroides finegoldii | | scientific name | 338188 338188 | Bacteroides finegoldii Bakir et al. 2006 | | authority | 338188 338188 | DSM 17565 | | type material | 338188 338188 | JCM 13345 | | type material | 338188 338188 | strain 199 | | type material | 354276 354276 | Enterobacter cloacae complex | | scientific name | 357276 357276 | Bacteroides dorei | | scientific name | 357276 357276 | Bacteroides dorei Bakir et al. 2006 | | authority | 357276 357276 | Bacteroides sp. 175T | | includes | 357276 357276 | Bacteroides sp. 219 | | includes | 357276 357276 | DSM 17855 | | type material | 357276 357276 | JCM 13471 | | type material | 357276 357276 | strain 175 | | type material | 362663 362663 | Escherichia coli 536 | | scientific name | 362663 362663 | Escherichia coli str. 536 | | equivalent name | 362663 362663 | Escherichia coli strain 536 | | equivalent name | 363265 363265 | DSM 18206 | | type material | 363265 363265 | JCM 13469 | | type material | 363265 363265 | Prevotella sp. CB35 | | includes | 363265 363265 | Prevotella stercorea | | scientific name | 363265 363265 | Prevotella stercorea Hayashi et al. 2007 | | authority | 363265 363265 | strain CB35 | | type material | 365048 365048 | Bacteriophage GBSV1 | | synonym | 365048 365048 | Geobacillus phage GBSV1 | | scientific name | 371601 371601 | Bacteroides xylanisolvens | | scientific name | 371601 371601 | Bacteroides xylanisolvens Chassard et al. 2008 | | authority | 371601 371601 | CCUG 53782 | | type material | 371601 371601 | DSM 18836 | | type material | 371601 371601 | JCM 15633 | | type material | 371601 371601 | strain XB1A | | type material | 375288 375288 | Parabacteroides | | scientific name | 375288 375288 | Parabacteroides Sakamoto and Benno 2006 | | authority | 379891 379891 | Plutella xylostella multiple nucleopolyhedrovirus | | scientific name | 387661 387661 | DSM 18315 | | type material | 387661 387661 | JCM 13406 | | type material | 387661 387661 | Parabacteroides johnsonii | | scientific name | 387661 387661 | Parabacteroides johnsonii Sakamoto et al. 2007 | | authority | 387661 387661 | strain M-165 | | type material | 400667 400667 | Acinetobacter baumannii ATCC 17978 | | scientific name | 400667 400667 | Acinetobacter baumannii str. ATCC 17978 | | equivalent name | 400667 400667 | Acinetobacter baumannii strain ATCC 17978 | | equivalent name | 409438 409438 | Escherichia coli SE11 | | scientific name | 409438 409438 | Escherichia coli str. SE11 | | equivalent name | 409438 409438 | Escherichia coli strain SE11 | | equivalent name | 410072 410072 | ATCC 27758 | | type material | 410072 410072 | Coprococcus comes | | scientific name | 410072 410072 | Coprococcus comes Holdeman and Moore 1974 | | authority | 410072 410072 | VPI C1-38 | | type material | 420247 420247 | Methanobrevibacter smithii ATCC 35061 | | scientific name | 420247 420247 | Methanobrevibacter smithii DSM 861 | | synonym | 420247 420247 | Methanobrevibacter smithii PS | | synonym | 420247 420247 | Methanobrevibacter smithii str. ATCC 35061 | | equivalent name | 420247 420247 | Methanobrevibacter smithii strain ATCC 35061 | | equivalent name | 435590 435590 | Bacteroides vulgatus ATCC 8482 | | scientific name | 435590 435590 | Bacteroides vulgatus str. ATCC 8482 | | equivalent name | 435590 435590 | Bacteroides vulgatus strain ATCC 8482 | | equivalent name | 437897 437897 | DSM 19343 | | type material | 437897 437897 | JCM 14723 | | type material | 437897 437897 | Megamonas funiformis | | scientific name | 437897 437897 | Megamonas funiformis Sakon et al. 2008 | | authority | 437897 437897 | YIT 11815 | | type material | 437898 437898 | DSM 19354 | | type material | 437898 437898 | JCM 14724 | | type material | 437898 437898 | Sutterella parvirubra | | scientific name | 437898 437898 | Sutterella parvirubra Sakon et al. 2008 | | authority | 437898 437898 | YIT 11816 | | type material | 479436 479436 | Veillonella parvula DSM 2008 | | scientific name | 479436 479436 | Veillonella parvula str. DSM 2008 | | equivalent name | 479436 479436 | Veillonella parvula strain DSM 2008 | | equivalent name | 487173 487173 | DSM 21274 | | type material | 487173 487173 | Dialister succinatiphilus | | scientific name | 487173 487173 | Dialister succinatiphilus Morotomi et al. 2008 | | authority | 487173 487173 | JCM 15077 | | type material | 487173 487173 | YIT 11850 | | type material | 487174 487174 | Barnesiella intestinihominis | | scientific name | 487174 487174 | Barnesiella intestinihominis Morotomi et al. 2008 | | authority | 487174 487174 | Barnesiella sp. YIT 11860 | | includes | 487174 487174 | DSM 21032 | | type material | 487174 487174 | JCM 15079 | | type material | 487174 487174 | YIT 11860 | | type material | 487175 487175 | DSM 21040 | | type material | 487175 487175 | JCM 15078 | | type material | 487175 487175 | Parasutterella excrementihominis | | scientific name | 487175 487175 | Parasutterella excrementihominis Nagai et al. 2009 | | authority | 487175 487175 | strain YIT 11859 | | type material | 502102 502102 | Rat coronavirus Parker | | scientific name | 502102 502102 | Rat coronavirus strain Parker | | synonym | 502105 502105 | Bovine respiratory coronavirus bovine/US/OH-440-TC/1996 | | scientific name | 502108 502108 | Bovine respiratory coronavirus AH187 | | scientific name | 525146 525146 | Desulfovibrio desulfuricans subsp. desulfuricans ATCC 27774 | | equivalent name | 525146 525146 | Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774 | | scientific name | 525146 525146 | Desulfovibrio desulfuricans subsp. desulfuricans strain ATCC 27774 | | equivalent name | 548476 548476 | Corynebacterium aurimucosum ATCC 700975 | | scientific name | 548476 548476 | Corynebacterium aurimucosum CCUG 48176 | | synonym | 548476 548476 | Corynebacterium aurimucosum CIP 107436 | | synonym | 548476 548476 | Corynebacterium aurimucosum CN-1 | | synonym | 548476 548476 | Corynebacterium aurimucosum DSM 44827 | | synonym | 548476 548476 | Corynebacterium aurimucosum str. ATCC 700975 | | equivalent name | 548476 548476 | Corynebacterium aurimucosum strain ATCC 700975 | | equivalent name | 548476 548476 | Corynebacterium nigricans CN-1 | | synonym | 548479 548479 | Falcivibrio vaginalis ATCC 43063 | | synonym | 548479 548479 | Mobiluncus curtisii ATCC 43063 | | scientific name | 548479 548479 | Mobiluncus curtisii str. ATCC 43063 | | equivalent name | 548479 548479 | Mobiluncus curtisii strain ATCC 43063 | | equivalent name | 553199 553199 | Propionibacterium acnes SK137 | | scientific name | 553199 553199 | Propionibacterium acnes str. SK137 | | equivalent name | 553199 553199 | Propionibacterium acnes strain SK137 | | equivalent name | 573174 573174 | Vibrio phage henriette 12B8 | | scientific name | 573174 573174 | Vibriophage henriette 12B8 | | synonym | 576790 576790 | Enterobacteria phage JS10 | | scientific name | 607711 607711 | CIP 109934 | | type material | 607711 607711 | DSM 22247 | | type material | 607711 607711 | Neisseria sp. WC 05-2507 | | includes | 607711 607711 | Neisseria wadsworthii | | scientific name | 607711 607711 | Neisseria wadsworthii Wolfgang et al. 2011 | | authority | 607711 607711 | WC 05-9715 | | type material | 607711 607711 | strain 9715 | | type material | 607712 607712 | CIP 109933 | | type material | 607712 607712 | DSM 22246 | | type material | 607712 607712 | Neisseria shayeganii | | scientific name | 607712 607712 | Neisseria shayeganii Wolfgang et al. 2011 | | authority | 607712 607712 | Neisseria sp. WC 04-12337 | | includes | 607712 607712 | WC 08-871 | | type material | 607712 607712 | strain 871 | | type material | 626930 626930 | Bacteroides fluxus | | scientific name | 626930 626930 | Bacteroides fluxus Watanabe et al. 2010 | | authority | 626930 626930 | DSM 22534 | | type material | 626930 626930 | JCM 16101 | | type material | 626930 626930 | YIT 12057 | | type material | 626932 626932 | Alistipes indistinctus | | scientific name | 626932 626932 | Alistipes indistinctus Nagai et al. 2010 | | authority | 626932 626932 | DSM 22520 | | type material | 626932 626932 | JCM 16068 | | type material | 626932 626932 | YIT 12060 | | type material | 626933 626933 | DSM 22474 | | type material | 626933 626933 | JCM 16069 | | type material | 626933 626933 | Odoribacter laneus | | scientific name | 626933 626933 | Odoribacter laneus Nagai et al. 2010 | | authority | 626933 626933 | YIT 12061 | | type material | 626940 626940 | "Phascolarctobacterium succinatutens" Watanabe et al. 2012 | | authority | 626940 626940 | DSM 22533 | | type material | 626940 626940 | JCM 16074 | | type material | 626940 626940 | Phascolarctobacterium sp. YIT 12068 | | includes | 626940 626940 | Phascolarctobacterium succinatutens | | scientific name | 626940 626940 | YIT 12067 | | type material | 626962 626962 | Olive latent virus 3 | | scientific name | 627439 627439 | Human enteric coronavirus strain 4408 | | scientific name | 633135 633135 | Streptococcus phage Abc2 | | scientific name | 633135 633135 | Streptococcus thermophilus phage Abc2 | | synonym | 634176 634176 | Aggregatibacter aphrophilus NJ8700 | | scientific name | 634176 634176 | Aggregatibacter aphrophilus str. NJ8700 | | equivalent name | 634176 634176 | Aggregatibacter aphrophilus strain NJ8700 | | equivalent name | 646413 646413 | Streptococcus phage 5093 | | scientific name | 646413 646413 | Streptococcus thermophilus phage 5093 | | synonym | 663954 663954 | Streptococcus dysgalactiae subsp. equisimilis ATCC 12394 | | scientific name | 663954 663954 | Streptococcus dysgalactiae subsp. equisimilis str. ATCC 12394 | | equivalent name | 663954 663954 | Streptococcus dysgalactiae subsp. equisimilis strain ATCC 12394 | | equivalent name | 694569 694569 | Aggregatibacter actinomycetemcomitans D7S-1 | | scientific name | 694569 694569 | Aggregatibacter actinomycetemcomitans str. D7S-1 | | equivalent name | 694569 694569 | Aggregatibacter actinomycetemcomitans strain D7S-1 | | equivalent name | 697227 697227 | Enterobacteria phage IME08 | | scientific name | 751585 751585 | Coprococcus sp. ART55/1 | | scientific name | 754037 754037 | Cyanophage S-CAM1 | | synonym | 754037 754037 | Synechococcus phage S-CAM1 | | scientific name | 754064 754064 | Ostreococcus lucimarinus virus OlV5 | | scientific name | 759851 759851 | 'Sporosarcina newyorkensis' | | synonym | 759851 759851 | CCUG 59649 | | type material | 759851 759851 | DSM 23544 | | type material | 759851 759851 | LMG 26022 | | type material | 759851 759851 | Sporosarcina newyorkensis | | scientific name | 759851 759851 | Sporosarcina sp. 1655 | | includes | 759851 759851 | Sporosarcina sp. 3418 | | includes | 759851 759851 | Sporosarcina sp. 4331 | | includes | 759851 759851 | Sporosarcina sp. 4469 | | includes | 759851 759851 | Sporosarcina sp. 4974 | | includes | 759851 759851 | Sporosarcina sp. 4984 | | includes | 759851 759851 | Sporosarcina sp. 5353 | | includes | 759851 759851 | Sporosarcina sp. 57 | | includes | 759851 759851 | Sporosarcina sp. 5868 | | includes | 759851 759851 | Sporosarcina sp. 6062 | | includes | 759851 759851 | Sporosarcina sp. R-31323 | | includes | 759851 759851 | strain 6062 | | type material | 760732 760732 | Acinetobacter phage Acj61 | | scientific name | 796942 796942 | 'Stomatobaculum longum' | | synonym | 796942 796942 | Lachnospiraceae bacterium ACC2 | | includes | 796942 796942 | Stomatobaculum longum | | scientific name | 908937 908937 | Prevotella dentalis ATCC 49559 | | synonym | 908937 908937 | Prevotella dentalis DSM 3688 | | scientific name | 908937 908937 | Prevotella dentalis JCM 13448 | | synonym | 908937 908937 | Prevotella dentalis str. DSM 3688 | | equivalent name | 908937 908937 | Prevotella dentalis strain DSM 3688 | | equivalent name | 927666 927666 | Streptococcus oralis Uo5 | | scientific name | 927666 927666 | Streptococcus oralis str. Uo5 | | equivalent name | 927666 927666 | Streptococcus oralis strain Uo5 | | equivalent name | 932662 932662 | Mud crab dicistrovirus | | scientific name | 1116482 1116482 | Pectobacterium phage phiTE | | scientific name | 1116482 1116482 | bacteriophage phiTE | | synonym | 1160968 1160968 | Rabbit coronavirus HKU14 | | scientific name | 1161927 1161927 | Pseudomonas phage Lu11 | | scientific name | 1172562 1172562 | Helicobacter cinaedi PAGU611 | | scientific name | 1172562 1172562 | Helicobacter cinaedi str. PAGU611 | | equivalent name | 1172562 1172562 | Helicobacter cinaedi strain PAGU611 | | equivalent name | 1235559 1235559 | Providencia phage Redjac | | scientific name | metaMix/inst/extdata/dat1/names_example.dmp0000644000176200001440000031520513403500106020434 0ustar liggesusers72 | "Caryophanon muelleri" (Schmid 1922) Peshkoff 1948 | | authority | 72 | ATCC 29453 | | type material | 72 | CCUG 30554 | | type material | 72 | CIP 103436 | | type material | 72 | Caryophanon muelleri | | synonym | 72 | DSM 2579 | | type material | 72 | LMG 7828 | | type material | 72 | Scheibenbakterien | | common name | 72 | Scheibenbakterien Muller 1911 | | common name | 72 | Simonsiella muelleri | | scientific name | 72 | Simonsiella muelleri Schmid 1922 | | authority | 158 | "Spirillum dentium" (Miller 1889) Sternberg 1892 | | authority | 158 | "Spirochaeta ambigua" Seguin and Vinzent 1936 | | authority | 158 | "Spirochaeta comandonii" Seguin and Vinzent 1936 | | authority | 158 | "Spirochaeta dentium" (Miller 1889) Migula 1895 | | authority | 158 | "Spirochaeta microdentium" (Noguchi 1912) Heim 1922 | | authority | 158 | "Spirochaeta orthodonta" Hoffmann 1920 | | authority | 158 | "Spirochaete denticola" Flugge 1886 | | authority | 158 | "Spirochaete dentium" Miller 1889 | | authority | 158 | "Spironema dentium" (Miller 1889) Gross 1912 | | authority | 158 | "Treponema ambiguum" (Seguin and Vinzent 1936) Prevot 1940 | | authority | 158 | "Treponema comandonii" (Seguin and Vinzent 1936) Prevot 1940 | | authority | 158 | "Treponema dentium" (Miller 1889) Dobell 1912 | | authority | 158 | "Treponema dentium-stenogyratum" Pettit 1928 | | authority | 158 | "Treponema microdentium" Noguchi 1912 | | authority | 158 | "Treponema orthodontum" (Hoffmann 1920) Noguchi 1928 | | authority | 158 | ATCC 35405 | | type material | 158 | CIP 103919 | | type material | 158 | DSM 14222 | | type material | 158 | JCM 8153 | | type material | 158 | Spirillum dentium | | synonym | 158 | Spirochaeta ambigua | | synonym | 158 | Spirochaeta comandonii | | synonym | 158 | Spirochaeta dentium | | synonym | 158 | Spirochaeta microdentium | | synonym | 158 | Spirochaeta orthodonta | | synonym | 158 | Spirochaete denticola | | synonym | 158 | Spirochaete dentium | | synonym | 158 | Spironema dentium | | synonym | 158 | Treponema ambiguum | | synonym | 158 | Treponema comandonii | | synonym | 158 | Treponema denticola | | scientific name | 158 | Treponema denticola (ex Brumpt 1925) Chan et al. 1993 | | authority | 158 | Treponema denticola (ex Flugge 1886) Chan et al. 1993 | | authority | 158 | Treponema dentium | | synonym | 158 | Treponema dentium-stenogyratum | | synonym | 158 | Treponema microdentium | | synonym | 158 | Treponema orthodontum | | synonym | 204 | ATCC 51146 | | type material | 204 | CCUG 30254 | | type material | 204 | CIP 103970 | | type material | 204 | Campylobacter showae | | scientific name | 204 | Campylobacter showae Etoh et al. 1993 | | authority | 204 | JCM 12989 | | type material | 204 | LMG 12635 | | type material | 204 | strain SU A4 | | type material | 222 | Achromobacter | | scientific name | 222 | Achromobacter Yabuuchi and Yano 1981 emend. Yabuuchi et al. 1998 | | authority | 250 | ATCC 35910 | | type material | 250 | CCUG 14555 | | type material | 250 | CIP 103039 | | type material | 250 | Chryseobacterium gleum | | scientific name | 250 | Chryseobacterium gleum (Holmes et al. 1984) Vandamme et al. 1994 | | authority | 250 | DSM 16776 | | type material | 250 | Flavobacterium gleum | | synonym | 250 | Flavobacterium gleum Holmes et al. 1984 | | authority | 250 | IFO 15054 | | type material | 250 | JCM 2410 | | type material | 250 | LMG 8334 | | type material | 250 | NBRC 15054 | | type material | 250 | NCTC 11432 | | type material | 250 | strain F93 | | type material | 258 | ATCC 33861 | | type material | 258 | CCUG 13224 | | type material | 258 | CDC E7288 | | type material | 258 | CIP 100542 | | type material | 258 | DSM 11722 | | type material | 258 | Flavibacterium yabuuchiae | | synonym | 258 | Flavobacterium spiritivorum | | synonym | 258 | Flavobacterium spiritivorum Holmes et al. 1982 | | authority | 258 | Flavobacterium yabuuchiae | | synonym | 258 | Flavobacterium yabuuchiae Holmes et al. 1988 | | authority | 258 | GIFU 3101 | | type material | 258 | IFO 14948 | | type material | 258 | JCM 1277 | | type material | 258 | JCM 6897 | | type material | 258 | LMG 8347 | | type material | 258 | NBRC 14948 | | type material | 258 | NCTC 11386 | | type material | 258 | Sphingobacter spiritivorum | | misspelling | 258 | Sphingobacterium spiritivorum | | scientific name | 258 | Sphingobacterium spiritivorum (Holmes et al. 1982) Yabuuchi et al. 1983 | | authority | 258 | strain E7288 | | type material | 469 | Acinetobacter | | scientific name | 469 | Acinetobacter Brisou and Prevot 1954 | | authority | 471 | "Micrococcus calco-aceticus" Beijerinck 1911 | | authority | 471 | ATCC 23055 | | type material | 471 | Acinetobacter calcoaceticus | | scientific name | 471 | Acinetobacter calcoaceticus (Beijerinck 1911) Baumann et al. 1968 (Approved Lists 1980) emend. Bouvet and Grimont 1986 | | authority | 471 | Acinetobacter genomosp. 1 | | synonym | 471 | Acinetobacter genomospecies 1 | | synonym | 471 | Acinetobacter sp. AV6 | | includes | 471 | Acinetobacter sp. HNR | | includes | 471 | Acinetobacter sp. STB1 | | includes | 471 | CAIM 17 | | type material | 471 | CCUG 12804 | | type material | 471 | CIP 81.8 | | type material | 471 | DSM 30006 | | type material | 471 | JCM 6842 | | type material | 471 | LMG 1046 | | type material | 471 | Micrococcus calcoaceticus | | synonym | 471 | Moraxella calcoacetica | | synonym | 471 | NCCB 22016 | | type material | 471 | NCTC 12983 | | type material | 471 | Neisseria winogradskyi | | synonym | 482 | "Gonococcus" Lindau 1898 | | synonym | 482 | "Merismopedia" Zopf 1885 | | synonym | 482 | Gonococcus | | synonym | 482 | Neisseria | | scientific name | 482 | Neisseria Trevisan 1885 | | synonym | 482 | Nesseira | | misspelling | 483 | "Micrococcus cinereus" von Lingelsheim 1906 | | authority | 483 | ATCC 14685 | | type material | 483 | CCUG 2156 | | type material | 483 | CCUG 346 | | type material | 483 | CIP 73.16 | | type material | 483 | DSM 4630 | | type material | 483 | LMG 8380 | | type material | 483 | Micrococcus cinereus | | synonym | 483 | NCTC 10294 | | type material | 483 | Neisseria cinerea | | scientific name | 483 | Neisseria cinerea (von Lingelsheim 1906) Murray 1939 | | authority | 484 | ATCC 13120 | | type material | 484 | CCUG 17913 | | type material | 484 | CCUG 345 | | type material | 484 | CIP 73.15 | | type material | 484 | DSM 17633 | | type material | 484 | LMG 5297 | | type material | 484 | NCTC 8263 | | type material | 484 | Neisseria flavescens | | scientific name | 484 | Neisseria flavescens Branham 1930 | | authority | 486 | "Neisseria lactamicus" (sic) Hollis et al. 1969 | | authority | 486 | ATCC 23970 | | type material | 486 | CCUG 5853 | | type material | 486 | CIP 72.17 | | type material | 486 | DSM 4691 | | type material | 486 | NCTC 10617 | | type material | 486 | Neisseria lactamica | | scientific name | 486 | Neisseria lactamica Hollis et al. 1969 | | authority | 486 | Neisseria lactamicus | | synonym | 487 | "Diplokokkus intracellularis meningitidis" (sic) Weichselbaum 1887 | | authority | 487 | "Micrococcus intracellularis" (Jaeger) Migula 1900 | | authority | 487 | "Micrococcus meningitidis cerebrospinalis" Albrecht and Ghon 1901 | | authority | 487 | "Micrococcus meningitidis" Albrecht and Ghon 1903 | | authority | 487 | "Neisseria weichselbaumii" Trevisan 1889 | | authority | 487 | ATCC 13077 | | type material | 487 | CCUG 3269 | | type material | 487 | CIP 73.10 | | type material | 487 | DSM 10036 | | type material | 487 | Diplokokkus intracellularis meningitidis | | synonym | 487 | Micrococcus intracellularis | | synonym | 487 | Micrococcus meningitidis | | synonym | 487 | Micrococcus meningitidis cerebrospinalis | | synonym | 487 | NCTC 10025 | | type material | 487 | Neisseria meningitidis | | scientific name | 487 | Neisseria meningitidis (Albrecht and Ghon 1901) Murray 1929 | | authority | 487 | Neisseria meningitidis. | | misspelling | 487 | Neisseria weichselbaumii | | synonym | 487 | strain Sara E. Branham M1027 | | type material | 488 | "Diplococcus mucosus" von Lingelsheim 1906 | | authority | 488 | ATCC 19696 | | type material | 488 | CCUG 26877 | | type material | 488 | CIP 59.51 | | type material | 488 | DSM 17611 | | type material | 488 | Diplococcus mucosus | | synonym | 488 | JCM 12992 | | type material | 488 | NCTC 12978 | | type material | 488 | Neisseria mucosa | | scientific name | 488 | Neisseria mucosa (von Lingelsheim 1906) Veron et al. 1959 | | authority | 488 | Neisseria mucosa Veron et al. 1959 (sic) | | authority | 489 | "Neisseria polysacchareae" Riou et al. 1983 | | authority | 489 | ATCC 43768 | | type material | 489 | CCUG 18030 | | type material | 489 | CIP 100113 | | type material | 489 | NCTC 11858 | | type material | 489 | Neisseria polysaccharea | | scientific name | 489 | Neisseria polysaccharea Riou and Guibourdenche 1987 | | authority | 489 | Neisseria polysacchareae | | synonym | 496 | ATCC 33926 | | type material | 496 | CIP 103346 | | type material | 496 | Neisseria macaca | | misspelling | 496 | Neisseria macacae | | scientific name | 496 | Neisseria macacae Vedros et al. 1983 | | authority | 496 | strain M-740 | | type material | 502 | ATCC 33394 | | type material | 502 | CCUG 6516 | | type material | 502 | CCUG 9125 | | type material | 502 | CIP 103473 | | type material | 502 | DSM 10202 | | type material | 502 | Kingella denitrificans | | scientific name | 502 | Kingella denitrificans Snell and Lapage 1976 | | authority | 502 | NCTC 10995 | | type material | 504 | "Moraxella kingae" Bovre et al. 1974 | | authority | 504 | "Moraxella kingii" (sic) Henriksen and Bovre 1968 | | authority | 504 | ATCC 23330 | | type material | 504 | CCUG 352 | | type material | 504 | CIP 80.16 | | type material | 504 | DSM 7536 | | type material | 504 | Kingella kingae | | scientific name | 504 | Kingella kingae (Henriksen and Bovre 1968) Henriksen and Bovre 1976 | | authority | 504 | Kingella kingii | | equivalent name | 504 | Moraxella kingae | | synonym | 504 | Moraxella kingii | | synonym | 504 | NCTC 10529 | | type material | 505 | ATCC 51147 | | type material | 505 | CCUG 30450 | | type material | 505 | CIP 103803 | | type material | 505 | DSM 18271 | | type material | 505 | Kingella orale | | synonym | 505 | Kingella oralis | | scientific name | 505 | Kingella oralis corrig. Dewhirst et al. 1993 | | authority | 505 | strain UB-38 | | type material | 539 | "Bacteroides corrodens" Eiken 1958 (in part) | | synonym | 539 | "Ristella corrodens" (Eiken 1958) Prevot 1966 | | synonym | 539 | ATCC 23834 | | type material | 539 | Bacteroides corrodens | Bacteroides corrodens | synonym | 539 | CCUG 2138 | | type material | 539 | CIP 70.75 | | type material | 539 | DSM 8340 | | type material | 539 | Eikenella corrodens | | scientific name | 539 | Eikenella corrodens (Eiken 1958) Jackson and Goodman 1972 | | synonym | 539 | JCM 12952 | | type material | 539 | LMG 15557 | | type material | 539 | NCTC 10596 | | type material | 539 | Ristella corrodens | | synonym | 587 | "Bacterium rettgeri" Hadley 1918 | | authority | 587 | "Shigella rettgeri" (Hadley et al. 1918) Weldin 1927 | | authority | 587 | ATCC 29944 | | type material | 587 | Bacterium rettgeri | | synonym | 587 | CCUG 14804 | | type material | 587 | CIP 103182 | | type material | 587 | DSM 4542 | | type material | 587 | JCM 1675 | | type material | 587 | LMG 3259 | | type material | 587 | NCTC 11801 | | type material | 587 | Proteus rettgeri | | synonym | 587 | Proteus rettgeri (Hadley et al. 1918) Rustigian and Stuart 1943 (Approved Lists 1980) | | authority | 587 | Providencia rettgeri | | scientific name | 587 | Providencia rettgeri (Hadley 1918) Brenner et al. 1978 | | authority | 587 | Shigella rettgeri | | synonym | 588 | "Proteus stuartii" Buttiaux et al. 1954 | | authority | 588 | ATCC 29914 | | type material | 588 | CCUG 14805 | | type material | 588 | CIP 104687 | | type material | 588 | DSM 4539 | | type material | 588 | LMG 3260 | | type material | 588 | NCTC 11800 | | type material | 588 | Proteus stuartii | | synonym | 588 | Providencia stuartii | | scientific name | 588 | Providencia stuartii (Buttiaux et al. 1954) Ewing 1962 | | authority | 618 | ATCC 33077 | | type material | 618 | CCUG 14508 | | type material | 618 | CDC 1979-77 | | type material | 618 | CIP 79.1 | | type material | 618 | DSM 4582 | | type material | 618 | JCM 1243 | | type material | 618 | NBRC 102598 | | type material | 618 | NCTC 11214 | | type material | 618 | Serratia odorifera | | scientific name | 618 | Serratia odorifera Grimont et al. 1978 | | authority | 618 | Serratia odorifora | | misspelling | 636 | "Paracolobactrum anguillimortiferum" Hoshina 1962 | | authority | 636 | ATCC 15947 | | type material | 636 | CCUG 1638 | | type material | 636 | CIP 78.61 | | type material | 636 | DSM 30052 | | type material | 636 | Edwardsiella anguillimortifera | | synonym | 636 | Edwardsiella anguillimortifera (Hoshina 1962) Sakazaki and Tamura 1975 | | authority | 636 | Edwardsiella tarda | | scientific name | 636 | Edwardsiella tarda Ewing and McWhorter 1965 | | authority | 636 | JCM 1656 | | type material | 636 | LMG 2793 | | type material | 636 | NCCB 73021 | | type material | 636 | NCTC 10396 | | type material | 636 | Paracolobactrum anguillimortiferum | | synonym | 816 | "Ristella" Prevot 1938 | | authority | 816 | Bacteroides | Bacteroides | scientific name | 816 | Bacteroides Castellani and Chalmers 1919 (Approved Lists 1980) emend. Shah and Collins 1989 | | authority | 816 | Capsularis | | synonym | 816 | Capsularis Prevot 1938 (Approved Lists 1980) | | authority | 816 | Ristella | Ristella | synonym | 817 | "Bacteroides inaequalis" Eggerth and Gagnon 1933 | | authority | 817 | "Bacteroides incommunis" Eggerth and Gagnon 1933 | | authority | 817 | "Bacteroides uncatus" Eggerth and Gagnon 1933 | | authority | 817 | "Fusiformis fragilis" Topley and Wilson 1929 | | authority | 817 | "Pseudobacterium fragilis" Krasil'nikov 1949 | | authority | 817 | "Pseudobacterium inaequalis" (Eggerth and Gagnon 1933) Krasil'nikov 1949 | | authority | 817 | "Pseudobacterium incommunis" (Eggerth and Gagnon 1933) Krasil'nikov 1949 | | authority | 817 | "Pseudobacterium uncatum" (Eggerth and Gagnon 1933) Krasil'nikov 1949 | | authority | 817 | "Ristella fragilis" Prevot 1938 | | authority | 817 | "Ristella incommunis" (Eggerth and Gagnon 1933) Prevot 1938 | | authority | 817 | "Ristella uncata" (Eggerth and Gagnon 1933) Prevot 1938 | | authority | 817 | "Sphaerophorus inaequalis" (Eggerth and Gagnon 1933) Prevot 1938 | | authority | 817 | "Sphaerophorus intermedius" Bergan and Hovig 1968 | | authority | 817 | ATCC 25285 | | type material | 817 | Bacillus fragilis | | synonym | 817 | Bacillus fragilis Veillon and Zuber 1898 | | authority | 817 | Bacteroides fragili | | misspelling | 817 | Bacteroides fragilis | | scientific name | 817 | Bacteroides fragilis (Veillon and Zuber 1898) Castellani and Chalmers 1919 | | authority | 817 | Bacteroides inaequalis | | synonym | 817 | Bacteroides incommunis | | synonym | 817 | Bacteroides uncatus | | synonym | 817 | CCUG 4856 | | type material | 817 | CIP 77.16 | | type material | 817 | DSM 2151 | | type material | 817 | Fusiformis fragilis | | synonym | 817 | JCM 11019 | | type material | 817 | LMG 10263 | | type material | 817 | NCTC 9343 | | type material | 817 | Pseudobacterium fragilis | | synonym | 817 | Pseudobacterium inaequalis | | synonym | 817 | Pseudobacterium incommunis | | synonym | 817 | Pseudobacterium uncatum | | synonym | 817 | Ristella fragilis | | synonym | 817 | Ristella incommunis | | synonym | 817 | Ristella uncata | | synonym | 817 | Sphaerophorus inaequalis | | synonym | 817 | Sphaerophorus intermedius | | synonym | 823 | "Bacteroides fragilis subsp. distasonis" (Eggerth and Gagnon 1933) Holdeman and Moore 1970 | | authority | 823 | "Pseudobacterium distasonis" (Eggerth and Gagnon 1933) Krasil'nikov 1949 | | authority | 823 | "Ristella distasonis" (Eggerth and Gagnon 1933) Prevot 1938 | | authority | 823 | ATCC 8503 | | type material | 823 | Bacteroides distasonis | | synonym | 823 | Bacteroides distasonis Eggerth and Gagnon 1933 (Approved Lists 1980) | | authority | 823 | Bacteroides fragilis subsp. distasoni | | synonym | 823 | CCUG 4941 | | type material | 823 | CIP 104284 | | type material | 823 | DSM 20701 | | type material | 823 | JCM 5825 | | type material | 823 | NCTC 11152 | | type material | 823 | Parabacteroides distasonis | | scientific name | 823 | Parabacteroides distasonis (Eggerth and Gagnon 1933) Sakamoto and Benno 2006 | | authority | 823 | Pseudobacterium distasonis | | synonym | 823 | Ristella distasonis | | synonym | 824 | ATCC 33236 | | type material | 824 | Bacteroides gracilis | | synonym | 824 | Bacteroides gracilis Tanner et al. 1981 | | synonym | 824 | CCUG 27720 | | type material | 824 | Campylobacter gracilis | | scientific name | 824 | Campylobacter gracilis (Tanner et al. 1981) Vandamme et al. 1995 | | synonym | 824 | DSM 19528 | | type material | 824 | FDC 1084 | | type material | 824 | JCM 8538 | | type material | 824 | NCTC 12738 | | type material | 847 | ATCC 35274 | | type material | 847 | CIP 106513 | | type material | 847 | Oxalobacter formigenes | | scientific name | 847 | Oxalobacter formigenes Allison et al. 1985 | | authority | 847 | strain OxB | | type material | 1017 | ATCC 33624 | | type material | 1017 | CCUG 9715 | | type material | 1017 | CIP 102945 | | type material | 1017 | Capnocytophaga gingivalis | | scientific name | 1017 | Capnocytophaga gingivalis Leadbetter et al. 1982 emend. London et al. 1985 | | authority | 1017 | DSM 3290 | | type material | 1017 | JCM 12953 | | type material | 1017 | LMG 11514 | | type material | 1017 | NCTC 12372 | | type material | 1017 | strain 27 | strain 27 | type material | 1019 | ATCC 33612 | | type material | 1019 | CCUG 9714 | | type material | 1019 | CIP 104301 | | type material | 1019 | Capnocytophaga sputigena | | scientific name | 1019 | Capnocytophaga sputigena Leadbetter et al. 1982 | | authority | 1019 | DSM 3292 | | type material | 1019 | DSM 7273 | | type material | 1019 | JCM 12967 | | type material | 1019 | LMG 11518 | | type material | 1019 | NCTC 11653 | | type material | 1019 | strain 4 | | type material | 1033 | Afipia | | scientific name | 1033 | Afipia Brenner et al. 1992 emend. La Scola et al. 2002 | | authority | 1034 | ATCC 49720 | | type material | 1034 | Afipia clevelandensis | | scientific name | 1034 | Afipia clevelandensis Brenner et al. 1992 | | authority | 1034 | CCUG 30457 | | type material | 1034 | CIP 103516 | | type material | 1034 | DSM 7315 | | type material | 1034 | NCTC 12721 | | type material | 1034 | strain B-91-007353 | | type material | 1035 | AFIP strain BV | | type material | 1035 | ATCC 53690 | | type material | 1035 | Afipia felis | | scientific name | 1035 | Afipia felis Brenner et al. 1992 | | authority | 1035 | CCUG 30456 | | type material | 1035 | CIP 103515 | | type material | 1035 | DSM 7326 | | type material | 1035 | NCTC 12499 | | type material | 1035 | cat scratch disease bacillus | | genbank common name | 1035 | strain B-91-007352 | | type material | 1260 | "Diplococcus magnus" Prevot 1933 | | authority | 1260 | ATCC 15794 | | type material | 1260 | CCUG 17636 | | type material | 1260 | DSM 20470 | | type material | 1260 | Finegoldia magna | | scientific name | 1260 | Finegoldia magna (Prevot 1933) Murdoch and Shah 2000 | | authority | 1260 | GIFU 7629 | | type material | 1260 | JCM 1766 | | type material | 1260 | NCTC 11804 | | type material | 1260 | Peptococcus magnus | | synonym | 1260 | Peptococcus magnus (Prevot 1933) Holdeman and Moore 1972 (Approved Lists 1980) | | authority | 1260 | Peptostreptococcus magnus | | synonym | 1260 | Peptostreptococcus magnus (Prevot 1933) Ezaki et al. 1983 | | authority | 1270 | "Bacteridium luteum" Schroeter 1872 | | authority | 1270 | "Micrococcus flavus" Trevisan | | authority | 1270 | "Micrococcus lysodeikticus" Fleming 1933 | | authority | 1270 | "Sarcina lutea" (Schroeter 1872) Schroeter 1886 | | authority | 1270 | ATCC 4698 | | type material | 1270 | Bacteridium luteum | | synonym | 1270 | CCM 169 | | type material | 1270 | CCUG 5858 | | type material | 1270 | CIP A270 | | type material | 1270 | DSM 20030 | | type material | 1270 | HAMBI 1399 | | type material | 1270 | HAMBI 26 | | type material | 1270 | IEGM 391 | | type material | 1270 | IFO 3333 | | type material | 1270 | JCM 1464 | | type material | 1270 | LMG 4050 | | type material | 1270 | Micrococcus luteus | | scientific name | 1270 | Micrococcus luteus (Schroeter 1872) Cohn 1872 (Approved Lists 1980) emend. Wieser et al. 2002 | | authority | 1270 | Micrococcus lysodeikticus | | synonym | 1270 | NBRC 3333 | | type material | 1270 | NCCB 78001 | | type material | 1270 | NCTC 2665 | | type material | 1270 | NRRL B-287 | | type material | 1270 | Sarcina lutea | | synonym | 1270 | VKM B-1314 | | type material | 1270 | not "Micrococcus luteus" Lehmann and Neumann 1896 | | authority | 1279 | "Aurococcus" Winslow and Rogers 1906 | | authority | 1279 | Aurococcus | | synonym | 1279 | Staphylococcus | | scientific name | 1279 | Staphylococcus Rosenbach 1884 | | authority | 1301 | Streptococcus | | scientific name | 1301 | Streptococcus Rosenbach 1884 | | authority | 1303 | ATCC 35037 | | type material | 1303 | CCUG 13229 | | type material | 1303 | CCUG 24891 | | type material | 1303 | CIP 102922 | | type material | 1303 | DSM 20627 | | type material | 1303 | JCM 12997 | | type material | 1303 | LMG 14532 | | type material | 1303 | NCTC 11427 | | type material | 1303 | Streptococcus oralis | | scientific name | 1303 | Streptococcus oralis Bridge and Sneath 1982 emend. Kilian et al. 1989 | | authority | 1303 | Streptococcus oralis Bridge and Sneath 1982 emend. Kilpper-Balz et al. 1985 | | authority | 1303 | strain LVG 1 | | type material | 1303 | strain PB 182 | | type material | 1303 | strain SK23 | | type material | 1305 | ATCC 10556 | | type material | 1305 | CCUG 17826 | | type material | 1305 | CCUG 35770 | | type material | 1305 | CIP 55.128 | | type material | 1305 | DSM 20567 | | type material | 1305 | JCM 5708 | | type material | 1305 | LMG 14702 | | type material | 1305 | NCTC 7863 | | type material | 1305 | Streptococcus sanguinis | | scientific name | 1305 | Streptococcus sanguinis corrig. White and Niven 1946 (Approved Lists 1980) emend. Kilian et al. 1989 | | authority | 1305 | Streptococcus sanguis | | misspelling | 1305 | strain SK1 | strain SK1 | type material | 1317 | ATCC 33748 | | type material | 1317 | CCUG 24890 | | type material | 1317 | CIP 103222 | | type material | 1317 | DSM 5635 | | type material | 1317 | LMG 14514 | | type material | 1317 | NCTC 11391 | | type material | 1317 | Streptococcus downei | | scientific name | 1317 | Streptococcus downei Whiley et al. 1988 | | authority | 1317 | Streptococcus downensis | | equivalent name | 1317 | strain MFe28 | | type material | 1322 | ATCC 27752 | | type material | 1322 | Blautia hansenii | | scientific name | 1322 | Blautia hansenii (Holdeman and Moore 1974) Liu et al. 2008 | | authority | 1322 | CIP 104219 | | type material | 1322 | DSM 20583 | | type material | 1322 | JCM 14655 | | type material | 1322 | Ruminococcus hansenii | | synonym | 1322 | Ruminococcus hansenii (Holdeman and Moore 1974) Ezaki et al. 1994 | | authority | 1322 | Streptococcus hansenii | | synonym | 1322 | Streptococcus hansenii Holdeman and Moore 1974 (Approved Lists 1980) | | authority | 1343 | ATCC 49124 | | type material | 1343 | CCUG 24893 | | type material | 1343 | CIP 103363 | | type material | 1343 | DSM 5636 | | type material | 1343 | LMG 13516 | | type material | 1343 | NCTC 12166 | | type material | 1343 | Streptococcus vestibularis | | scientific name | 1343 | Streptococcus vestibularis Whiley and Hardie 1988 | | authority | 1343 | strain MM1 | strain MM1 | type material | 1352 | ATCC 19434 | | type material | 1352 | CCUG 542 | | type material | 1352 | CFBP 4248 | | type material | 1352 | CIP 103014 | | type material | 1352 | DSM 20477 | | type material | 1352 | Enterococcus faecium | | scientific name | 1352 | Enterococcus faecium (Orla-Jensen 1919) Schleifer and Kilpper-Balz 1984 | | authority | 1352 | HAMBI 1710 | | type material | 1352 | JCM 5804 | | type material | 1352 | JCM 8727 | | type material | 1352 | LMG 11423 | | type material | 1352 | NBRC 100485 | | type material | 1352 | NBRC 100486 | | type material | 1352 | NCDO 942 | | type material | 1352 | NCIMB 11508 | | type material | 1352 | NCTC 7171 | | type material | 1352 | Streptococcus faecium | | synonym | 1352 | Streptococcus faecium Orla-Jensen 1919 (Approved Lists 1980) | | authority | 1383 | ATCC 49626 | | type material | 1383 | Atopobium rimae | | scientific name | 1383 | Atopobium rimae (Olsen et al. 1991) Collins and Wallbanks 1993 | | synonym | 1383 | CCUG 31168 | | type material | 1383 | DSM 7090 | | type material | 1383 | IFO 15546 | | type material | 1383 | JCM 10299 | | type material | 1383 | LMG 11476 | | type material | 1383 | Lactobacillus rimae | | synonym | 1383 | Lactobacillus rimae Olsen et al. 1991 | | synonym | 1383 | NBRC 15546 | | type material | 1383 | VPI D140H-11A | | type material | 1496 | "Bacillus difficilis" Hall and O'Toole 1935 | | authority | 1496 | AS 1.2184 | | type material | 1496 | ATCC 9689 | | type material | 1496 | BCRC 10642 | | type material | 1496 | Bacillus difficilis | | synonym | 1496 | CCRC 10642 | | type material | 1496 | CCUG 4938 | | type material | 1496 | CIP 104282 | | type material | 1496 | Clostridium difficile | | equivalent name | 1496 | Clostridium difficile (Hall and O'Toole 1935) Prevot 1938 | | authority | 1496 | DSM 1296 | | type material | 1496 | JCM 1296 | | type material | 1496 | LMG 15861 | | type material | 1496 | NCIMB 10666 | | type material | 1496 | NCTC 11209 | | type material | 1496 | [Clostridium] difficile | | scientific name | 1509 | "Bacillus sporogenes var. A" Metchnikoff 1908 | | authority | 1509 | "Clostridium sporogenes var. A" (Metchnikoff 1908) Prevot 1938 | | authority | 1509 | "Clostridium sporogenes" (Heller 1922) Bergey et al. 1923 | | authority | 1509 | "Metchnikovillus sporogenes" (sic) Heller 1922 | | authority | 1509 | ATCC 3584 | | type material | 1509 | BCRC 11259 | | type material | 1509 | Bacillus sporogenes var. A | | synonym | 1509 | CCRC 11259 | | type material | 1509 | CCUG 15941 | | type material | 1509 | CIP 106155 | | type material | 1509 | Clostridium sporogenes | | scientific name | 1509 | Clostridium sporogenes (Metchnikoff 1908) Bergey et al. 1923 | | authority | 1509 | Clostridium sporogenes var. A | | synonym | 1509 | DSM 795 | | type material | 1509 | JCM 1416 | | type material | 1509 | LMG 8421 | | type material | 1509 | Metchnikovillus sporogenes | | synonym | 1509 | NCIMB 10696 | | type material | 1509 | NCTC 13020 | | type material | 1535 | ATCC 29065 | | type material | 1535 | CCUG 48287 | | type material | 1535 | Clostridium leptum | | scientific name | 1535 | Clostridium leptum Moore et al. 1976 | | authority | 1535 | DSM 753 | | type material | 1535 | [Clostridium] leptum | | equivalent name | 1623 | ATCC 27780 | | type material | 1623 | CCUG 39465 | | type material | 1623 | CIP 103153 | | type material | 1623 | DSM 20403 | | type material | 1623 | JCM 1152 | | type material | 1623 | LMG 10756 | | type material | 1623 | Lactobacillus ruminis | | scientific name | 1623 | Lactobacillus ruminis Sharpe et al. 1973 | | authority | 1623 | NBRC 102161 | | type material | 1623 | NRRL B-14853 | | type material | 1633 | ATCC 49540 | | type material | 1633 | CCUG 31452 | | type material | 1633 | CIP 105932 | | type material | 1633 | DSM 5837 | | type material | 1633 | JCM 9505 | | type material | 1633 | LMG 12891 | | type material | 1633 | Lactobacillus vaginalis | | scientific name | 1633 | Lactobacillus vaginalis Embley et al. 1989 | | synonym | 1633 | NCTC 12197 | | type material | 1656 | "Odontomyces viscosus" Howell et al. 1965 | | synonym | 1656 | ATCC 15987 | | type material | 1656 | Actinomyces viscosus | | scientific name | 1656 | Actinomyces viscosus (Howell et al. 1965) Georg et al. 1969 | | synonym | 1656 | CCUG 14476 | | type material | 1656 | CIP 103147 | | type material | 1656 | DSM 43327 | | type material | 1656 | JCM 8353 | | type material | 1656 | NCTC 10951 | | type material | 1656 | Odontomyces viscosus | | synonym | 1660 | ATCC 17929 | | type material | 1660 | Actinomyces odontolyticus | | scientific name | 1660 | Actinomyces odontolyticus Batty 1958 | | synonym | 1660 | CCUG 20536 | | type material | 1660 | CIP 101124 | | type material | 1660 | DSM 19120 | | type material | 1660 | DSM 43760 | | type material | 1660 | JCM 14871 | | type material | 1660 | LMG 18080 | | type material | 1660 | NCTC 9935 | | type material | 1681 | "Actinobacterium bifidum" (Tissier 1900) Puntoni 1937 | | authority | 1681 | "Actinomyces bifidus" (Tissier 1900) Nannizzi 1934 | | authority | 1681 | "Actinomyces parabifidus" (Weiss and Rettger 1938) Pine and Georg 1965 | | authority | 1681 | "Bacillus bifidus communis" Tissier 1900 | | authority | 1681 | "Bacillus bifidus" Tissier 1900 | | authority | 1681 | "Bacterium bifidum" (Tissier 1900) Lehmann and Neumann 1927 | | authority | 1681 | "Bacteroides bifidus" (Tissier 1900) Castellani and Chalmers 1919 | | authority | 1681 | "Bifidibacterium bifidum" (Tissier 1900) Prevot 1938 | | authority | 1681 | "Cohnistreptothrix bifidus" (Tissier 1900) Negroni and Fischer 1944 | | authority | 1681 | "Lactobacillus bifidus type II" Weiss and Rettger 1938 | | authority | 1681 | "Lactobacillus parabifidus" Weiss and Rettger 1938 | | authority | 1681 | "Nocardia bifida" (Tissier 1900) Vuillemin 1931 | | authority | 1681 | "Tissieria bifida" (Tissier 1900) Pribram 1929 | | authority | 1681 | AS 1.2212 | | type material | 1681 | ATCC 29521 | | type material | 1681 | Actinobacterium bifidum | | synonym | 1681 | Actinomyces bifidus | | synonym | 1681 | Actinomyces parabifidus | | synonym | 1681 | BCRC 14615 | | type material | 1681 | Bacillus bifidus | | synonym | 1681 | Bacillus bifidus communis | | synonym | 1681 | Bacterium bifidum | | synonym | 1681 | Bacteroides bifidus | | synonym | 1681 | Bifidibacterium bifidum | | synonym | 1681 | Bifidobacterium bifidum | | scientific name | 1681 | Bifidobacterium bifidum (Tissier 1900) Orla-Jensen 1924 | | authority | 1681 | CCRC 14615 | | type material | 1681 | CCUG 18364 | | type material | 1681 | CCUG 45217 | | type material | 1681 | CIP 56.7 | | type material | 1681 | Cohnistreptothrix bifidus | | synonym | 1681 | DSM 20456 | | type material | 1681 | HAMBI 1380 | | type material | 1681 | IFO 14252 | | type material | 1681 | JCM 1255 | | type material | 1681 | KCTC 3202 | | type material | 1681 | LMG 11041 | | type material | 1681 | LMG 8810 | | type material | 1681 | Lactobacillus bifidus type II | | synonym | 1681 | Lactobacillus parabifidus | | synonym | 1681 | NBRC 100015 | | type material | 1681 | NBRC 14252 | | type material | 1681 | NCFB 2715 | | type material | 1681 | NCIMB 702715 | | type material | 1681 | NCTC 13001 | | type material | 1681 | Nocardia bifida | | synonym | 1681 | Tissieria bifida | | synonym | 1681 | strain Ti | | type material | 1689 | AS 1.2188 | | type material | 1689 | ATCC 27534 | | type material | 1689 | Actinomyces eriksonii | | synonym | 1689 | BCRC 14662 | | type material | 1689 | Bifidobacterium dentium | | scientific name | 1689 | Bifidobacterium dentium Scardovi and Crociani 1974 | | authority | 1689 | CCRC 14662 | | type material | 1689 | CCUG 18367 | | type material | 1689 | CIP 104176 | | type material | 1689 | DSM 20436 | | type material | 1689 | HAMBI 556 | | type material | 1689 | JCM 1195 | | type material | 1689 | LMG 10506 | | type material | 1689 | LMG 11045 | | type material | 1689 | NCFB 2243 | | type material | 1689 | NCIMB 702243 | | type material | 1689 | NCTC 11816 | | type material | 1747 | "Bacillus acnes" Gilchrist 1900 | | authority | 1747 | "Corynebacterium acnes" (Gilchrist 1900) Eberson 1918 | | authority | 1747 | ATCC 6919 | | type material | 1747 | Bacillus acnes | | synonym | 1747 | CCUG 1794 | | type material | 1747 | CIP 53.117 | | type material | 1747 | Corynebacterium acnes | | synonym | 1747 | DSM 1897 | | type material | 1747 | JCM 6425 | | type material | 1747 | LMG 16711 | | type material | 1747 | NCTC 737 | | type material | 1747 | NRRL B-4224 | | type material | 1747 | Propionibacterium acnes | | scientific name | 1747 | Propionibacterium acnes (sic) (Gilchrist 1900) Douglas and Gunter 1946 | | authority | 1747 | Propionicibacterium acnes | | equivalent name | 1747 | VKM Ac-1450 | | type material | 1827 | Rhodococcus | | scientific name | 1827 | Rhodococcus Zopf 1891 | | authority | 2051 | ATCC 35241 | | type material | 2051 | ATCC 43063 [[Falcivibrio vaginalis]] | | type material | 2051 | CCUG 21018 | | type material | 2051 | CCUG 24716 [[Falcivibrio vaginalis]] | | type material | 2051 | DSM 23059 | | type material | 2051 | DSM 2711 [[Falcivibrio vaginalis]] | | type material | 2051 | Falcivibrio vaginalis | | synonym | 2051 | Falcivibrio vaginalis Hammann et al. 1984 | | authority | 2051 | LMG 7856 [[Falcivibrio vaginalis]] | | type material | 2051 | Mobiluncus curtisii | | scientific name | 2051 | Mobiluncus curtisii Spiegel and Roberts 1984 emend. Hoyles et al. 2004 | | authority | 2051 | NCTC 11656 | | type material | 2051 | NCTC 11820 [[Falcivibrio vaginalis]] | | type material | 2051 | strain BV345-16 | | type material | 2051 | strain V125 [[Falcivibrio vaginalis]] | | type material | 2173 | ATCC 35061 | | type material | 2173 | DSM 861 | | type material | 2173 | Methanobrevibacter smithii | | scientific name | 2173 | Methanobrevibacter smithii Balch and Wolfe 1981 | | authority | 2173 | OCM 144 | | type material | 2173 | strain PS | | type material | 9606 | Homo sapiens | | scientific name | 9606 | Homo sapiens Linnaeus, 1758 | | authority | 9606 | human | | genbank common name | 9606 | man | | common name | 10090 | LK3 transgenic mice | | includes | 10090 | Mus muscaris | | misnomer | 10090 | Mus musculus | | scientific name | 10090 | Mus musculus Linnaeus, 1758 | | authority | 10090 | Mus sp. 129SV | | includes | 10090 | house mouse | | genbank common name | 10090 | mice C57BL/6xCBA/CaJ hybrid | | misspelling | 10090 | mouse | | common name | 10090 | nude mice | | includes | 10090 | transgenic mice | | includes | 10401 | Channel catfish virus | | genbank common name | 10401 | IcHV-1 | | genbank acronym | 10401 | Ictalurid herpesvirus 1 | | scientific name | 10401 | channel catfish virus CCV | | synonym | 10493 | FV3 | | acronym | 10493 | Frog virus 3 | | scientific name | 10493 | Frog virus 3 iridovirus | | synonym | 10493 | frog virus 3 FV3 | | synonym | 10493 | frog virus 3, FV3 | | synonym | 10506 | Chlorella PBCV-1 virus | | synonym | 10506 | Chlorella virus PBCV-1 | | synonym | 10506 | PBCV-1 | | acronym | 10506 | Paramecium bursaria Chlorella virus 1 | | scientific name | 10506 | Paramecium bursaria Chlorella virus 1, PBCV-1 | | synonym | 10506 | Paramecium bursaria Chlorella virus PBCV-1 | | synonym | 10726 | Bacteriophage T5 | | synonym | 10726 | Enterobacteria phage T5 | | scientific name | 10726 | phage T5 | | synonym | 11128 | BCV | | acronym | 11128 | BECV | | acronym | 11128 | Bovine coronavirus | | scientific name | 11128 | Bovine enteritic coronavirus | | synonym | 11128 | Bovine enteritic coronavirus BECV | | synonym | 11128 | bovine coronavirus BCV | | synonym | 11128 | bovine enteric coronavirus | | synonym | 11128 | calf diarrheal coronavirus | | synonym | 11128 | neonatal calf diarrhea virus | | synonym | 11142 | Murine coronavirus mhv (STRAIN A59) | | synonym | 11142 | Murine hepatitis virus (strain A59) | | synonym | 11142 | Murine hepatitis virus strain A59 | | scientific name | 11144 | Murine coronavirus mhv (STRAIN JHM) | | synonym | 11144 | Murine hepatitis virus (strain JHM) | | synonym | 11144 | Murine hepatitis virus strain JHM | | scientific name | 13690 | ATCC 51230 | | type material | 13690 | Beijerinckia B1 | | includes | 13690 | Beijerinckia sp. B1 | | includes | 13690 | CCUG 28380 | | type material | 13690 | CCUG 31205 | | type material | 13690 | CIP 106726 | | type material | 13690 | DSM 7462 | | type material | 13690 | GIFU 9882 | | type material | 13690 | HAMBI 1842 | | type material | 13690 | IFO 15102 | | type material | 13690 | JCM 7371 | | type material | 13690 | LMG 11252 | | type material | 13690 | NBRC 15102 | | type material | 13690 | Sphingobium yanoikuyae | | scientific name | 13690 | Sphingobium yanoikuyae (Yabuuchi et al. 1990) Takeuchi et al. 2001 | | synonym | 13690 | Sphingomonas yanoikuyae | | genbank synonym | 13690 | Sphingomonas yanoikuyae Yabuuchi et al. 1990 | | synonym | 28037 | ATCC 49456 | ATCC 49456 | type material | 28037 | CCUG 31611 | CCUG 31611 | type material | 28037 | CCUG 35790 | CCUG 35790 | type material | 28037 | CIP 103335 | CIP 103335 | type material | 28037 | DSM 12643 | DSM 12643 | type material | 28037 | JCM 12971 | JCM 12971 | type material | 28037 | LMG 14557 | LMG 14557 | type material | 28037 | NCTC 12261 | NCTC 12261 | type material | 28037 | Streptococcus mitis | | scientific name | 28037 | Streptococcus mitis Andrewes and Horder 1906 (Approved Lists 1980) emend. Kilian et al. 1989 | | authority | 28037 | Streptococcus mitis Andrewes and Horder 1906 emend. Judicial Commission 1993 | | authority | 28037 | strain NS 51 | strain NS 51 | type material | 28080 | ATCC 43954 | | type material | 28080 | CCUG 14913 | | type material | 28080 | CIP 103681 | | type material | 28080 | CNW group | | synonym | 28080 | Campylobacter upsaliensis | | scientific name | 28080 | Campylobacter upsaliensis Sandstedt and Ursing 1991 | | authority | 28080 | DSM 5365 | | type material | 28080 | NCTC 11541 | | type material | 28080 | catalase-negative or weak group of campylobacteria | | synonym | 28111 | ATCC 27754 | | type material | 28111 | Bacteroides eggerthii | | scientific name | 28111 | Bacteroides eggerthii Holdeman and Moore 1974 | | authority | 28111 | CCUG 9559 | | type material | 28111 | CIP 104285 | | type material | 28111 | DSM 20697 | | type material | 28111 | JCM 12986 | | type material | 28111 | NCTC 11155 | | type material | 28116 | "Bacteroides fragilis subsp. ovatus" (Eggerth and Gagnon 1933) Holdeman and Moore 1970 | | authority | 28116 | "Pasteurella ovata" (Eggerth and Gagnon 1933) Prevot 1938 | | authority | 28116 | "Pseudobacterium ovatum" (Eggerth and Gagnon 1933) Krasil'nikov 1949 | | authority | 28116 | ATCC 8483 | | type material | 28116 | BCRC 10623 | | type material | 28116 | Bacteroides fragilis subsp. ovatus | | synonym | 28116 | Bacteroides ovatus | | scientific name | 28116 | Bacteroides ovatus Eggerth and Gagnon 1933 | | authority | 28116 | CCRC 10623 | | type material | 28116 | CCUG 4943 | | type material | 28116 | CIP 103756 | | type material | 28116 | DSM 1896 | | type material | 28116 | JCM 5824 | | type material | 28116 | NCTC 11153 | | type material | 28116 | Pasteurella ovata | | synonym | 28116 | Pseudobacterium ovatum | | synonym | 28117 | "Bacillus putredinis" Weinberg et al. 1937 | | authority | 28117 | "Pseudobacterium putredinis" (Weinberg et al. 1937) Krasil'nikov 1949 | | authority | 28117 | "Ristella putredinis" (Weinberg et al. 1937) Prevot 1938 | | authority | 28117 | ATCC 29800 | | type material | 28117 | Alistipes putredinis | | scientific name | 28117 | Alistipes putredinis (Weinberg et al. 1937) Rautio et al. 2003 | | authority | 28117 | Bacillus putredinis | | synonym | 28117 | Bacteroides putredenis | | misspelling | 28117 | Bacteroides putredinis | | synonym | 28117 | Bacteroides putredinis (Weinberg et al. 1937) Kelly 1957 (Approved Lists 1980) | | authority | 28117 | CCUG 45780 | | type material | 28117 | CIP 104286 | | type material | 28117 | DSM 17216 | | type material | 28117 | JCM 16772 | | type material | 28117 | Pseudobacterium putredinis | | synonym | 28117 | Ristella putredinis | | synonym | 28124 | ATCC 35406 | | type material | 28124 | Bacteroides endodontalis | | synonym | 28124 | Bacteroides endodontalis van Steenbergen et al. 1984 | | authority | 28124 | DSM 24491 | | type material | 28124 | JCM 8526 | | type material | 28124 | NCTC 13058 | | type material | 28124 | Porphyromonas endodontalis | | scientific name | 28124 | Porphyromonas endodontalis (van Steenbergen et al. 1984) Shah and Collins 1988 | | authority | 28124 | strain HG370 | | type material | 28127 | ATCC 35310 | | type material | 28127 | Bacteroides buccalis | | synonym | 28127 | Bacteroides buccalis Shah and Collins 1982 | | synonym | 28127 | CCUG 15557 | | type material | 28127 | DSM 20616 | | type material | 28127 | JCM 12246 | | type material | 28127 | NCDO 2354 | | type material | 28127 | NCTC 13064 | | type material | 28127 | Prevotella buccalis | | scientific name | 28127 | Prevotella buccalis (Shah and Collins 1982) Shah and Collins 1990 | | synonym | 28133 | ATCC 33563 | | type material | 28133 | CCUG 9560 | | type material | 28133 | CIP 105552 | | type material | 28133 | DSM 13386 | | type material | 28133 | JCM 12250 | | type material | 28133 | JCM 6322 | | type material | 28133 | NCTC 9336 | | type material | 28133 | Prevotella nigrescens | | scientific name | 28133 | Prevotella nigrescens Shah and Gharbia 1992 | | authority | 28133 | VPI 8944 | | type material | 28133 | strain Lambe 729-74 | | type material | 28134 | "Ristella oralis" (Loesche et al. 1964) Prevot et al. 1967 | | authority | 28134 | ATCC 33269 | | type material | 28134 | Bacteroides oralis | | synonym | 28134 | Bacteroides oralis Loesche et al. 1964 (Approved Lists 1980) | | authority | 28134 | CCUG 15408 | | type material | 28134 | DSM 20702 | | type material | 28134 | JCM 12251 | | type material | 28134 | NCTC 11459 | | type material | 28134 | Prevotella oralis | | scientific name | 28134 | Prevotella oralis (Loesche et al. 1964) Shah and Collins 1990 | | authority | 28134 | Ristella oralis | | synonym | 28134 | VPI D27B-24 | | type material | 28135 | ATCC 33573 | | type material | 28135 | Bacteroides oris | | synonym | 28135 | Bacteroides oris Holdeman et al. 1982 | | authority | 28135 | CCUG 15405 | | type material | 28135 | CIP 104480 | | type material | 28135 | DSM 18711 | | type material | 28135 | JCM 12252 | | type material | 28135 | JCM 8540 | | type material | 28135 | NCTC 13071 | | type material | 28135 | Prevotella oris | | scientific name | 28135 | Prevotella oris (Holdeman et al. 1982) Shah and Collins 1990 | | authority | 28135 | VPI D1A-1A | | type material | 28137 | ATCC 33779 | | type material | 28137 | Bacteroides veroralis | | synonym | 28137 | Bacteroides veroralis Watabe et al. 1983 | | authority | 28137 | CCUG 15422 | | type material | 28137 | JCM 6290 | | type material | 28137 | Prevotella veroralis | | scientific name | 28137 | Prevotella veroralis (Watabe et al. 1983) Shah and Collins 1990 emend. Wu et al. 1992 | | authority | 28137 | VPI D22A-7 | | type material | 28197 | ATCC 49616 | | type material | 28197 | Arcibacter butzleri | | equivalent name | 28197 | Arcobacter butzleri | | scientific name | 28197 | Arcobacter butzleri (Kiehlbauch et al. 1991) Vandamme et al. 1992 | | authority | 28197 | Arcobacter butzlerii | | misspelling | 28197 | Arquibacter butzleri | | equivalent name | 28197 | CCUG 30485 | | type material | 28197 | CDC D2686 | | type material | 28197 | CIP 103493 | | type material | 28197 | CIP 103537 | | type material | 28197 | Campylobacter butzleri | | synonym | 28197 | Campylobacter butzleri Kiehlbauch et al. 1991 | | authority | 28197 | DSM 8739 | | type material | 28197 | LMG 10828 | | type material | 28197 | NCTC 12481 | | type material | 28197 | strain D2686 | | type material | 28211 | "Alphabacteria" Cavalier-Smith 1992 | | authority | 28211 | Alphabacteria | | synonym | 28211 | Alphabacteria Cavalier-Smith 2002 | | authority | 28211 | Alphaproteobacteria | | scientific name | 28211 | Alphaproteobacteria Garrity et al. 2006 | | authority | 28211 | Proteobacteria alpha subdivision | | synonym | 28211 | Purple bacteria, alpha subdivision | | synonym | 28211 | a-proteobacteria | alpha proteos | blast name | 28211 | alpha proteobacteria | | synonym | 28211 | alpha subdivision | | synonym | 28211 | alpha subgroup | | synonym | 28449 | "Micrococcus subflavus" Flugge 1886 | | authority | 28449 | ATCC 49275 | | type material | 28449 | CCUG 23930 | | type material | 28449 | CIP 103343 | | type material | 28449 | DSM 17610 | | type material | 28449 | LMG 5313 | | type material | 28449 | Micrococcus subflavus | | synonym | 28449 | NRL 30,017 | | type material | 28449 | Neisseria subflava | | scientific name | 28449 | Neisseria subflava (Flugge 1886) Trevisan 1889 | | authority | 28449 | strain U37 | | type material | 29321 | ATCC 51513 | | type material | 29321 | CCUG 32254 | | type material | 29321 | CDC coryneform group ANF-1 like | | synonym | 29321 | CIP 104075 | | type material | 29321 | Corynebacterium otitidis | | synonym | 29321 | DSM 8821 | | type material | 29321 | JCM 12146 | | type material | 29321 | LMG 19071 | | type material | 29321 | Turicella otitidis | | scientific name | 29321 | Turicella otitidis Funke et al. 1994 | | authority | 29321 | strain 234/92 | | type material | 29347 | ATCC 35704 | | type material | 29347 | CIP 106687 | | type material | 29347 | Clostridium scindens | | scientific name | 29347 | Clostridium scindens Morris et al. 1985 | | authority | 29347 | DSM 5676 | | type material | 29347 | Eubacterium VPI-12708 | | includes | 29347 | Eubacterium sp. (strain VPI 12708) | | includes | 29347 | Eubacterium sp. VPI 12708 | | includes | 29347 | Eubacterium sp. VPI-12708 | | includes | 29347 | JCM 6567 | | type material | 29347 | [Clostridium] scindens | | equivalent name | 29347 | strain Bokkenheuser 19 | | type material | 29348 | ATCC 29900 | | type material | 29348 | CCUG 46510 | | type material | 29348 | CIP 106966 | | type material | 29348 | Clostridium spiroforme | | equivalent name | 29348 | Clostridium spiroforme Kaneuchi et al. 1979 | | authority | 29348 | DSM 1552 | | type material | 29348 | JCM 1432 | | type material | 29348 | NCTC 11211 | | type material | 29348 | VPI C28-23-1A | | type material | 29348 | [Clostridium] spiroforme | | scientific name | 29361 | ATCC 27757 | | type material | 29361 | Clostridium nexile | | scientific name | 29361 | Clostridium nexile Holdeman and Moore 1974 | | authority | 29361 | DSM 1787 | | type material | 29361 | [Clostridium] nexile | | equivalent name | 29380 | ATCC 35538 | | type material | 29380 | CCM 3573 | | type material | 29380 | CCUG 15604 | | type material | 29380 | CIP 104000 | | type material | 29380 | DSM 20608 | | type material | 29380 | NCTC 12196 | | type material | 29380 | NRRL B-14757 | | type material | 29380 | Staphylococcus caprae | | scientific name | 29380 | Staphylococcus caprae Devriese et al. 1983 emend. Kawamura et al. 1998 | | synonym | 29380 | strain 143.22 | | type material | 29388 | ATCC 27840 | | type material | 29388 | CCM 2734 | | type material | 29388 | CCUG 7326 | | type material | 29388 | CIP 81.53 | | type material | 29388 | DSM 20326 | | type material | 29388 | JCM 2420 | | type material | 29388 | LMG 13353 | | type material | 29388 | NCTC 11045 | | type material | 29388 | NRRL B-14752 | | type material | 29388 | Staphylococcus capiti | | misspelling | 29388 | Staphylococcus capitis | | scientific name | 29388 | Staphylococcus capitis Kloos and Schleifer 1975 | | synonym | 29466 | "Micrococcus gazogenes alcalescens anaerobius" Lewkowicz 1901 | | authority | 29466 | "Micrococcus gazogenes" Hall and Howitt 1925 | | authority | 29466 | "Micrococcus lactilyticus" Foubert and Douglas 1948 | | authority | 29466 | "Staphylococcus parvulus" Veillon and Zuber 1898 | | authority | 29466 | "Veillonella gazogenes" (Hall and Howitt 1925) Murray 1939 | | authority | 29466 | ATCC 10790 | | type material | 29466 | CCUG 5123 | | type material | 29466 | DSM 2008 | | type material | 29466 | JCM 12972 | | type material | 29466 | Micrococcus gazogenes | | synonym | 29466 | Micrococcus gazogenes alcalescens anaerobius | | synonym | 29466 | Micrococcus lactilyticus | | synonym | 29466 | NCTC 11810 | | type material | 29466 | Staphylococcus parvulus | | synonym | 29466 | Veillonella alcalescens | | synonym | 29466 | Veillonella alcalescens Prevot 1933 | | authority | 29466 | Veillonella gazogenes | | synonym | 29466 | Veillonella parvula | | scientific name | 29466 | Veillonella parvula (Veillon and Zuber 1898) Prevot 1933 (AL 1980) emend. Mays et al. 1982 | | authority | 29466 | not "Micrococcus gazogenes" Choukevitch 1911 | | authority | 31631 | HCoV-OC43 | | genbank acronym | 31631 | Human coronavirus (strain OC43) | | synonym | 31631 | Human coronavirus OC43 | | scientific name | 31631 | Human coronavirus strain OC43 | | synonym | 31732 | PWV | | acronym | 31732 | Passion fruit woodiness potyvirus | | synonym | 31732 | Passion fruit woodiness virus | | scientific name | 31732 | Passionfruit woodiness virus | | synonym | 33030 | "Micrococcus indolicus" Christiansen 1934 | | authority | 33030 | "Schleiferella indolica" Rajendram et al. 2001 | | authority | 33030 | ATCC 29427 | | type material | 33030 | CCUG 17639 | | type material | 33030 | CCUG 46591 | | type material | 33030 | DSM 20464 | | type material | 33030 | Micrococcus indolicus | | synonym | 33030 | NCTC 11088 | | type material | 33030 | Peptococcus indolicus | | synonym | 33030 | Peptococcus indolicus (Christiansen 1934) Sorensen 1975 (Approved Lists 1980) | | authority | 33030 | Peptoniphilus indolicus | | scientific name | 33030 | Peptoniphilus indolicus (Christiansen 1934) Ezaki et al. 2001 | | authority | 33030 | Peptostreptococcus indolicus | | synonym | 33030 | Peptostreptococcus indolicus (Christiansen 1934) Ezaki et al. 1983 | | authority | 33030 | Schleiferella indolica | | synonym | 33032 | ATCC 51172 | | type material | 33032 | Anaerococcus lactolyticus | | scientific name | 33032 | Anaerococcus lactolyticus (Li et al. 1992) Ezaki et al. 2001 | | authority | 33032 | CCUG 31351 | | type material | 33032 | CIP 103725 | | type material | 33032 | DSM 7456 | | type material | 33032 | GIFU 8586 | | type material | 33032 | JCM 8140 | | type material | 33032 | Peptostreptococcus lactolyticus | | synonym | 33032 | Peptostreptococcus lactolyticus Li et al. 1992 | | authority | 33033 | "Streptococcus anaerobius micros" Lewkowicz 1901 | | authority | 33033 | "Streptococcus micros" Prevot 1933 | | authority | 33033 | 'Diplococcus glycinophilus' | | synonym | 33033 | ATCC 33270 | | type material | 33033 | CCUG 17638 | | type material | 33033 | CCUG 17638 A | | type material | 33033 | CCUG 46357 | | type material | 33033 | CIP 105294 | | type material | 33033 | DSM 20468 | | type material | 33033 | Diplococcus glycinophilus | | synonym | 33033 | JCM 12970 | | type material | 33033 | KCTC 5196 | | type material | 33033 | Micromonas micros | | misnomer | 33033 | Micromonas micros (Prevot 1933) Murdoch and Shah 2000 | | authority | 33033 | NCTC 11808 | | type material | 33033 | Parvimonas micra | | scientific name | 33033 | Parvimonas micra (Prevot 1933) Tindall and Euzeby 2006 | | authority | 33033 | Peptococcus glycinophilus | | synonym | 33033 | Peptostreptococcus micros | | synonym | 33033 | Peptostreptococcus micros (Prevot 1933) Smith 1957 (Approved Lists 1980) | | authority | 33033 | Streptococcus anaerobius micros | | synonym | 33033 | Streptococcus micros | | synonym | 33033 | strain 3119B | | type material | 33036 | "Gaffkya anaerobius" (sic) (Choukevitch 1911) Prevot 1933 | | authority | 33036 | "Tetracoccus anaerobius" Choukevitch 1911 | | authority | 33036 | ATCC 35098 | | type material | 33036 | Anaerococcus tetradius | | scientific name | 33036 | Anaerococcus tetradius (Ezaki et al. 1983) Ezaki et al. 2001 | | authority | 33036 | CCM 3634 | | type material | 33036 | CCUG 17637 | | type material | 33036 | CCUG 46590 | | type material | 33036 | CIP 103927 | | type material | 33036 | DSM 2951 | | type material | 33036 | GIFU 7672 | | type material | 33036 | Gaffkya anaerobius | | synonym | 33036 | JCM 1964 | | type material | 33036 | LMG 14264 | | type material | 33036 | Peptostreptococcus tetradius | | synonym | 33036 | Peptostreptococcus tetradius (ex Choukevitch 1911) Ezaki et al. 1983 | | authority | 33036 | Tetracoccus anaerobius | | synonym | 33038 | ATCC 29149 | | type material | 33038 | Ruminococcus gnavus | | equivalent name | 33038 | Ruminococcus gnavus Moore et al. 1976 | | authority | 33038 | Ruminococcus gravus | | misspelling | 33038 | VPI C7-9 | | type material | 33038 | [Ruminococcus] gnavus | | scientific name | 33043 | ATCC 27759 | | type material | 33043 | Coprococcus eutactus | | scientific name | 33043 | Coprococcus eutactus Holdeman and Moore 1974 | | synonym | 37372 | ATCC 51630 | | type material | 37372 | CCUG 38995 B | | type material | 37372 | CIP 104752 | | type material | 37372 | Flexispira rappini species 8 | | includes | 37372 | Flexispira taxon 9 | | includes | 37372 | Helicobacter bilis | | scientific name | 37372 | Helicobacter bilis Fox et al. 1997 | | authority | 37372 | Helicobacter sp. 'Flexispira taxon 2' | | includes | 37372 | Helicobacter sp. 'Flexispira taxon 3' | | includes | 37372 | Helicobacter sp. 'Flexispira taxon 8' | | includes | 37372 | Helicobacter sp. 'Flexispira taxon 9' | | includes | 37372 | Helicobacter sp. ATCC 43879 | | includes | 37372 | Helicobacter sp. ATCC 49314 | | includes | 37372 | Helicobacter sp. ATCC 49317 | | includes | 37372 | Helicobacter sp. ATCC 49320 | | includes | 37372 | strain Hb1 | strain Hb1 | type material | 38303 | "Corynebacterium pseudogenitalium" Furness et al. 1979 | | synonym | 38303 | Corynebacterium pseudogenitalium | | scientific name | 38304 | "Corynebacterium tuberculostearicum" Brown et al. 1984 | | synonym | 38304 | ATCC 35692 | | type material | 38304 | CCUG 45418 | | type material | 38304 | CIP 107291 | | type material | 38304 | Corynebacterium sp. CIP101775 | | includes | 38304 | Corynebacterium sp. CIP102076 | | includes | 38304 | Corynebacterium sp. CIP102124 | | includes | 38304 | Corynebacterium sp. CIP102211 | | includes | 38304 | Corynebacterium sp. CIP102346 | | includes | 38304 | Corynebacterium sp. CIP102590 | | includes | 38304 | Corynebacterium sp. CIP102622 | | includes | 38304 | Corynebacterium sp. CIP102645 | | includes | 38304 | Corynebacterium sp. CIP102857 | | includes | 38304 | Corynebacterium sp. CIP107067 | | includes | 38304 | Corynebacterium sp. CIP107291 | | includes | 38304 | Corynebacterium tuberculostearicum | | scientific name | 38304 | Corynebacterium tuberculostearicum Feurer et al. 2004 | | synonym | 38304 | DSM 44922 | | type material | 38304 | JCM 13389 | | type material | 38304 | strain LDC-20 | | type material | 38304 | strain Medalle X | | type material | 39488 | ATCC 27751 | | type material | 39488 | DSM 3353 | | type material | 39488 | Eubacterium halii | | misspelling | 39488 | Eubacterium hallii | | scientific name | 39488 | Eubacterium hallii Holdeman and Moore 1974 | | authority | 39488 | VPI B4-27 | | type material | 39488 | [Eubacterium] hallii | | equivalent name | 39496 | "Bacillus ventriosus" Tissier 1908 | | authority | 39496 | "Bacteroides ventriosus" (Tissier 1908) Eggerth 1935 | | authority | 39496 | "Pseudobacterium ventriosum" (Tissier 1908) Krasil'nikov 1949 | | authority | 39496 | ATCC 27560 | | type material | 39496 | Bacillus ventriosus | | synonym | 39496 | Bacteroides ventriosus | | synonym | 39496 | DSM 3988 | | type material | 39496 | Eubacterium ventriosum | | scientific name | 39496 | Eubacterium ventriosum (Tissier 1908) Prevot 1938 | | authority | 39496 | Pseudobacterium ventriosum | | synonym | 39496 | [Eubacterium] ventriosum | | equivalent name | 39778 | ATCC 17748 | | type material | 39778 | DSM 20735 | | type material | 39778 | NCTC 11831 | | type material | 39778 | Veillonella alcalescens subsp. dispar | | synonym | 39778 | Veillonella dispar | | scientific name | 39778 | Veillonella dispar (Rogosa 1965) Mays et al. 1982 | | synonym | 40091 | ATCC 51366 | | type material | 40091 | CCUG 32213 | | type material | 40091 | CIP 103932 | | type material | 40091 | DSM 10548 | | type material | 40091 | Helcococcus kunzii | | scientific name | 40091 | Helcococcus kunzii Collins et al. 1993 | | authority | 40091 | Helococcus kunzii | | misspelling | 40091 | IFO 15552 | | type material | 40091 | LMG 15123 | | type material | 40091 | NBRC 15552 | | type material | 40091 | NCFB 2900 | | type material | 40091 | NCIMB 702900 | | type material | 40091 | strain n. 22 | | type material | 40215 | ATCC 17908 | | type material | 40215 | Acinetobacter genomosp. 5 | | synonym | 40215 | Acinetobacter genomospecies 5 | | synonym | 40215 | Acinetobacter grimontii | | genbank synonym | 40215 | Acinetobacter grimontii Carr et al. 2003 | | authority | 40215 | Acinetobacter junii | | scientific name | 40215 | Acinetobacter junii Bouvet and Grimont 1986 | | authority | 40215 | CCUG 889 | | type material | 40215 | CIP 64.5 | | type material | 40215 | DSM 6964 | | type material | 40215 | LMG 998 | | type material | 40215 | NCTC 12153 | | type material | 40215 | strain Mannheim 2723/59 | | type material | 40216 | ATCC 43998 | | type material | 40216 | Acinetobacter genomosp. 12 | | synonym | 40216 | Acinetobacter genomospecies 12 | | synonym | 40216 | Acinetobacter radiiresistens | | misspelling | 40216 | Acinetobacter radioresistens | | scientific name | 40216 | Acinetobacter radioresistens Nishimura et al. 1988 | | authority | 40216 | CIP 103788 | | type material | 40216 | DSM 6976 | | type material | 40216 | IAM 13186 | | type material | 40216 | JCM 9326 | | type material | 40216 | LMG 10613 | | type material | 40216 | NBRC 102413 | | type material | 40216 | strain FO-1 | | type material | 40520 | ATCC 29174 | | type material | 40520 | DSM 25238 | | type material | 40520 | Eubacterium obeum | | misspelling | 40520 | Ruminococcus obeum | | equivalent name | 40520 | Ruminococcus obeum Moore et al. 1976 | | authority | 40520 | [Ruminococcus] obeum | | scientific name | 41294 | 'Bradyrhizobiaceae' | | synonym | 41294 | BANA domain | | synonym | 41294 | Bradyrhizobiaceae | | scientific name | 41294 | Bradyrhizobium group | | synonym | 41294 | Nitrobacteraceae | | includes | 41294 | Nitrobacteraceae Buchanan 1917 | | includes | 41294 | Nitrobacteriaceae | | misspelling | 41294 | alpha-2 proteobacteria | alpha-2 proteobacteria <2> | in-part | 42005 | HEV | HEV <#2> | acronym | 42005 | Hemagglutinating encephalomyelitis virus | | synonym | 42005 | PHEV | | acronym | 42005 | Porcine hemagglutinating encephalomyelitis coronavirus | | synonym | 42005 | Porcine hemagglutinating encephalomyelitis virus | | scientific name | 42005 | porcine hemagglutinating encephalomyelitis virus HEV | | misspelling | 42475 | RRSV | | acronym | 42475 | Rice ragged stunt virus | | scientific name | 42475 | rice ragged stunt oryzavirus | | synonym | 43675 | "Micrococcus mucilaginosus" Migula 1900 | | authority | 43675 | ATCC 25296 | | type material | 43675 | CCM 2417 | | type material | 43675 | CCUG 20962 | | type material | 43675 | CIP 71.14 | | type material | 43675 | DSM 20746 | | type material | 43675 | IFO 15673 | | type material | 43675 | JCM 10910 | | type material | 43675 | Micrococcus mucilaginosus | | synonym | 43675 | NBRC 15673 | | type material | 43675 | NCTC 10663 | | type material | 43675 | Rothia mucilaginosa | | scientific name | 43675 | Rothia mucilaginosa (Bergan and Kocur 1982) Collins et al. 2000 | | authority | 43675 | Stomatococcus mucilaginosus | | synonym | 43675 | Stomatococcus mucilaginosus (ex Migula 1900) Bergan and Kocur 1982 | | authority | 43765 | 'Corynebacterium asperum' | | synonym | 43765 | ATCC 49368 | | type material | 43765 | CCUG 35685 | | type material | 43765 | CDC coryneform group F-2 | | includes | 43765 | CDC coryneform group I-2 | | includes | 43765 | CIP 103452 | | type material | 43765 | Corynebacterium amycolatum | | scientific name | 43765 | Corynebacterium amycolatum Collins et al. 1988 | | synonym | 43765 | Corynebacterium asperum | | synonym | 43765 | DSM 6922 | | type material | 43765 | IFO 15207 | | type material | 43765 | JCM 7447 | | type material | 43765 | NBRC 15207 | | type material | 43765 | NCFB 2768 | | type material | 43765 | NCIMB 13130 | | type material | 43765 | strain S160 | | type material | 43768 | "Actinomyces matruchoti" (Mendel 1919) Nannizzi 1934 | | synonym | 43768 | "Cladothrix matruchoti" (sic) Mendel 1919 | | synonym | 43768 | "Oospora matruchoti" (Mendel 1919) Sartory 1930 | | synonym | 43768 | ATCC 14266 | | type material | 43768 | Actinomyces matruchoti | | synonym | 43768 | Bacterionema matruchotii | | synonym | 43768 | Bacterionema matruchotii (Mendel 1919) Gilmour et al. 1961 (Approved Lists 1980) | | synonym | 43768 | CCUG 27545 | | type material | 43768 | CCUG 46620 | | type material | 43768 | CIP 81.82 | | type material | 43768 | Cladothrix matruchoti | | synonym | 43768 | Corynebacterium matruchotii | | scientific name | 43768 | Corynebacterium matruchotii (Mendel 1919) Collins 1983 | | synonym | 43768 | DSM 20635 | | type material | 43768 | IFO 15360 | | type material | 43768 | JCM 9386 | | type material | 43768 | NBRC 15360 | | type material | 43768 | NCTC 10254 | | type material | 43768 | Oospora matruchoti | | synonym | 43770 | "Bacterium striatum" Chester 1901 | | synonym | 43770 | ATCC 6940 | | type material | 43770 | Bacterium striatum | | synonym | 43770 | CCUG 27949 | | type material | 43770 | CIP 81.15 | | type material | 43770 | Corynebacterium striatum | | scientific name | 43770 | Corynebacterium striatum (Chester 1901) Eberson 1918 | | synonym | 43770 | DSM 20668 | | type material | 43770 | IFO 15291 | | type material | 43770 | JCM 9390 | | type material | 43770 | NBRC 15291 | | type material | 43770 | NCTC 764 | | type material | 44088 | Avipoxvirus clade B1 | | synonym | 44088 | Canarypox virus | | scientific name | 45851 | ATCC 29175 | | type material | 45851 | Butyrivibrio crossotus | | scientific name | 45851 | Butyrivibrio crossotus Moore et al. 1976 | | synonym | 45851 | DSM 2876 | | type material | 45851 | VPI T9-40A | | type material | 46015 | AcMNPV | | acronym | 46015 | Autographa californica multicapsid nuclear polyhedrosis virus | | synonym | 46015 | Autographa californica multicapsid nuclear polyhedrosis virus AcMNPV | | synonym | 46015 | Autographa californica nuclear polyhedrosis virus | | synonym | 46015 | Autographa californica nuclear polyhedrosis virus AcMNPV | | synonym | 46015 | Autographa californica nuclear polyhedrosis virus AcNPV | | synonym | 46015 | Autographa californica nuclear polyhedrosis virus, AcMNPV | | synonym | 46015 | Autographa californica nucleopolyhedrovirus | | scientific name | 46503 | ATCC 43184 | | type material | 46503 | Bacteroides merdae | | synonym | 46503 | Bacteroides merdae Johnson et al. 1986 | | authority | 46503 | CCUG 38734 | | type material | 46503 | CIP 104202 | | type material | 46503 | JCM 9497 | | type material | 46503 | NCTC 13052 | | type material | 46503 | Parabacteroides merdae | | scientific name | 46503 | Parabacteroides merdae (Johnson et al. 1986) Sakamoto and Benno 2006 | | authority | 46503 | VPI T4-1 | | type material | 47229 | CCUG 45783 | | type material | 47229 | CIP 105350 | | type material | 47229 | Janthinobacterium sp. R2-11 | | includes | 47229 | Massilia timonae | | scientific name | 47229 | Massilia timonae La Scola et al. 2000 emend. Lindquist et al. 2003 | | authority | 47229 | Timone isolate | | synonym | 47229 | strain UR/MT95 | | type material | 47671 | ATCC 51599 | | type material | 47671 | CCUG 34794 | | type material | 47671 | CIP 106317 | | type material | 47671 | DSM 11362 | | type material | 47671 | Lautropia mirabilis | | scientific name | 47671 | Lautropia mirabilis Gerner-Smidt et al. 1995 | | authority | 47671 | NCTC 12852 | | type material | 47671 | strain AB2188 | | type material | 47678 | ATCC 43185 | | type material | 47678 | Bacteroides caccae | | scientific name | 47678 | Bacteroides caccae Johnson et al. 1986 | | authority | 47678 | CCUG 38735 | | type material | 47678 | CIP 104201 | | type material | 47678 | DSM 19024 | | type material | 47678 | JCM 9498 | | type material | 47678 | NCTC 13051 | | type material | 47678 | VPI 3452A | | type material | 49338 | DSM 10664 | | type material | 49338 | Desulfitobacterium frappieri | | synonym | 49338 | Desulfitobacterium frappieri Bouchard et al. 1996 | | authority | 49338 | Desulfitobacterium hafniense | | scientific name | 49338 | Desulfitobacterium hafniense Christiansen and Ahring 1996 emend. Niggemyer et al. 2001 | | authority | 49338 | anaerobic eubacterium PCP-1 | | includes | 49338 | strain DCB-2 | | type material | 52226 | ATCC 27723 | | type material | 52226 | Bacteroides multiacidus Mitsuoka et al. 1974 (Approved Lists 1980) | | synonym | 52226 | CCUG 21055 | | type material | 52226 | CIP 107116 | | type material | 52226 | DSM 20544 | | type material | 52226 | JCM 2054 | | type material | 52226 | Mitsuokella multacida | | scientific name | 52226 | Mitsuokella multacida corrig. (Mitsuoka et al. 1974) Shah and Collins 1983 | | synonym | 52226 | Mitsuokella multiacidus | | synonym | 52226 | NCTC 10934 | | type material | 53443 | Blautia hydrogenotrophica | | scientific name | 53443 | Blautia hydrogenotrophica (Bernalier et al. 1997) Liu et al. 2008 | | authority | 53443 | DSM 10507 | | type material | 53443 | JCM 14656 | | type material | 53443 | Ruminococcus hydrogenotrophicus | | synonym | 53443 | Ruminococcus hydrogenotrophicus Bernalier et al. 1997 | | authority | 53443 | strain S5a33 | | type material | 55565 | Actinomyces graevenitzii | | scientific name | 55565 | Actinomyces graevenitzii Pascual Ramos et al. 1997 | | authority | 55565 | CCUG 27294 | | type material | 55565 | CIP 105737 | | type material | 55565 | DSM 15540 | | type material | 56774 | Eubacterium infirmum | | equivalent name | 56774 | Eubacterium infirmum Cheeseman et al. 1996 | | authority | 56774 | Eubacterium sp. (strain W 1417) | | includes | 56774 | NCTC 12940 | | type material | 56774 | [Eubacterium] infirmum | | scientific name | 56946 | ATCC 49717 | | type material | 56946 | Afipia broomae | | misspelling | 56946 | Afipia broomeae | | scientific name | 56946 | Afipia broomeae Brenner et al. 1992 | | authority | 56946 | CCUG 30458 | | type material | 56946 | CIP 103517 | | type material | 56946 | DSM 7327 | | type material | 56946 | NCTC 12720 | | type material | 56946 | strain B-91-007286 | | type material | 60133 | AHN 10371 | | type material | 60133 | ATCC 700821 | | type material | 60133 | CCUG 39484 | | type material | 60133 | CIP 105551 | | type material | 60133 | DSM 18710 | | type material | 60133 | JCM 11140 | | type material | 60133 | NCTC 13042 | | type material | 60133 | Prevotella intermedia / Prevotella nigrescens-like organism (PINLO) | | synonym | 60133 | Prevotella pallens | | scientific name | 60133 | Prevotella pallens Kononen et al. 1998 | | authority | 61171 | ATCC 51649 | | type material | 61171 | DSM 12042 | | type material | 61171 | Eubacterium-like group S14 | | synonym | 61171 | Holdemania filiformis | | scientific name | 61171 | Holdemania filiformis Willems et al. 1997 | | synonym | 61171 | strain J1-31B-1 | | type material | 68892 | ATCC 700779 | | type material | 68892 | CCUG 39817 | | type material | 68892 | CIP 105949 | | type material | 68892 | DSM 12492 | | type material | 68892 | GTC 849 | | type material | 68892 | JCM 10157 | | type material | 68892 | LMG 18720 | | type material | 68892 | Streptococcus infantis | | scientific name | 68892 | Streptococcus infantis Kawamura et al. 1998 | | authority | 68892 | strain O-122 | | type material | 69218 | ATCC 33241 | | type material | 69218 | CCUG 25231 | | type material | 69218 | CDC Enteric Group 19 | | synonym | 69218 | CFBP 4167 | | type material | 69218 | CIP 103787 | | type material | 69218 | DSM 17580 | | type material | 69218 | Enterobacter cancerogenus | | scientific name | 69218 | Enterobacter cancerogenus (Urosevic 1966) Dickey and Zumoff 1988 | | authority | 69218 | Enterobacter taylorae | | synonym | 69218 | Enterobacter taylorae Farmer et al. 1985 | | authority | 69218 | Erwinia cancerogena | | synonym | 69218 | Erwinia cancerogena Urosevic 1966 (Approved Lists 1980) | | authority | 69218 | ICMP 5706 | | type material | 69218 | LMG 2693 | | type material | 69218 | NCPPB 2176 | | type material | 69823 | "Spirillum sputigenum" Flugge 1886 | | authority | 69823 | "Vibrio sputigenus" Prevot 1940 | | authority | 69823 | ATCC 35185 | ATCC 35185 | type material | 69823 | CCUG 44933 | CCUG 44933 | type material | 69823 | DSM 20758 | DSM 20758 | type material | 69823 | Selenomonas sputigena | | scientific name | 69823 | Selenomonas sputigena (Flugge 1886) Boskamp 1922 (Approved Lists 1980) emend. Judicial Commission 1992 | | authority | 69823 | Spirillum sputigenum | | synonym | 69823 | VPI D 19B-28 | VPI D 19B-28 | type material | 69823 | Vibrio sputigenus | | synonym | 72556 | ATCC 43552 | | type material | 72556 | Achromobacter piechaudii | | scientific name | 72556 | Achromobacter piechaudii (Kiredjian et al. 1986) Yabuuchi et al. 1998 | | authority | 72556 | Alcaligenes piechaudii | | synonym | 72556 | Alcaligenes piechaudii Kiredjian et al. 1986 | | authority | 72556 | CCUG 724 | | type material | 72556 | CIP 60.75 | | type material | 72556 | DSM 10342 | | type material | 72556 | IAM 12591 | | type material | 72556 | JCM 20668 | | type material | 72556 | LMG 1873 | | type material | 72556 | NBRC 102461 | | type material | 72556 | NCTC 11970 | | type material | 72556 | strain Hugh 366-5 | | type material | 74426 | "Bacteroides aerofaciens" Eggerth 1935 | | synonym | 74426 | "Pseudobacterium aerofaciens" (Eggerth 1935) Krasil'nikov 1949 | | synonym | 74426 | ATCC 25986 | | type material | 74426 | Bacteroides aerofaciens | | synonym | 74426 | CCUG 28087 | | type material | 74426 | Collinsella aerofaciens | | scientific name | 74426 | Collinsella aerofaciens (Eggerth 1935) Kageyama et al. 1999 | | synonym | 74426 | DSM 3979 | | type material | 74426 | Eubacterium aerofaciens | | synonym | 74426 | Eubacterium aerofaciens (Eggerth 1935) Prevot 1938 (Approved Lists 1980) | | synonym | 74426 | JCM 10188 | | type material | 74426 | NCTC 11838 | | type material | 74426 | Pseudobacterium aerofaciens | | synonym | 74426 | VPI 1003 | | type material | 76831 | Myroides | | scientific name | 76831 | Myroides Vancanneyt et al. 1996 emend. Yan et al. 2012 | | authority | 76832 | CCUG 39352 | | type material | 76832 | CIP 105170 | | type material | 76832 | JCM 7460 | | type material | 76832 | LMG 4029 | | type material | 76832 | Myroides odoratimimus | | scientific name | 76832 | Myroides odoratimimus Vancanneyt et al. 1996 | | authority | 76832 | NCTC 11180 | | type material | 78342 | AS 1.2274 | | type material | 78342 | ATCC 49850 | | type material | 78342 | Bifidobacterium gallicum | | scientific name | 78342 | Bifidobacterium gallicum Lauer 1990 | | synonym | 78342 | CCUG 34979 | | type material | 78342 | CIP 103417 | | type material | 78342 | DSM 20093 | | type material | 78342 | JCM 8224 | | type material | 78342 | LMG 11596 | | type material | 80366 | NOT Rachiplusia nu MNPV | | equivalent name | 80366 | Rachiplusia ou MNPV | | scientific name | 80366 | Rachiplusia ou multiple nucleopolyhedrovirus | | synonym | 80366 | Rachiplusia ou nuclear polyhedrosis virus | | synonym | 82135 | ATCC BAA-55 | | type material | 82135 | Atopobium vaginae | | scientific name | 82135 | Atopobium vaginae Rodriguez Jovita et al. 1999 | | authority | 82135 | CCUG 38953 | | type material | 82135 | CIP 106431 | | type material | 82135 | DSM 15829 | | type material | 84026 | ATCC 43829 | | type material | 84026 | Clostridium methylpentosum | | scientific name | 84026 | Clostridium methylpentosum Himelbloom and Canale-Parola 1989 | | authority | 84026 | DSM 5476 | | type material | 84026 | [Clostridium] methylpentosum | | equivalent name | 84026 | strain R2 | strain R2 | type material | 85698 | "Achromobacter xylosoxidans" Yabuuchi and Ohyama 1971 | | authority | 85698 | ATCC 27061 | | type material | 85698 | Achromobacter xylosoxidans | | scientific name | 85698 | Achromobacter xylosoxidans (ex Yabuuchi and Ohyama 1971) Yabuuchi and Yano 1981 | | authority | 85698 | Achromobacter xylosoxidans KF701 | | includes | 85698 | Achromobacter xylosoxidans subsp. xylosoxidans | | includes | 85698 | Achromobacter xylosoxidans subsp. xylosoxidans (ex Yabuuchi & Ohyama 1971) Yabuuchi & Yano 1981 | | authority | 85698 | Achromobacter xylosoxydans | | equivalent name | 85698 | Alcaligenes denitrificans subsp. xylosoxydans | | includes | 85698 | Alcaligenes denitrificans subsp. xylosoxydans (Yabuuchi and Yano 1981) Kersters and De Ley 1984 | | authority | 85698 | Alcaligenes denitrificans xylosoxydans | | includes | 85698 | Alcaligenes xylosoxidans | | synonym | 85698 | Alcaligenes xylosoxidans (Yabuuchi and Yano 1981) Kiredjian et al. 1986 | | authority | 85698 | Alcaligenes xylosoxidans subsp. xylosoxidans | | includes | 85698 | Alcaligenes xylosoxidans subsp. xylosoxidans (Yabuuchi and Yano 1981) Kiredjian et al. 1986 | | authority | 85698 | Alcaligenes xylosoxydans | | equivalent name | 85698 | Alcaligenes xylosoxydans xylosoxydans | | includes | 85698 | CCUG 12689 | | type material | 85698 | CIP 71.32 | | type material | 85698 | DSM 10346 | | type material | 85698 | DSM 2402 | | type material | 85698 | Flavobacterium sp. 650 | | includes | 85698 | IFO 15126 | | type material | 85698 | JCM 9659 | | type material | 85698 | LMG 1863 | | type material | 85698 | NBRC 15126 | | type material | 85698 | NCTC 10807 | | type material | 85698 | NRRL B-4082 | | type material | 85698 | strain Hugh 2838 | | type material | 85698 | strain KM 543 | | type material | 85698 | strain Yabuuchi KM 543 | | type material | 89153 | CIP 106689 | | type material | 89153 | Clostridium hylemonae | | scientific name | 89153 | Clostridium hylemonae Kitahara et al. 2000 | | authority | 89153 | DSM 15053 | | type material | 89153 | JCM 10539 | | type material | 89153 | [Clostridium] hylemonae | | equivalent name | 89153 | strain TN-271 | | type material | 91753 | CABYV | | acronym | 91753 | Cucurbit aphid borne yellowing virus | | misnomer | 91753 | Cucurbit aphid-borne yellows virus | | scientific name | 101850 | Thysanoplusia orichalcea MNPV | | synonym | 101850 | Thysanoplusia orichalcea NPV | | synonym | 101850 | Thysanoplusia orichalcea multicapsid nucleopolyhedrovirus | | synonym | 101850 | Thysanoplusia orichalcea multiple nucleopolyhedrovirus | | synonym | 101850 | Thysanoplusia orichalcea nucleopolyhedrovirus | | scientific name | 102148 | Bulleidia moorei | | misspelling | 102148 | CIP 106864 | | type material | 102148 | JCM 10645 | | type material | 102148 | Solobacterium moorei | | scientific name | 102148 | Solobacterium moorei Kageyama and Benno 2000 | | authority | 102148 | strain RCA59-74 | | type material | 102148 | unclassified Clostridium group RCA59 | | synonym | 102862 | ATCC 33519 | | type material | 102862 | CCUG 15722 | | type material | 102862 | CDC 1808-73 | | type material | 102862 | CIP 103030 | | type material | 102862 | DSM 4544 | | type material | 102862 | JCM 3948 | | type material | 102862 | NCTC 12737 | | type material | 102862 | Proteus genomosp. 1 | | synonym | 102862 | Proteus genomospecies 1 | | synonym | 102862 | Proteus penneri | | scientific name | 102862 | Proteus penneri Hickman et al. 1983 | | synonym | 102862 | Proteus vulgaris biogroup 1 | | synonym | 102862 | Proteus vulgaris indole negative | | synonym | 103618 | Actinomyces coleocanis | | scientific name | 103618 | Actinomyces coleocanis Hoyles et al. 2002 | | authority | 103618 | Actinomyces sp. CCUG 41708 | | includes | 103618 | CCUG 41708 | | type material | 103618 | CIP 106873 | | type material | 103618 | DSM 15436 | | type material | 103618 | strain M343/98/2 | | type material | 103621 | Actinomyces sp. CCUG 28744 | | includes | 103621 | Actinomyces sp. CCUG 42029 | | equivalent name | 103621 | Actinomyces urogenitalis | | scientific name | 103621 | Actinomyces urogenitalis Nikolaitchouk et al. 2000 | | synonym | 103621 | CCUG 38702 | | type material | 103621 | CIP 106421 | | type material | 103621 | DSM 15434 | | type material | 106588 | "Bacillus capillosus" Tissier 1908 | | authority | 106588 | "Pseudobacterium capillosum" (Tissier 1908) Krasil'nikov 1949 | | authority | 106588 | "Ristella capillosa" (Tissier 1908) Prevot 1938 | | authority | 106588 | ATCC 29799 | | type material | 106588 | Bacillus capillosus | | synonym | 106588 | Bacteroides capillosus | | synonym | 106588 | Bacteroides capillosus (Tissier 1908) Kelly 1957 | | authority | 106588 | CCUG 15402 A | | type material | 106588 | DSM 23940 | | type material | 106588 | Pseudobacterium capillosum | | synonym | 106588 | Pseudoflavonifractor capillosus | | scientific name | 106588 | Pseudoflavonifractor capillosus (Tissier 1908) Carlier et al. 2010 | | authority | 106588 | Ristella capillosa | | synonym | 106588 | VPI R2-29-1 | | type material | 112023 | Streptococcus phage 7201 | | scientific name | 112023 | Streptococcus thermophilus bacteriophage 7201 | | synonym | 113287 | "Ramibacterium alactolyticum" Prevot and Taffanel 1942 | | authority | 113287 | "Ramibacterium dentium" Vinzent and Reynes 1947 | | authority | 113287 | "Ramibacterium pleuriticum" Prevot et al. 1947 | | authority | 113287 | ATCC 23263 | | type material | 113287 | CIP 106365 | | type material | 113287 | DSM 3980 | | type material | 113287 | Eubacterium alactolyticum | | synonym | 113287 | Eubacterium alactolyticum (Prevot and Taffanel 1942) Holdeman and Moore 1970 (Approved Lists 1980) | | authority | 113287 | JCM 6480 | | type material | 113287 | Pseudoramibacter alactolyticus | | scientific name | 113287 | Pseudoramibacter alactolyticus (Prevot and Taffanel 1942) Willems and Collins 1996 | | authority | 113287 | Ramibacterium alactolyticum | | synonym | 113287 | Ramibacterium dentium | | synonym | 113287 | Ramibacterium pleuriticum | | synonym | 118748 | ATCC BAA-170 | | type material | 118748 | Bulleidia extructa | | scientific name | 118748 | Bulleidia extructa Downes et al. 2000 | | synonym | 118748 | DSM 13220 | | type material | 118748 | strain W 1219 | | type material | 133448 | ATCC 29935 | | type material | 133448 | CCUG 30791 | | type material | 133448 | CDC 460-61 | | type material | 133448 | CIP 105016 | | type material | 133448 | Citrobacter genomospecies 5 | | synonym | 133448 | Citrobacter youngae | | scientific name | 133448 | Citrobacter youngae Brenner et al. 1993 | | authority | 133448 | DSM 17578 | | type material | 133448 | GTC 1314 | | type material | 135083 | ATCC 43541 | | type material | 135083 | DSM 19578 | | type material | 135083 | JCM 8546 | | type material | 135083 | Selenomonas noxia | | scientific name | 135083 | Selenomonas noxia Moore et al. 1987 | | authority | 135083 | VPI D9B-5 | | type material | 136187 | Equine coronavirus | | scientific name | 137732 | ATCC 700633 | | type material | 137732 | Abiotrophia elegans | | synonym | 137732 | Abiotrophia elegans Roggenkamp et al. 1999 | | authority | 137732 | Abiotrophia sp. B1333 | | includes | 137732 | CCUG 38949 | | type material | 137732 | CIP 105513 | | type material | 137732 | DSM 11693 | | type material | 137732 | Granulicatella elegans | | scientific name | 137732 | Granulicatella elegans (Roggenkamp et al. 1999) Collins and Lawson 2000 | | authority | 137732 | strain B1333 | | type material | 138119 | Desulfitobacterium hafniense Y51 | | scientific name | 138119 | Desulfitobacterium hafniense str. Y51 | | equivalent name | 138119 | Desulfitobacterium hafniense strain Y51 | | equivalent name | 138119 | Desulfitobacterium sp. Y51 | | equivalent name | 147207 | CCUG 45296 | | type material | 147207 | CIP 106914 | | type material | 147207 | Collinsella group 2 | | synonym | 147207 | Collinsella intestinalis | | scientific name | 147207 | Collinsella intestinalis Kageyama and Benno 2000 | | synonym | 147207 | Collinsella sp. RCA56-68 | | includes | 147207 | Collinsella sp. RCA56-80 | | includes | 147207 | DSM 13280 | | type material | 147207 | JCM 10643 | | type material | 147207 | strain RCA56-68 | | type material | 154046 | CCUG 43506 | | type material | 154046 | Clostridium hathewayi | | scientific name | 154046 | Clostridium hathewayi Steer et al. 2002 | | authority | 154046 | Clostridium sp. DSM 13479 | | includes | 154046 | DSM 13479 | | type material | 154046 | [Clostridium] hathewayi | | equivalent name | 154046 | strain 1313 | | type material | 158877 | ATCC 49455 | | type material | 158877 | BCRC 12225 | | type material | 158877 | CCRC 12225 | | type material | 158877 | CIP 105435 | | type material | 158877 | Enteric Group 45 | | synonym | 158877 | JCM 2403 | | type material | 158877 | Koserella trabulsii | | synonym | 158877 | Koserella trabulsii Hickman-Brenner et al. 1985 | | authority | 158877 | NBRC 102600 | | type material | 158877 | NCTC 11966 | | type material | 158877 | NIH 725-83 | | type material | 158877 | Yokenella regensburgei | | scientific name | 158877 | Yokenella regensburgei Kosako et al. 1985 | | authority | 161889 | ATCC 700352 | | type material | 161889 | CCUG 37336 | | type material | 161889 | CIP 105127 | | type material | 161889 | Corynebacterium lipophiloflavum | | scientific name | 161889 | Corynebacterium lipophiloflavum Funke et al. 1997 | | synonym | 161889 | Corynebacterium sp. 1944 | | includes | 161889 | DMMZ 1944 | | type material | 161889 | DSM 44291 | | type material | 161889 | JCM 10383 | | type material | 163665 | CCUG 43457 | | type material | 163665 | CDC F9489 | | type material | 163665 | CIP 107079 | | type material | 163665 | Dysgonomonas mossii | | scientific name | 163665 | Dysgonomonas mossii Lawson et al. 2002 | | authority | 163665 | Dysgonomonas shahii | | misspelling | 163665 | JCM 16699 | | type material | 168384 | Bryantella formatexigens | | synonym | 168384 | Bryantella formatexigens Wolin et al. 2004 | | authority | 168384 | CCUG 46960 | | type material | 168384 | DSM 14469 | | type material | 168384 | Marvinbryantia formatexigens | | scientific name | 168384 | Marvinbryantia formatexigens (Wolin et al. 2004) Wolin et al. 2008 | | authority | 168384 | strain I-52 | | type material | 169435 | Anaerotruncus colihominis | | scientific name | 169435 | Anaerotruncus colihominis Lawson et al. 2004 | | synonym | 169435 | CCUG 45055 | | type material | 169435 | CIP 107754 | | type material | 169435 | DSM 17241 | | type material | 169435 | JCM 15631 | | type material | 169435 | Ruminococcus sp. 14565 | | includes | 169435 | WAL 14565 | | type material | 171549 | "Bacteroidales" Krieg 2011 | | authority | 171549 | Bacteroidales | | scientific name | 177972 | CCUG 45864 | | type material | 177972 | DSM 14600 | | type material | 177972 | Shuttleworthia satelles | | scientific name | 177972 | Shuttleworthia satelles Downes et al. 2002 | | authority | 177972 | VPI D143K-13 | | type material | 181082 | EhV-86 | | acronym | 181082 | Emiliana huxleyi virus 86 | | misspelling | 181082 | Emiliania huxleyi virus 86 | | scientific name | 186802 | Clostridiales | | scientific name | 186802 | Clostridiales Prevot 1953 | | authority | 186803 | Lachnospiraceae | | scientific name | 186803 | Lachnospiraceae Rainey 2010 | | authority | 189723 | CCUG 56105 | | type material | 189723 | DSM 21469 | | type material | 189723 | JCM 16134 | | type material | 189723 | Prevotella genomosp. E3 | | synonym | 189723 | Prevotella genomospecies E3 | | synonym | 189723 | Prevotella micans | | scientific name | 189723 | Prevotella micans Downes et al. 2009 | | authority | 189723 | Prevotella sp. E7.56 | | includes | 189723 | Prevotella sp. E7_56 | | misspelling | 189723 | strain E7.56 | | type material | 195099 | Campylobacter jejuni RM1221 | | scientific name | 195099 | Campylobacter jejuni str. RM1221 | | equivalent name | 195099 | Campylobacter jejuni strain RM1221 | | equivalent name | 199310 | Escherichia coli CFT073 | | scientific name | 199310 | Escherichia coli str. CFT073 | | equivalent name | 199310 | Escherichia coli strain CFT073 | | equivalent name | 204525 | ATCC 49957 | | type material | 204525 | CIP 104027 | | type material | 204525 | Roseomonas cervicalis | | scientific name | 204525 | Roseomonas cervicalis Rihs et al. 1998 | | synonym | 204525 | strain E7107 | | type material | 207244 | Anaerostipes | | scientific name | 207244 | Anaerostipes Schwiertz et al. 2002 emend. Eeckhaut et al. 2010 | | authority | 211110 | Streptococcus agalactiae NEM316 | | scientific name | 211110 | Streptococcus agalactiae str. NEM316 | | synonym | 214853 | ATCC BAA-858 | | type material | 214853 | Anaerofustis stercorihominis | | scientific name | 214853 | Anaerofustis stercorihominis Finegold et al 2004 | | synonym | 214853 | CCUG 47767 | | type material | 214853 | DSM 17244 | | type material | 214853 | Pseudoramibacter sp. wal 14563 | | includes | 214853 | WAL 14563 | | type material | 218538 | CCUG 47026 | | type material | 218538 | DSM 15470 | | type material | 218538 | Dialister invisus | | scientific name | 218538 | Dialister invisus Downes et al. 2003 | | authority | 218538 | JCM 17566 | | type material | 218538 | strain E7.25 | | type material | 219314 | Aeromicrobium marinum | | scientific name | 219314 | Aeromicrobium marinum Bruns et al. 2003 | | authority | 219314 | DSM 15272 | | type material | 219314 | JCM 13314 | | type material | 219314 | LMG 21768 | | type material | 225324 | ATCC 27094 | | type material | 225324 | Enhydrobacter aerosaccus | | scientific name | 225324 | Enhydrobacter aerosaccus Staley et al. 1987 | | synonym | 225324 | LMG 21877 | | type material | 228604 | DSM 15606 | | type material | 228604 | JCM 12084 | | type material | 228604 | Prevotella salivae | | scientific name | 228604 | Prevotella salivae Sakamoto et al. 2004 | | authority | 228604 | strain EPSA11 | | type material | 243275 | Treponema denticola ATCC 35405 | | scientific name | 243275 | Treponema denticola str. ATCC 35405 | | equivalent name | 245018 | Clostridiales bacterium SSC/2 | | synonym | 245018 | Clostridiales sp. SSC/2 | | misspelling | 245018 | butyrate-producing bacterium SSC/2 | | scientific name | 262177 | OpMNPV | | acronym | 262177 | Orgya pseudotsugata MNPV | | misspelling | 262177 | Orgya pseudotsugata nucleopolyhedrovirus | | synonym | 262177 | Orgyia pseudotsugata MNPV | | synonym | 262177 | Orgyia pseudotsugata multicapsid nuclear polyhedrosis virus | | synonym | 262177 | Orgyia pseudotsugata multicapsid nuclear polyhedrosis virus OpMNPV | | synonym | 262177 | Orgyia pseudotsugata multicapsid nucleopolyhedrovirus | | synonym | 262177 | Orgyia pseudotsugata multicapsid polyhedrosis virus | | synonym | 262177 | Orgyia pseudotsugata multinucleocapsid nuclear polyhedrosis virus | | synonym | 262177 | Orgyia pseudotsugata multiple nucleopolyhedrovirus | | scientific name | 282402 | DSM 16608 | | type material | 282402 | JCM 12541 | | type material | 282402 | Prevotella multiformis | | scientific name | 282402 | Prevotella multiformis Sakamoto et al. 2005 | | authority | 282402 | strain PPPA21 | | type material | 290028 | CoV-HKU1 | | synonym | 290028 | HCoV-HKU1 | | genbank acronym | 290028 | Human CoV/HKU1 | | synonym | 290028 | Human coronavirus HKU1 | | scientific name | 291644 | ATCC BAA-997 | | type material | 291644 | Bacteroides salyersae | | synonym | 291644 | Bacteroides salyersiae | | scientific name | 291644 | Bacteroides salyersiae corrig. Song et al. 2005 | | authority | 291644 | Bacteroides sp. WAL 10018 | | includes | 291644 | CCUG 48945 | | type material | 291644 | DSM 18765 | | type material | 291644 | JCM 12988 | | type material | 291644 | WAL 10018 | | type material | 291645 | ATCC BAA-998 | | type material | 291645 | Bacteroides nordii | | scientific name | 291645 | Bacteroides nordii Song et al. 2005 | | authority | 291645 | Bacteroides sp. WAL 11050 | | includes | 291645 | CCUG 48943 | | type material | 291645 | JCM 12987 | | type material | 291645 | WAL 11050 | | type material | 292800 | "Bacille de Plaut, Kritchevsky and Seguin 1921" | | authority | 292800 | "Bacillus plauti" (sic) Seguin 1928 | | authority | 292800 | "Fusocillus plauti" (sic) (Seguin 1928) Prevot 1938 | | authority | 292800 | "Zuberella plauti" (sic) (Seguin 1928) Sebald 1962 | | authority | 292800 | ATCC 29863 | | type material | 292800 | ATCC 49531 [[Clostridium orbiscindens]] | | type material | 292800 | Bacillus plauti | | synonym | 292800 | CCUG 28093 | | type material | 292800 | Clostridium orbiscindens | | synonym | 292800 | Clostridium orbiscindens Winter et al. 1991 | | authority | 292800 | DSM 4000 | | type material | 292800 | DSM 6740 [[Clostridium orbiscindens]] | | type material | 292800 | DSM 6749 [[Clostridium orbiscindens]] | | type material | 292800 | Eubacterium plautii | | synonym | 292800 | Eubacterium plautii (Seguin 1928) Hofstad and Aasjord 1982 | | authority | 292800 | Flavonifractor plautii | | scientific name | 292800 | Flavonifractor plautii (Seguin 1928) Carlier et al. 2010 | | authority | 292800 | Fusobacterium plautii | | synonym | 292800 | Fusobacterium plautii corrig. Seguin 1928 (Approved Lists 1980) | | authority | 292800 | Fusocillus plauti | | synonym | 292800 | Zuberella plauti | | synonym | 293178 | Enterobacteria phage JS98 | | scientific name | 295405 | Bacteroides fragilis YCH46 | | scientific name | 295405 | Bacteroides fragilis str. YCH46 | | equivalent name | 295405 | Bacteroides fragilis strain YCH46 | | equivalent name | 310297 | Bacteroides plebeius | | scientific name | 310297 | Bacteroides plebeius Kitahara et al. 2005 | | authority | 310297 | DSM 17135 | | type material | 310297 | JCM 12973 | | type material | 310297 | strain M12 | strain M12 | type material | 312008 | Citrus sudden death marafivirus | | synonym | 312008 | Citrus sudden death-associated virus | | scientific name | 328812 | ATCC BAA-1180 | | type material | 328812 | Bacteroides goldsteinii | | synonym | 328812 | Bacteroides goldsteinii Song et al. 2006 | | authority | 328812 | Bacteroides sp. WAL 12034 | | includes | 328812 | CCUG 48944 | | type material | 328812 | DSM 19448 | | type material | 328812 | JCM 13446 | | type material | 328812 | Parabacteroides goldsteinii | | scientific name | 328812 | Parabacteroides goldsteinii (Song et al. 2006) Sakamoto and Benno 2006 | | authority | 328812 | WAL 12034 | | type material | 331278 | Bacteriophage phiR1-37 | | synonym | 331278 | Yersinia phage phiR1-37 | | scientific name | 331278 | Yersiniophage phiR1-37 | | synonym | 334390 | Lactobacillus fermentum IFO 3956 | | scientific name | 334390 | Lactobacillus fermentum IFO3956 | | misspelling | 334390 | Lactobacillus fermentum NBRC 3956 | | synonym | 334390 | Lactobacillus fermentum str. IFO 3956 | | equivalent name | 334390 | Lactobacillus fermentum strain IFO 3956 | | equivalent name | 338188 | Bacteroides finegoldii | | scientific name | 338188 | Bacteroides finegoldii Bakir et al. 2006 | | authority | 338188 | DSM 17565 | | type material | 338188 | JCM 13345 | | type material | 338188 | strain 199 | | type material | 354276 | Enterobacter cloacae complex | | scientific name | 357276 | Bacteroides dorei | | scientific name | 357276 | Bacteroides dorei Bakir et al. 2006 | | authority | 357276 | Bacteroides sp. 175T | | includes | 357276 | Bacteroides sp. 219 | | includes | 357276 | DSM 17855 | | type material | 357276 | JCM 13471 | | type material | 357276 | strain 175 | | type material | 362663 | Escherichia coli 536 | | scientific name | 362663 | Escherichia coli str. 536 | | equivalent name | 362663 | Escherichia coli strain 536 | | equivalent name | 363265 | DSM 18206 | | type material | 363265 | JCM 13469 | | type material | 363265 | Prevotella sp. CB35 | | includes | 363265 | Prevotella stercorea | | scientific name | 363265 | Prevotella stercorea Hayashi et al. 2007 | | authority | 363265 | strain CB35 | | type material | 365048 | Bacteriophage GBSV1 | | synonym | 365048 | Geobacillus phage GBSV1 | | scientific name | 371601 | Bacteroides xylanisolvens | | scientific name | 371601 | Bacteroides xylanisolvens Chassard et al. 2008 | | authority | 371601 | CCUG 53782 | | type material | 371601 | DSM 18836 | | type material | 371601 | JCM 15633 | | type material | 371601 | strain XB1A | | type material | 375288 | Parabacteroides | | scientific name | 375288 | Parabacteroides Sakamoto and Benno 2006 | | authority | 379891 | Plutella xylostella multiple nucleopolyhedrovirus | | scientific name | 387661 | DSM 18315 | | type material | 387661 | JCM 13406 | | type material | 387661 | Parabacteroides johnsonii | | scientific name | 387661 | Parabacteroides johnsonii Sakamoto et al. 2007 | | authority | 387661 | strain M-165 | | type material | 400667 | Acinetobacter baumannii ATCC 17978 | | scientific name | 400667 | Acinetobacter baumannii str. ATCC 17978 | | equivalent name | 400667 | Acinetobacter baumannii strain ATCC 17978 | | equivalent name | 409438 | Escherichia coli SE11 | | scientific name | 409438 | Escherichia coli str. SE11 | | equivalent name | 409438 | Escherichia coli strain SE11 | | equivalent name | 410072 | ATCC 27758 | | type material | 410072 | Coprococcus comes | | scientific name | 410072 | Coprococcus comes Holdeman and Moore 1974 | | authority | 410072 | VPI C1-38 | | type material | 420247 | Methanobrevibacter smithii ATCC 35061 | | scientific name | 420247 | Methanobrevibacter smithii DSM 861 | | synonym | 420247 | Methanobrevibacter smithii PS | | synonym | 420247 | Methanobrevibacter smithii str. ATCC 35061 | | equivalent name | 420247 | Methanobrevibacter smithii strain ATCC 35061 | | equivalent name | 435590 | Bacteroides vulgatus ATCC 8482 | | scientific name | 435590 | Bacteroides vulgatus str. ATCC 8482 | | equivalent name | 435590 | Bacteroides vulgatus strain ATCC 8482 | | equivalent name | 437897 | DSM 19343 | | type material | 437897 | JCM 14723 | | type material | 437897 | Megamonas funiformis | | scientific name | 437897 | Megamonas funiformis Sakon et al. 2008 | | authority | 437897 | YIT 11815 | | type material | 437898 | DSM 19354 | | type material | 437898 | JCM 14724 | | type material | 437898 | Sutterella parvirubra | | scientific name | 437898 | Sutterella parvirubra Sakon et al. 2008 | | authority | 437898 | YIT 11816 | | type material | 479436 | Veillonella parvula DSM 2008 | | scientific name | 479436 | Veillonella parvula str. DSM 2008 | | equivalent name | 479436 | Veillonella parvula strain DSM 2008 | | equivalent name | 487173 | DSM 21274 | | type material | 487173 | Dialister succinatiphilus | | scientific name | 487173 | Dialister succinatiphilus Morotomi et al. 2008 | | authority | 487173 | JCM 15077 | | type material | 487173 | YIT 11850 | | type material | 487174 | Barnesiella intestinihominis | | scientific name | 487174 | Barnesiella intestinihominis Morotomi et al. 2008 | | authority | 487174 | Barnesiella sp. YIT 11860 | | includes | 487174 | DSM 21032 | | type material | 487174 | JCM 15079 | | type material | 487174 | YIT 11860 | | type material | 487175 | DSM 21040 | | type material | 487175 | JCM 15078 | | type material | 487175 | Parasutterella excrementihominis | | scientific name | 487175 | Parasutterella excrementihominis Nagai et al. 2009 | | authority | 487175 | strain YIT 11859 | | type material | 502102 | Rat coronavirus Parker | | scientific name | 502102 | Rat coronavirus strain Parker | | synonym | 502105 | Bovine respiratory coronavirus bovine/US/OH-440-TC/1996 | | scientific name | 502108 | Bovine respiratory coronavirus AH187 | | scientific name | 525146 | Desulfovibrio desulfuricans subsp. desulfuricans ATCC 27774 | | equivalent name | 525146 | Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774 | | scientific name | 525146 | Desulfovibrio desulfuricans subsp. desulfuricans strain ATCC 27774 | | equivalent name | 548476 | Corynebacterium aurimucosum ATCC 700975 | | scientific name | 548476 | Corynebacterium aurimucosum CCUG 48176 | | synonym | 548476 | Corynebacterium aurimucosum CIP 107436 | | synonym | 548476 | Corynebacterium aurimucosum CN-1 | | synonym | 548476 | Corynebacterium aurimucosum DSM 44827 | | synonym | 548476 | Corynebacterium aurimucosum str. ATCC 700975 | | equivalent name | 548476 | Corynebacterium aurimucosum strain ATCC 700975 | | equivalent name | 548476 | Corynebacterium nigricans CN-1 | | synonym | 548479 | Falcivibrio vaginalis ATCC 43063 | | synonym | 548479 | Mobiluncus curtisii ATCC 43063 | | scientific name | 548479 | Mobiluncus curtisii str. ATCC 43063 | | equivalent name | 548479 | Mobiluncus curtisii strain ATCC 43063 | | equivalent name | 553199 | Propionibacterium acnes SK137 | | scientific name | 553199 | Propionibacterium acnes str. SK137 | | equivalent name | 553199 | Propionibacterium acnes strain SK137 | | equivalent name | 573174 | Vibrio phage henriette 12B8 | | scientific name | 573174 | Vibriophage henriette 12B8 | | synonym | 576790 | Enterobacteria phage JS10 | | scientific name | 607711 | CIP 109934 | | type material | 607711 | DSM 22247 | | type material | 607711 | Neisseria sp. WC 05-2507 | | includes | 607711 | Neisseria wadsworthii | | scientific name | 607711 | Neisseria wadsworthii Wolfgang et al. 2011 | | authority | 607711 | WC 05-9715 | | type material | 607711 | strain 9715 | | type material | 607712 | CIP 109933 | | type material | 607712 | DSM 22246 | | type material | 607712 | Neisseria shayeganii | | scientific name | 607712 | Neisseria shayeganii Wolfgang et al. 2011 | | authority | 607712 | Neisseria sp. WC 04-12337 | | includes | 607712 | WC 08-871 | | type material | 607712 | strain 871 | | type material | 626930 | Bacteroides fluxus | | scientific name | 626930 | Bacteroides fluxus Watanabe et al. 2010 | | authority | 626930 | DSM 22534 | | type material | 626930 | JCM 16101 | | type material | 626930 | YIT 12057 | | type material | 626932 | Alistipes indistinctus | | scientific name | 626932 | Alistipes indistinctus Nagai et al. 2010 | | authority | 626932 | DSM 22520 | | type material | 626932 | JCM 16068 | | type material | 626932 | YIT 12060 | | type material | 626933 | DSM 22474 | | type material | 626933 | JCM 16069 | | type material | 626933 | Odoribacter laneus | | scientific name | 626933 | Odoribacter laneus Nagai et al. 2010 | | authority | 626933 | YIT 12061 | | type material | 626940 | "Phascolarctobacterium succinatutens" Watanabe et al. 2012 | | authority | 626940 | DSM 22533 | | type material | 626940 | JCM 16074 | | type material | 626940 | Phascolarctobacterium sp. YIT 12068 | | includes | 626940 | Phascolarctobacterium succinatutens | | scientific name | 626940 | YIT 12067 | | type material | 626962 | Olive latent virus 3 | | scientific name | 627439 | Human enteric coronavirus strain 4408 | | scientific name | 633135 | Streptococcus phage Abc2 | | scientific name | 633135 | Streptococcus thermophilus phage Abc2 | | synonym | 634176 | Aggregatibacter aphrophilus NJ8700 | | scientific name | 634176 | Aggregatibacter aphrophilus str. NJ8700 | | equivalent name | 634176 | Aggregatibacter aphrophilus strain NJ8700 | | equivalent name | 646413 | Streptococcus phage 5093 | | scientific name | 646413 | Streptococcus thermophilus phage 5093 | | synonym | 663954 | Streptococcus dysgalactiae subsp. equisimilis ATCC 12394 | | scientific name | 663954 | Streptococcus dysgalactiae subsp. equisimilis str. ATCC 12394 | | equivalent name | 663954 | Streptococcus dysgalactiae subsp. equisimilis strain ATCC 12394 | | equivalent name | 694569 | Aggregatibacter actinomycetemcomitans D7S-1 | | scientific name | 694569 | Aggregatibacter actinomycetemcomitans str. D7S-1 | | equivalent name | 694569 | Aggregatibacter actinomycetemcomitans strain D7S-1 | | equivalent name | 697227 | Enterobacteria phage IME08 | | scientific name | 751585 | Coprococcus sp. ART55/1 | | scientific name | 754037 | Cyanophage S-CAM1 | | synonym | 754037 | Synechococcus phage S-CAM1 | | scientific name | 754064 | Ostreococcus lucimarinus virus OlV5 | | scientific name | 759851 | 'Sporosarcina newyorkensis' | | synonym | 759851 | CCUG 59649 | | type material | 759851 | DSM 23544 | | type material | 759851 | LMG 26022 | | type material | 759851 | Sporosarcina newyorkensis | | scientific name | 759851 | Sporosarcina sp. 1655 | | includes | 759851 | Sporosarcina sp. 3418 | | includes | 759851 | Sporosarcina sp. 4331 | | includes | 759851 | Sporosarcina sp. 4469 | | includes | 759851 | Sporosarcina sp. 4974 | | includes | 759851 | Sporosarcina sp. 4984 | | includes | 759851 | Sporosarcina sp. 5353 | | includes | 759851 | Sporosarcina sp. 57 | | includes | 759851 | Sporosarcina sp. 5868 | | includes | 759851 | Sporosarcina sp. 6062 | | includes | 759851 | Sporosarcina sp. R-31323 | | includes | 759851 | strain 6062 | | type material | 760732 | Acinetobacter phage Acj61 | | scientific name | 796942 | 'Stomatobaculum longum' | | synonym | 796942 | Lachnospiraceae bacterium ACC2 | | includes | 796942 | Stomatobaculum longum | | scientific name | 908937 | Prevotella dentalis ATCC 49559 | | synonym | 908937 | Prevotella dentalis DSM 3688 | | scientific name | 908937 | Prevotella dentalis JCM 13448 | | synonym | 908937 | Prevotella dentalis str. DSM 3688 | | equivalent name | 908937 | Prevotella dentalis strain DSM 3688 | | equivalent name | 927666 | Streptococcus oralis Uo5 | | scientific name | 927666 | Streptococcus oralis str. Uo5 | | equivalent name | 927666 | Streptococcus oralis strain Uo5 | | equivalent name | 932662 | Mud crab dicistrovirus | | scientific name | 1116482 | Pectobacterium phage phiTE | | scientific name | 1116482 | bacteriophage phiTE | | synonym | 1160968 | Rabbit coronavirus HKU14 | | scientific name | 1161927 | Pseudomonas phage Lu11 | | scientific name | 1172562 | Helicobacter cinaedi PAGU611 | | scientific name | 1172562 | Helicobacter cinaedi str. PAGU611 | | equivalent name | 1172562 | Helicobacter cinaedi strain PAGU611 | | equivalent name | 1235559 | Providencia phage Redjac | | scientific name | metaMix/inst/extdata/names_example.dmp0000644000176200001440000031253113403500106017602 0ustar liggesusers2 | Bacteria | Bacteria | scientific name | 2 | Monera | Monera | in-part | 2 | Procaryotae | Procaryotae | in-part | 2 | Prokaryota | Prokaryota | in-part | 2 | Prokaryotae | Prokaryotae | in-part | 2 | bacteria | bacteria | blast name | 2 | eubacteria | | genbank common name | 2 | not Bacteria Haeckel 1894 | | synonym | 2 | prokaryote | prokaryote | in-part | 2 | prokaryotes | prokaryotes | in-part | 72 | "Caryophanon muelleri" (Schmid 1922) Peshkoff 1948 | | authority | 72 | ATCC 29453 | | type material | 72 | CCUG 30554 | | type material | 72 | CIP 103436 | | type material | 72 | Caryophanon muelleri | | synonym | 72 | DSM 2579 | | type material | 72 | LMG 7828 | | type material | 72 | Scheibenbakterien | | common name | 72 | Scheibenbakterien Muller 1911 | | common name | 72 | Simonsiella muelleri | | scientific name | 72 | Simonsiella muelleri Schmid 1922 | | authority | 158 | "Spirillum dentium" (Miller 1889) Sternberg 1892 | | authority | 158 | "Spirochaeta ambigua" Seguin and Vinzent 1936 | | authority | 158 | "Spirochaeta comandonii" Seguin and Vinzent 1936 | | authority | 158 | "Spirochaeta dentium" (Miller 1889) Migula 1895 | | authority | 158 | "Spirochaeta microdentium" (Noguchi 1912) Heim 1922 | | authority | 158 | "Spirochaeta orthodonta" Hoffmann 1920 | | authority | 158 | "Spirochaete denticola" Flugge 1886 | | authority | 158 | "Spirochaete dentium" Miller 1889 | | authority | 158 | "Spironema dentium" (Miller 1889) Gross 1912 | | authority | 158 | "Treponema ambiguum" (Seguin and Vinzent 1936) Prevot 1940 | | authority | 158 | "Treponema comandonii" (Seguin and Vinzent 1936) Prevot 1940 | | authority | 158 | "Treponema dentium" (Miller 1889) Dobell 1912 | | authority | 158 | "Treponema dentium-stenogyratum" Pettit 1928 | | authority | 158 | "Treponema microdentium" Noguchi 1912 | | authority | 158 | "Treponema orthodontum" (Hoffmann 1920) Noguchi 1928 | | authority | 158 | ATCC 35405 | | type material | 158 | CIP 103919 | | type material | 158 | DSM 14222 | | type material | 158 | JCM 8153 | | type material | 158 | Spirillum dentium | | synonym | 158 | Spirochaeta ambigua | | synonym | 158 | Spirochaeta comandonii | | synonym | 158 | Spirochaeta dentium | | synonym | 158 | Spirochaeta microdentium | | synonym | 158 | Spirochaeta orthodonta | | synonym | 158 | Spirochaete denticola | | synonym | 158 | Spirochaete dentium | | synonym | 158 | Spironema dentium | | synonym | 158 | Treponema ambiguum | | synonym | 158 | Treponema comandonii | | synonym | 158 | Treponema denticola | | scientific name | 158 | Treponema denticola (ex Brumpt 1925) Chan et al. 1993 | | authority | 158 | Treponema denticola (ex Flugge 1886) Chan et al. 1993 | | authority | 158 | Treponema dentium | | synonym | 158 | Treponema dentium-stenogyratum | | synonym | 158 | Treponema microdentium | | synonym | 158 | Treponema orthodontum | | synonym | 195 | "Vibrio coli" Doyle 1948 | | authority | 195 | ATCC 33559 | | type material | 195 | CCUG 11283 | | type material | 195 | CCUG 14540 | | type material | 195 | CIP 70.80 | | type material | 195 | Campylobacter coli | | scientific name | 195 | Campylobacter coli (Doyle 1948) Veron and Chatelain 1973 | | authority | 195 | Campylobacter hyoilei | | genbank synonym | 195 | Campylobacter hyoilei Alderton et al. 1995 | | authority | 195 | DSM 4689 | | type material | 195 | JCM 2529 | | type material | 195 | LMG 6440 | | type material | 195 | NCTC 11366 | | type material | 195 | Vibrio coli | | synonym | 204 | ATCC 51146 | | type material | 204 | CCUG 30254 | | type material | 204 | CIP 103970 | | type material | 204 | Campylobacter showae | | scientific name | 204 | Campylobacter showae Etoh et al. 1993 | | authority | 204 | JCM 12989 | | type material | 204 | LMG 12635 | | type material | 204 | strain SU A4 | | type material | 250 | ATCC 35910 | | type material | 250 | CCUG 14555 | | type material | 250 | CIP 103039 | | type material | 250 | Chryseobacterium gleum | | scientific name | 250 | Chryseobacterium gleum (Holmes et al. 1984) Vandamme et al. 1994 | | authority | 250 | DSM 16776 | | type material | 250 | Flavobacterium gleum | | synonym | 250 | Flavobacterium gleum Holmes et al. 1984 | | authority | 250 | IFO 15054 | | type material | 250 | JCM 2410 | | type material | 250 | LMG 8334 | | type material | 250 | NBRC 15054 | | type material | 250 | NCTC 11432 | | type material | 250 | strain F93 | | type material | 258 | ATCC 33861 | | type material | 258 | CCUG 13224 | | type material | 258 | CDC E7288 | | type material | 258 | CIP 100542 | | type material | 258 | DSM 11722 | | type material | 258 | Flavibacterium yabuuchiae | | synonym | 258 | Flavobacterium spiritivorum | | synonym | 258 | Flavobacterium spiritivorum Holmes et al. 1982 | | authority | 258 | Flavobacterium yabuuchiae | | synonym | 258 | Flavobacterium yabuuchiae Holmes et al. 1988 | | authority | 258 | GIFU 3101 | | type material | 258 | IFO 14948 | | type material | 258 | JCM 1277 | | type material | 258 | JCM 6897 | | type material | 258 | LMG 8347 | | type material | 258 | NBRC 14948 | | type material | 258 | NCTC 11386 | | type material | 258 | Sphingobacter spiritivorum | | misspelling | 258 | Sphingobacterium spiritivorum | | scientific name | 258 | Sphingobacterium spiritivorum (Holmes et al. 1982) Yabuuchi et al. 1983 | | authority | 258 | strain E7288 | | type material | 469 | Acinetobacter | | scientific name | 469 | Acinetobacter Brisou and Prevot 1954 | | authority | 470 | ATCC 19606 | | type material | 470 | Acinetobacter baumanii | | misspelling | 470 | Acinetobacter baumanni | | misspelling | 470 | Acinetobacter baumannii | | scientific name | 470 | Acinetobacter baumannii Bouvet and Grimont 1986 | | authority | 470 | Acinetobacter genomosp. 2 | | synonym | 470 | Acinetobacter genomospecies 2 | | synonym | 470 | Bacterium anitratum | | synonym | 470 | CCUG 19096 | | type material | 470 | CIP 70.34 | | type material | 470 | DSM 30007 | | type material | 470 | JCM 6841 | | type material | 470 | LMG 1041 | | type material | 470 | NCCB 85021 | | type material | 470 | NCTC 12156 | | type material | 471 | "Micrococcus calco-aceticus" Beijerinck 1911 | | authority | 471 | ATCC 23055 | | type material | 471 | Acinetobacter calcoaceticus | | scientific name | 471 | Acinetobacter calcoaceticus (Beijerinck 1911) Baumann et al. 1968 (Approved Lists 1980) emend. Bouvet and Grimont 1986 | | authority | 471 | Acinetobacter genomosp. 1 | | synonym | 471 | Acinetobacter genomospecies 1 | | synonym | 471 | Acinetobacter sp. AV6 | | includes | 471 | Acinetobacter sp. HNR | | includes | 471 | Acinetobacter sp. STB1 | | includes | 471 | CAIM 17 | | type material | 471 | CCUG 12804 | | type material | 471 | CIP 81.8 | | type material | 471 | DSM 30006 | | type material | 471 | JCM 6842 | | type material | 471 | LMG 1046 | | type material | 471 | Micrococcus calcoaceticus | | synonym | 471 | Moraxella calcoacetica | | synonym | 471 | NCCB 22016 | | type material | 471 | NCTC 12983 | | type material | 471 | Neisseria winogradskyi | | synonym | 483 | "Micrococcus cinereus" von Lingelsheim 1906 | | authority | 483 | ATCC 14685 | | type material | 483 | CCUG 2156 | | type material | 483 | CCUG 346 | | type material | 483 | CIP 73.16 | | type material | 483 | DSM 4630 | | type material | 483 | LMG 8380 | | type material | 483 | Micrococcus cinereus | | synonym | 483 | NCTC 10294 | | type material | 483 | Neisseria cinerea | | scientific name | 483 | Neisseria cinerea (von Lingelsheim 1906) Murray 1939 | | authority | 484 | ATCC 13120 | | type material | 484 | CCUG 17913 | | type material | 484 | CCUG 345 | | type material | 484 | CIP 73.15 | | type material | 484 | DSM 17633 | | type material | 484 | LMG 5297 | | type material | 484 | NCTC 8263 | | type material | 484 | Neisseria flavescens | | scientific name | 484 | Neisseria flavescens Branham 1930 | | authority | 486 | "Neisseria lactamicus" (sic) Hollis et al. 1969 | | authority | 486 | ATCC 23970 | | type material | 486 | CCUG 5853 | | type material | 486 | CIP 72.17 | | type material | 486 | DSM 4691 | | type material | 486 | NCTC 10617 | | type material | 486 | Neisseria lactamica | | scientific name | 486 | Neisseria lactamica Hollis et al. 1969 | | authority | 486 | Neisseria lactamicus | | synonym | 487 | "Diplokokkus intracellularis meningitidis" (sic) Weichselbaum 1887 | | authority | 487 | "Micrococcus intracellularis" (Jaeger) Migula 1900 | | authority | 487 | "Micrococcus meningitidis cerebrospinalis" Albrecht and Ghon 1901 | | authority | 487 | "Micrococcus meningitidis" Albrecht and Ghon 1903 | | authority | 487 | "Neisseria weichselbaumii" Trevisan 1889 | | authority | 487 | ATCC 13077 | | type material | 487 | CCUG 3269 | | type material | 487 | CIP 73.10 | | type material | 487 | DSM 10036 | | type material | 487 | Diplokokkus intracellularis meningitidis | | synonym | 487 | Micrococcus intracellularis | | synonym | 487 | Micrococcus meningitidis | | synonym | 487 | Micrococcus meningitidis cerebrospinalis | | synonym | 487 | NCTC 10025 | | type material | 487 | Neisseria meningitidis | | scientific name | 487 | Neisseria meningitidis (Albrecht and Ghon 1901) Murray 1929 | | authority | 487 | Neisseria meningitidis. | | misspelling | 487 | Neisseria weichselbaumii | | synonym | 487 | strain Sara E. Branham M1027 | | type material | 488 | "Diplococcus mucosus" von Lingelsheim 1906 | | authority | 488 | ATCC 19696 | | type material | 488 | CCUG 26877 | | type material | 488 | CIP 59.51 | | type material | 488 | DSM 17611 | | type material | 488 | Diplococcus mucosus | | synonym | 488 | JCM 12992 | | type material | 488 | NCTC 12978 | | type material | 488 | Neisseria mucosa | | scientific name | 488 | Neisseria mucosa (von Lingelsheim 1906) Veron et al. 1959 | | authority | 488 | Neisseria mucosa Veron et al. 1959 (sic) | | authority | 489 | "Neisseria polysacchareae" Riou et al. 1983 | | authority | 489 | ATCC 43768 | | type material | 489 | CCUG 18030 | | type material | 489 | CIP 100113 | | type material | 489 | NCTC 11858 | | type material | 489 | Neisseria polysaccharea | | scientific name | 489 | Neisseria polysaccharea Riou and Guibourdenche 1987 | | authority | 489 | Neisseria polysacchareae | | synonym | 490 | "Diplococcos pharyngis siccus" von Lingelsheim 1906 | | authority | 490 | "Diplococcus siccus" von Lingelsheim 1908 | | authority | 490 | ATCC 29256 | | type material | 490 | CCUG 23929 | | type material | 490 | CCUG 24959 | | type material | 490 | CIP 103345 | | type material | 490 | DSM 17713 | | type material | 490 | Diplococcos pharyngis siccus | | synonym | 490 | Diplococcus siccus | | synonym | 490 | LMG 5290 | | type material | 490 | NRL 30,016 | | type material | 490 | Neisseria sicca | | scientific name | 490 | Neisseria sicca (von Lingelsheim 1908) Bergey et al. 1923 | | authority | 496 | ATCC 33926 | | type material | 496 | CIP 103346 | | type material | 496 | Neisseria macaca | | misspelling | 496 | Neisseria macacae | | scientific name | 496 | Neisseria macacae Vedros et al. 1983 | | authority | 496 | strain M-740 | | type material | 502 | ATCC 33394 | | type material | 502 | CCUG 6516 | | type material | 502 | CCUG 9125 | | type material | 502 | CIP 103473 | | type material | 502 | DSM 10202 | | type material | 502 | Kingella denitrificans | | scientific name | 502 | Kingella denitrificans Snell and Lapage 1976 | | authority | 502 | NCTC 10995 | | type material | 504 | "Moraxella kingae" Bovre et al. 1974 | | authority | 504 | "Moraxella kingii" (sic) Henriksen and Bovre 1968 | | authority | 504 | ATCC 23330 | | type material | 504 | CCUG 352 | | type material | 504 | CIP 80.16 | | type material | 504 | DSM 7536 | | type material | 504 | Kingella kingae | | scientific name | 504 | Kingella kingae (Henriksen and Bovre 1968) Henriksen and Bovre 1976 | | authority | 504 | Kingella kingii | | equivalent name | 504 | Moraxella kingae | | synonym | 504 | Moraxella kingii | | synonym | 504 | NCTC 10529 | | type material | 505 | ATCC 51147 | | type material | 505 | CCUG 30450 | | type material | 505 | CIP 103803 | | type material | 505 | DSM 18271 | | type material | 505 | Kingella orale | | synonym | 505 | Kingella oralis | | scientific name | 505 | Kingella oralis corrig. Dewhirst et al. 1993 | | authority | 505 | strain UB-38 | | type material | 539 | "Bacteroides corrodens" Eiken 1958 (in part) | | synonym | 539 | "Ristella corrodens" (Eiken 1958) Prevot 1966 | | synonym | 539 | ATCC 23834 | | type material | 539 | Bacteroides corrodens | Bacteroides corrodens | synonym | 539 | CCUG 2138 | | type material | 539 | CIP 70.75 | | type material | 539 | DSM 8340 | | type material | 539 | Eikenella corrodens | | scientific name | 539 | Eikenella corrodens (Eiken 1958) Jackson and Goodman 1972 | | synonym | 539 | JCM 12952 | | type material | 539 | LMG 15557 | | type material | 539 | NCTC 10596 | | type material | 539 | Ristella corrodens | | synonym | 569 | "Enterobacter aerogenes subsp. hafniae" Ewing 1963 | | authority | 569 | "Enterobacter alvei" (Mller 1954) Sakazaki 1961 | | authority | 569 | "Enterobacter hafniae" Ewing and Fife 1968 | | authority | 569 | ATCC 13337 | | type material | 569 | CCUG 41547 | | type material | 569 | CIP 57.31 | | type material | 569 | DSM 30163 | | type material | 569 | Enterobacter aerogenes subsp. hafniae | | synonym | 569 | Enterobacter alvei | | synonym | 569 | Enterobacter hafniae | | synonym | 569 | HAMBI 1279 | | type material | 569 | HAMBI 1876 | | type material | 569 | Hafnia alvei | | scientific name | 569 | Hafnia alvei Moller 1954 | | authority | 569 | Hafnia alvei sensu stricto genomosp. 1 | | synonym | 569 | JCM 1666 | | type material | 569 | LMG 10392 | | type material | 569 | NCTC 8105 | | type material | 569 | NRRL B-4260 | | type material | 569 | not "Bacillus paratyphi-alvei" Bahr 1919 | | authority | 584 | ATCC 29906 | | type material | 584 | CCUG 26767 | | type material | 584 | CIP 103181 | | type material | 584 | DSM 4479 | | type material | 584 | JCM 1669 | | type material | 584 | LMG 3257 | | type material | 584 | NCTC 11938 | | type material | 584 | Proteus mirabilis | | scientific name | 584 | Proteus mirabilis Hauser 1885 | | authority | 587 | "Bacterium rettgeri" Hadley 1918 | | authority | 587 | "Shigella rettgeri" (Hadley et al. 1918) Weldin 1927 | | authority | 587 | ATCC 29944 | | type material | 587 | Bacterium rettgeri | | synonym | 587 | CCUG 14804 | | type material | 587 | CIP 103182 | | type material | 587 | DSM 4542 | | type material | 587 | JCM 1675 | | type material | 587 | LMG 3259 | | type material | 587 | NCTC 11801 | | type material | 587 | Proteus rettgeri | | synonym | 587 | Proteus rettgeri (Hadley et al. 1918) Rustigian and Stuart 1943 (Approved Lists 1980) | | authority | 587 | Providencia rettgeri | | scientific name | 587 | Providencia rettgeri (Hadley 1918) Brenner et al. 1978 | | authority | 587 | Shigella rettgeri | | synonym | 588 | "Proteus stuartii" Buttiaux et al. 1954 | | authority | 588 | ATCC 29914 | | type material | 588 | CCUG 14805 | | type material | 588 | CIP 104687 | | type material | 588 | DSM 4539 | | type material | 588 | LMG 3260 | | type material | 588 | NCTC 11800 | | type material | 588 | Proteus stuartii | | synonym | 588 | Providencia stuartii | | scientific name | 588 | Providencia stuartii (Buttiaux et al. 1954) Ewing 1962 | | authority | 615 | "Bacillus marcescens" (Bizio 1823) Trevisan in de Toni and Trevisan 1889 | | authority | 615 | ATCC 13880 | | type material | 615 | Bacillus marcescens | | synonym | 615 | CCUG 1647 | | type material | 615 | CFBP 4226 | | type material | 615 | CIP 103235 | | type material | 615 | DSM 30121 | | type material | 615 | Enterobacteriaceae bacterium KO4 | | includes | 615 | HAMBI 1286 | | type material | 615 | JCM 1239 | | type material | 615 | LMG 2792 | | type material | 615 | NBRC 102204 | | type material | 615 | NCTC 10211 | | type material | 615 | NRRL B-2544 | | type material | 615 | Pantoea sp. NAB7 | | includes | 615 | Serratia marcescens | | scientific name | 615 | Serratia marcescens Bizio 1823 | | authority | 615 | VKM B-1248 | | type material | 618 | ATCC 33077 | | type material | 618 | CCUG 14508 | | type material | 618 | CDC 1979-77 | | type material | 618 | CIP 79.1 | | type material | 618 | DSM 4582 | | type material | 618 | JCM 1243 | | type material | 618 | NBRC 102598 | | type material | 618 | NCTC 11214 | | type material | 618 | Serratia odorifera | | scientific name | 618 | Serratia odorifera Grimont et al. 1978 | | authority | 618 | Serratia odorifora | | misspelling | 636 | "Paracolobactrum anguillimortiferum" Hoshina 1962 | | authority | 636 | ATCC 15947 | | type material | 636 | CCUG 1638 | | type material | 636 | CIP 78.61 | | type material | 636 | DSM 30052 | | type material | 636 | Edwardsiella anguillimortifera | | synonym | 636 | Edwardsiella anguillimortifera (Hoshina 1962) Sakazaki and Tamura 1975 | | authority | 636 | Edwardsiella tarda | | scientific name | 636 | Edwardsiella tarda Ewing and McWhorter 1965 | | authority | 636 | JCM 1656 | | type material | 636 | LMG 2793 | | type material | 636 | NCCB 73021 | | type material | 636 | NCTC 10396 | | type material | 636 | Paracolobactrum anguillimortiferum | | synonym | 729 | ATCC 33392 | | type material | 729 | CCUG 12836 | | type material | 729 | CIP 102513 | | type material | 729 | DSM 8978 | | type material | 729 | Haemophilus parainfluenza | | misspelling | 729 | Haemophilus parainfluenzae | | scientific name | 729 | Haemophilus parainfluenzae Rivers 1922 | | authority | 729 | NCTC 7857 | | type material | 732 | ATCC 33389 | | type material | 732 | Aggregatibacter aphrophilus | | scientific name | 732 | Aggregatibacter aphrophilus (Khairat 1940) Norskov-Lauritsen and Kilian 2006 | | authority | 732 | CCUG 3715 | | type material | 732 | CIP 70.73 | | type material | 732 | Haemophilus aphrophilus | | synonym | 732 | Haemophilus aphrophilus Khairat 1940 (Approved Lists 1980) | | authority | 732 | Haemophilus paraphrophilus | | synonym | 732 | Haemophilus paraphrophilus Zinnemann et al. 1968 (Approved Lists 1980) | | authority | 732 | NCTC 5906 | | type material | 739 | ATCC 33393 | | type material | 739 | Aggregatibacter segnis | | scientific name | 739 | Aggregatibacter segnis (Kilian 1977) Norskov-Lauritsen and Kilian 2006 | | authority | 739 | CCUG 10787 | | type material | 739 | CCUG 12838 | | type material | 739 | CIP 103292 | | type material | 739 | DSM 21418 | | type material | 739 | Haemophilus segnis | | synonym | 739 | Haemophilus segnis Kilian 1977 | | authority | 739 | NCTC 10977 | | type material | 739 | strain HK316 | | type material | 754 | ATCC 43325 | | type material | 754 | CCUG 12397 | | type material | 754 | CIP 103293 | | type material | 754 | DSM 22969 | | type material | 754 | NCTC 11617 | | type material | 754 | Pasteurella dagmatis | | scientific name | 754 | Pasteurella dagmatis Mutters et al. 1985 | | authority | 816 | "Ristella" Prevot 1938 | | authority | 816 | Bacteroides | Bacteroides | scientific name | 816 | Bacteroides Castellani and Chalmers 1919 (Approved Lists 1980) emend. Shah and Collins 1989 | | authority | 816 | Capsularis | | synonym | 816 | Capsularis Prevot 1938 (Approved Lists 1980) | | authority | 816 | Ristella | Ristella | synonym | 817 | "Bacteroides inaequalis" Eggerth and Gagnon 1933 | | authority | 817 | "Bacteroides incommunis" Eggerth and Gagnon 1933 | | authority | 817 | "Bacteroides uncatus" Eggerth and Gagnon 1933 | | authority | 817 | "Fusiformis fragilis" Topley and Wilson 1929 | | authority | 817 | "Pseudobacterium fragilis" Krasil'nikov 1949 | | authority | 817 | "Pseudobacterium inaequalis" (Eggerth and Gagnon 1933) Krasil'nikov 1949 | | authority | 817 | "Pseudobacterium incommunis" (Eggerth and Gagnon 1933) Krasil'nikov 1949 | | authority | 817 | "Pseudobacterium uncatum" (Eggerth and Gagnon 1933) Krasil'nikov 1949 | | authority | 817 | "Ristella fragilis" Prevot 1938 | | authority | 817 | "Ristella incommunis" (Eggerth and Gagnon 1933) Prevot 1938 | | authority | 817 | "Ristella uncata" (Eggerth and Gagnon 1933) Prevot 1938 | | authority | 817 | "Sphaerophorus inaequalis" (Eggerth and Gagnon 1933) Prevot 1938 | | authority | 817 | "Sphaerophorus intermedius" Bergan and Hovig 1968 | | authority | 817 | ATCC 25285 | | type material | 817 | Bacillus fragilis | | synonym | 817 | Bacillus fragilis Veillon and Zuber 1898 | | authority | 817 | Bacteroides fragili | | misspelling | 817 | Bacteroides fragilis | | scientific name | 817 | Bacteroides fragilis (Veillon and Zuber 1898) Castellani and Chalmers 1919 | | authority | 817 | Bacteroides inaequalis | | synonym | 817 | Bacteroides incommunis | | synonym | 817 | Bacteroides uncatus | | synonym | 817 | CCUG 4856 | | type material | 817 | CIP 77.16 | | type material | 817 | DSM 2151 | | type material | 817 | Fusiformis fragilis | | synonym | 817 | JCM 11019 | | type material | 817 | LMG 10263 | | type material | 817 | NCTC 9343 | | type material | 817 | Pseudobacterium fragilis | | synonym | 817 | Pseudobacterium inaequalis | | synonym | 817 | Pseudobacterium incommunis | | synonym | 817 | Pseudobacterium uncatum | | synonym | 817 | Ristella fragilis | | synonym | 817 | Ristella incommunis | | synonym | 817 | Ristella uncata | | synonym | 817 | Sphaerophorus inaequalis | | synonym | 817 | Sphaerophorus intermedius | | synonym | 820 | ATCC 8492 | | type material | 820 | Bacteroides uniformis | | scientific name | 820 | Bacteroides uniformis Eggerth and Gagnon 1933 | | authority | 820 | CCUG 4942 | | type material | 820 | CIP 103695 | | type material | 820 | DSM 6597 | | type material | 820 | JCM 5828 | | type material | 820 | NCTC 13054 | | type material | 821 | ATCC 8482 | | type material | 821 | BCRC 12903 | | type material | 821 | Bacteroides vulgatus | | scientific name | 821 | Bacteroides vulgatus Eggerth and Gagnon 1933 | | authority | 821 | CCRC 12903 | | type material | 821 | CCUG 4940 | | type material | 821 | CIP 103714 | | type material | 821 | DSM 1447 | | type material | 821 | IFO 14291 | | type material | 821 | JCM 5826 | | type material | 821 | LMG 17767 | | type material | 821 | LMG 7956 | | type material | 821 | NBRC 14291 | | type material | 821 | NCTC 11154 | | type material | 847 | ATCC 35274 | | type material | 847 | CIP 106513 | | type material | 847 | Oxalobacter formigenes | | scientific name | 847 | Oxalobacter formigenes Allison et al. 1985 | | authority | 847 | strain OxB | | type material | 849 | "Actinomyces gonidiaformis" (Tunnicliff and Jackson 1925) Bergey et al. 1930 | | authority | 849 | "Bacillus gonidiaformans" Tunnicliff and Jackson 1925 | | authority | 849 | "Pseudobacterium gonidiaformans" (Tunnicliff and Jackson 1925) Krasil'nikov 1949 | | authority | 849 | "Sphaerophorus gonidiaformans" (Tunnicliff and Jackson 1925) Prevot 1938 | | authority | 849 | ATCC 25563 | | type material | 849 | Actinomyces gonidiaformis | | synonym | 849 | Bacillus gonidiaformans | | synonym | 849 | CCUG 16790 | | type material | 849 | DSM 19810 | | type material | 849 | Fusibacterium gonidiaformans | | synonym | 849 | Fusibacterium gonidiiformans | | equivalent name | 849 | Fusobacterium gonidiaformans | | scientific name | 849 | Fusobacterium gonidiaformans (Tunnicliff and Jackson 1925) Moore and Holdeman 1970 | | authority | 849 | Fusobacterium gonidiiformans | | synonym | 849 | Fusobacterium gonidoformans | | misspelling | 849 | Pseudobacterium gonidiaformans | | synonym | 849 | Sphaerophorus gonidiaformans | | synonym | 901 | ATCC 29098 | | type material | 901 | DSM 749 | | type material | 901 | Desulfomonas pigra | | synonym | 901 | Desulfomonas pigra Moore et al. 1976 | | authority | 901 | Desulfovibrio piger | | scientific name | 901 | Desulfovibrio piger (Moore et al. 1976) Loubinoux et al. 2002 | | authority | 1015 | ATCC 43767 | | type material | 1015 | Bergeyella zoohelcum | | scientific name | 1015 | Bergeyella zoohelcum (Holmes et al. 1987) Vandamme et al. 1994 | | authority | 1015 | CCUG 12568 | | type material | 1015 | CCUG 30535 | | type material | 1015 | CIP 103041 | | type material | 1015 | DSM 16783 | | type material | 1015 | IFO 16014 | | type material | 1015 | JCM 21249 | | type material | 1015 | LMG 12996 | | type material | 1015 | LMG 8351 | | type material | 1015 | NBRC 16014 | | type material | 1015 | NCTC 11660 | | type material | 1015 | Weeksella zoohelcum | | synonym | 1015 | Weeksella zoohelcum Holmes et al. 1987 | | authority | 1015 | group IIj | | synonym | 1015 | strain D658 | | type material | 1018 | "Fusiformis nucleatus var. ochraceus" Prevot et al. 1956 | | authority | 1018 | "Ristella ochraceus" (sic) (Prevot 1956) Sebald 1962 | | authority | 1018 | ATCC 27872 | | type material | 1018 | Bacteroides ochraceus | | synonym | 1018 | Bacteroides ochraceus (Prevot et al. 1956) Holdeman and Moore 1972 (Approved Lists 1980) | | authority | 1018 | Bacteroides ochraceus Prevot et al. 1956 (sic) | | authority | 1018 | CCUG 9716 | | type material | 1018 | CIP 103448 | | type material | 1018 | Capnocytophaga ochracaea | | misspelling | 1018 | Capnocytophaga ochracca | | misspelling | 1018 | Capnocytophaga ochracea | | scientific name | 1018 | Capnocytophaga ochracea (Prevot et al. 1956) Leadbetter et al. 1982 | | authority | 1018 | Capnocytophaga orchracea | | misspelling | 1018 | DSM 7271 | | type material | 1018 | Fusiformis nucleatus var. ochraceus | | synonym | 1018 | JCM 12966 | | type material | 1018 | NCTC 12371 | | type material | 1018 | Ristella ochraceus | | synonym | 1019 | ATCC 33612 | | type material | 1019 | CCUG 9714 | | type material | 1019 | CIP 104301 | | type material | 1019 | Capnocytophaga sputigena | | scientific name | 1019 | Capnocytophaga sputigena Leadbetter et al. 1982 | | authority | 1019 | DSM 3292 | | type material | 1019 | DSM 7273 | | type material | 1019 | JCM 12967 | | type material | 1019 | LMG 11518 | | type material | 1019 | NCTC 11653 | | type material | 1019 | strain 4 | | type material | 1034 | ATCC 49720 | | type material | 1034 | Afipia clevelandensis | | scientific name | 1034 | Afipia clevelandensis Brenner et al. 1992 | | authority | 1034 | CCUG 30457 | | type material | 1034 | CIP 103516 | | type material | 1034 | DSM 7315 | | type material | 1034 | NCTC 12721 | | type material | 1034 | strain B-91-007353 | | type material | 1035 | AFIP strain BV | | type material | 1035 | ATCC 53690 | | type material | 1035 | Afipia felis | | scientific name | 1035 | Afipia felis Brenner et al. 1992 | | authority | 1035 | CCUG 30456 | | type material | 1035 | CIP 103515 | | type material | 1035 | DSM 7326 | | type material | 1035 | NCTC 12499 | | type material | 1035 | cat scratch disease bacillus | | genbank common name | 1035 | strain B-91-007352 | | type material | 1236 | Gammaproteobacteria | | scientific name | 1236 | Gammaproteobacteria Garrity et al. 2005 | | synonym | 1236 | Proteobacteria gamma subdivision | | synonym | 1236 | Purple bacteria, gamma subdivision | | synonym | 1236 | g-proteobacteria | gamma proteos | blast name | 1236 | gamma proteobacteria | | synonym | 1236 | gamma subdivision | | synonym | 1236 | gamma subgroup | | synonym | 1270 | "Bacteridium luteum" Schroeter 1872 | | authority | 1270 | "Micrococcus flavus" Trevisan | | authority | 1270 | "Micrococcus lysodeikticus" Fleming 1933 | | authority | 1270 | "Sarcina lutea" (Schroeter 1872) Schroeter 1886 | | authority | 1270 | ATCC 4698 | | type material | 1270 | Bacteridium luteum | | synonym | 1270 | CCM 169 | | type material | 1270 | CCUG 5858 | | type material | 1270 | CIP A270 | | type material | 1270 | DSM 20030 | | type material | 1270 | HAMBI 1399 | | type material | 1270 | HAMBI 26 | | type material | 1270 | IEGM 391 | | type material | 1270 | IFO 3333 | | type material | 1270 | JCM 1464 | | type material | 1270 | LMG 4050 | | type material | 1270 | Micrococcus luteus | | scientific name | 1270 | Micrococcus luteus (Schroeter 1872) Cohn 1872 (Approved Lists 1980) emend. Wieser et al. 2002 | | authority | 1270 | Micrococcus lysodeikticus | | synonym | 1270 | NBRC 3333 | | type material | 1270 | NCCB 78001 | | type material | 1270 | NCTC 2665 | | type material | 1270 | NRRL B-287 | | type material | 1270 | Sarcina lutea | | synonym | 1270 | VKM B-1314 | | type material | 1270 | not "Micrococcus luteus" Lehmann and Neumann 1896 | | authority | 1282 | "Albococcus epidermidis" Winslow and Winslow 1908 | | authority | 1282 | "Micrococcus epidermidis" (Winslow and Winslow 1908) Hucker 1924 | | authority | 1282 | "Staphylococcus epidermidis albus" Welch 1891 | | authority | 1282 | ATCC 14990 | | type material | 1282 | Albococcus epidermidis | | synonym | 1282 | CCM 2124 | | type material | 1282 | CCUG 18000 A | | type material | 1282 | CCUG 39508 | | type material | 1282 | CIP 81.55 | | type material | 1282 | DSM 20044 | | type material | 1282 | JCM 2414 | | type material | 1282 | LMG 10474 | | type material | 1282 | Micrococcus epidermidis | | synonym | 1282 | NBRC 100911 | | type material | 1282 | NCAIM B.01066 | | type material | 1282 | NCTC 11047 | | type material | 1282 | Staphylococcus epidermidis | | scientific name | 1282 | Staphylococcus epidermidis (Winslow and Winslow 1908) Evans 1916 | | authority | 1282 | Staphylococcus epidermidis albus | | synonym | 1292 | ATCC 27836 | | type material | 1292 | CCUG 7325 | | type material | 1292 | CIP 81.65 | | type material | 1292 | DSM 20316 | | type material | 1292 | JCM 2415 | | type material | 1292 | LMG 13354 | | type material | 1292 | NCTC 11044 | | type material | 1292 | NRRL B-14736 | | type material | 1292 | Staphylococcus warneri | | scientific name | 1292 | Staphylococcus warneri Kloos and Schleifer 1975 | | authority | 1292 | Staphylococcus warnerii | | misspelling | 1305 | ATCC 10556 | | type material | 1305 | CCUG 17826 | | type material | 1305 | CCUG 35770 | | type material | 1305 | CIP 55.128 | | type material | 1305 | DSM 20567 | | type material | 1305 | JCM 5708 | | type material | 1305 | LMG 14702 | | type material | 1305 | NCTC 7863 | | type material | 1305 | Streptococcus sanguinis | | scientific name | 1305 | Streptococcus sanguinis corrig. White and Niven 1946 (Approved Lists 1980) emend. Kilian et al. 1989 | | authority | 1305 | Streptococcus sanguis | | misspelling | 1305 | strain SK1 | strain SK1 | type material | 1377 | "Gaffkya homari" Hitchner and Snieszko 1947 | | authority | 1377 | "Pediococcus homari" Deibel and Niven 1960 | | authority | 1377 | ATCC 11563 | | type material | 1377 | Aerococcus viridans | | scientific name | 1377 | Aerococcus viridans Williams et al. 1953 | | authority | 1377 | CCUG 4311 | | type material | 1377 | CIP 54.145 | | type material | 1377 | DSM 20340 | | type material | 1377 | Gaffkya homari | | synonym | 1377 | HAMBI 1583 | | type material | 1377 | IFO 12219 | | type material | 1377 | JCM 20461 | | type material | 1377 | LMG 17931 | | type material | 1377 | NBRC 12219 | | type material | 1377 | NCAIM B.01070 | | type material | 1377 | NCTC 8251 | | type material | 1377 | Pediococcus homari | | synonym | 1581 | "Bacillus Buchneri" (sic) Henneberg 1903 | | authority | 1581 | "Bacterium buchneri" (Henneberg 1903) Henneberg 1926 | | authority | 1581 | "Lactobacterium buchneri" (Henneberg 1903) Krasil'nikov 1949 | | authority | 1581 | "Ulvina buchneri" (Henneberg 1903) Pribram 1933 | | authority | 1581 | ATCC 4005 | | type material | 1581 | Bacillus Buchneri | | synonym | 1581 | Bacterium buchneri | | synonym | 1581 | CCUG 21532 | | type material | 1581 | CIP 103023 | | type material | 1581 | DSM 20057 | | type material | 1581 | JCM 1115 | | type material | 1581 | LMG 6892 | | type material | 1581 | Lactobacillus buchneri | | scientific name | 1581 | Lactobacillus buchneri (Henneberg 1903) Bergey et al. 1923 | | authority | 1581 | Lactobacterium buchneri | | synonym | 1581 | NCAIM B.01145 | | type material | 1581 | NRRL B-1837 | | type material | 1581 | Ulvina buchneri | | synonym | 1581 | VKM B-1599 | | type material | 1588 | "Lactobacillus Type II" Fornachon 1943 | | synonym | 1588 | ATCC 8290 | | type material | 1588 | CCUG 30140 | | type material | 1588 | CIP 103007 | | type material | 1588 | DSM 20176 | | type material | 1588 | IFO 15886 | | type material | 1588 | JCM 1155 | | type material | 1588 | LMG 6895 | | type material | 1588 | Lactobacillus Type II | | synonym | 1588 | Lactobacillus hilgardii | | scientific name | 1588 | Lactobacillus hilgardii Douglas and Cruess 1936 | | synonym | 1588 | NBRC 15886 | | type material | 1588 | NRRL B-1843 | | type material | 1641 | "Murraya grayi subsp. grayi" (Errebo Larsen and Seeliger 1966) Stuart and Welshimer 1974 | | authority | 1641 | "Murraya grayi" (Errebo Larsen and Seeliger 1966) Stuart and Welshimer 1974 | | authority | 1641 | ATCC 19120 | | type material | 1641 | CCUG 4983 | | type material | 1641 | CCUG 5118 | | type material | 1641 | CIP 105447 | | type material | 1641 | CIP 6818 | | type material | 1641 | DSM 20601 | | type material | 1641 | LMG 16490 | | type material | 1641 | Listeria grayi | | scientific name | 1641 | Listeria grayi Errebo Larsen and Seeliger 1966 (Approved Lists 1980) emend. Rocourt et al. 1992 | | authority | 1641 | Listeria grayi grayi | | equivalent name | 1641 | Listeria grayi subsp. grayi | | synonym | 1641 | Listeria murrayi | | synonym | 1641 | Listeria murrayi Welshimer and Meredith 1971 (Approved Lists 1980) | | authority | 1641 | Murraya grayi | | synonym | 1641 | Murraya grayi subsp. grayi | | synonym | 1641 | NCAIM B.01871 | | type material | 1641 | NCTC 10815 | | type material | 1642 | "Listeria innocua" Seeliger and Schoofs 1979 | | authority | 1642 | ATCC 33090 | | type material | 1642 | CCUG 15531 | | type material | 1642 | CIP 80.11 | | type material | 1642 | DSM 20649 | | type material | 1642 | LMG 11387 | | type material | 1642 | Listeria innocua | | scientific name | 1642 | Listeria innocua (ex Seeliger and Schoofs 1979) Seeliger 1983 | | authority | 1642 | Listeria innocua Seeliger 1983 | | misnomer | 1642 | NCTC 11288 | | type material | 1642 | SLCC 3379 | | type material | 1681 | "Actinobacterium bifidum" (Tissier 1900) Puntoni 1937 | | authority | 1681 | "Actinomyces bifidus" (Tissier 1900) Nannizzi 1934 | | authority | 1681 | "Actinomyces parabifidus" (Weiss and Rettger 1938) Pine and Georg 1965 | | authority | 1681 | "Bacillus bifidus communis" Tissier 1900 | | authority | 1681 | "Bacillus bifidus" Tissier 1900 | | authority | 1681 | "Bacterium bifidum" (Tissier 1900) Lehmann and Neumann 1927 | | authority | 1681 | "Bacteroides bifidus" (Tissier 1900) Castellani and Chalmers 1919 | | authority | 1681 | "Bifidibacterium bifidum" (Tissier 1900) Prevot 1938 | | authority | 1681 | "Cohnistreptothrix bifidus" (Tissier 1900) Negroni and Fischer 1944 | | authority | 1681 | "Lactobacillus bifidus type II" Weiss and Rettger 1938 | | authority | 1681 | "Lactobacillus parabifidus" Weiss and Rettger 1938 | | authority | 1681 | "Nocardia bifida" (Tissier 1900) Vuillemin 1931 | | authority | 1681 | "Tissieria bifida" (Tissier 1900) Pribram 1929 | | authority | 1681 | AS 1.2212 | | type material | 1681 | ATCC 29521 | | type material | 1681 | Actinobacterium bifidum | | synonym | 1681 | Actinomyces bifidus | | synonym | 1681 | Actinomyces parabifidus | | synonym | 1681 | BCRC 14615 | | type material | 1681 | Bacillus bifidus | | synonym | 1681 | Bacillus bifidus communis | | synonym | 1681 | Bacterium bifidum | | synonym | 1681 | Bacteroides bifidus | | synonym | 1681 | Bifidibacterium bifidum | | synonym | 1681 | Bifidobacterium bifidum | | scientific name | 1681 | Bifidobacterium bifidum (Tissier 1900) Orla-Jensen 1924 | | authority | 1681 | CCRC 14615 | | type material | 1681 | CCUG 18364 | | type material | 1681 | CCUG 45217 | | type material | 1681 | CIP 56.7 | | type material | 1681 | Cohnistreptothrix bifidus | | synonym | 1681 | DSM 20456 | | type material | 1681 | HAMBI 1380 | | type material | 1681 | IFO 14252 | | type material | 1681 | JCM 1255 | | type material | 1681 | KCTC 3202 | | type material | 1681 | LMG 11041 | | type material | 1681 | LMG 8810 | | type material | 1681 | Lactobacillus bifidus type II | | synonym | 1681 | Lactobacillus parabifidus | | synonym | 1681 | NBRC 100015 | | type material | 1681 | NBRC 14252 | | type material | 1681 | NCFB 2715 | | type material | 1681 | NCIMB 702715 | | type material | 1681 | NCTC 13001 | | type material | 1681 | Nocardia bifida | | synonym | 1681 | Tissieria bifida | | synonym | 1681 | strain Ti | | type material | 1697 | "Bacterium ammoniagenes" Cooke and Keith 1927 | | synonym | 1697 | ATCC 6871 | | type material | 1697 | Bacterium ammoniagenes | | synonym | 1697 | Brevibacterium ammoniagenes | | synonym | 1697 | Brevibacterium ammoniagenes (Cooke and Keith 1927) Breed 1953 (Approved Lists 1980) | | synonym | 1697 | CCUG 38796 | | type material | 1697 | CIP 101283 | | type material | 1697 | Corynebacterium ammoniagenes | | scientific name | 1697 | Corynebacterium ammoniagenes (Cooke and Keith 1927) Collins 1987 | | synonym | 1697 | Corynebacterium ammoniigenes | | equivalent name | 1697 | DSM 20306 | | type material | 1697 | IFO 12612 | | type material | 1697 | JCM 1305 | | type material | 1697 | NBRC 12612 | | type material | 1697 | NCCB 60030 | | type material | 1697 | NCIB 8143 | | type material | 1697 | NCIMB 8143 | | type material | 1697 | VKM B-672 | | type material | 1735 | "Bacteroides biformis" Eggerth 1935 | | authority | 1735 | "Pseudobacterium biforme" (Eggerth 1935) Krasil'nikov 1949 | | authority | 1735 | ATCC 27806 | | type material | 1735 | Bacteroides biformis | | synonym | 1735 | CCUG 28091 | | type material | 1735 | DSM 3989 | | type material | 1735 | Eubacterium biforme | | equivalent name | 1735 | Eubacterium biforme (Eggerth 1935) Prevot 1938 | | authority | 1735 | Pseudobacterium biforme | | synonym | 1735 | [Eubacterium] biforme | | scientific name | 1743 | Arachnia | | includes | 1743 | Arachnia Pine and Georg 1969 | | includes | 1743 | Propionibacterium | | scientific name | 1743 | Propionibacterium Orla-Jensen 1909 (Approved Lists 1980) emend. Charfreitag et al. 1988 | | synonym | 1743 | Propionicibacterium | | equivalent name | 1833 | "Mycobacterium erythropolis" Gray and Thornton 1928 | | authority | 1833 | ATCC 4277 | | type material | 1833 | Arthrobacter hydrocarboglutamicus | | synonym | 1833 | Arthrobacter oxamicetus | | synonym | 1833 | Arthrobacter oxamicetus subsp. propiophenicolus | | synonym | 1833 | Arthrobacter paraaffineus | | misspelling | 1833 | Arthrobacter paraffineus | | synonym | 1833 | Arthrobacter picolinophilus | | synonym | 1833 | Arthrobacter picolinophilus Tate and Ensign 1974 (Approved Lists 1980) | | authority | 1833 | Brevibacterium healii | | synonym | 1833 | Brevibacterium ketoglutamicum | | synonym | 1833 | Brevibacterium paraffinoliticum | | synonym | 1833 | CIP 104179 | | type material | 1833 | Corynebacterium alkanum | | synonym | 1833 | Corynebacterium aurantiacum | | synonym | 1833 | Corynebacterium humiferum | | synonym | 1833 | Corynebacterium sp. WS2071 | | includes | 1833 | Corynebacterium sp. WS2072 | | includes | 1833 | DSM 43066 | | type material | 1833 | HAMBI 1953 | | type material | 1833 | IEGM 7 | | type material | 1833 | IFO 15567 | | type material | 1833 | JCM 20419 | | type material | 1833 | JCM 3201 | | type material | 1833 | LMG 5359 | | type material | 1833 | Mycobacterium erythropolis | | synonym | 1833 | NBRC 15567 | | type material | 1833 | NCIB 9158 | | type material | 1833 | NCIMB 9158 | | type material | 1833 | NCTC 13021 | | type material | 1833 | NRRL B-16025 | | type material | 1833 | Nocardia calcarea | | synonym | 1833 | Nocardia calcarea Metcalf and Brown 1957 (Approved Lists 1980) | | authority | 1833 | Nocardioides simplex ATCC 13260 | | includes | 1833 | Nocardioides simplex ATCC 19565 | | includes | 1833 | Nocardioides simplex ATCC 19566 | | includes | 1833 | Rhodococcus NI86/21 | | includes | 1833 | Rhodococcus erythreus | | misnomer | 1833 | Rhodococcus erythropolis | | scientific name | 1833 | Rhodococcus erythropolis (Gray and Thornton 1928) Goodfellow and Alderson 1979 | | authority | 1833 | Rhodococcus sp. (strain NI86/21) | | includes | 1833 | Rhodococcus sp. ATCC 15108 | | includes | 1833 | Rhodococcus sp. ATCC 15961 | | includes | 1833 | Rhodococcus sp. ATCC 21035 | | includes | 1833 | Rhodococcus sp. BZ4 | | includes | 1833 | Rhodococcus sp. NCIB 9646 | | includes | 1833 | Rhodococcus sp. NI86/21 | | includes | 1833 | Rhodococcus sp. strain NI86/21 | | includes | 1833 | VKM Ac-858 | | type material | 1833 | strain N11 | | type material | 2173 | ATCC 35061 | | type material | 2173 | DSM 861 | | type material | 2173 | Methanobrevibacter smithii | | scientific name | 2173 | Methanobrevibacter smithii Balch and Wolfe 1981 | | authority | 2173 | OCM 144 | | type material | 2173 | strain PS | | type material | 2718 | ATCC 15826 | | type material | 2718 | CCUG 2711 | | type material | 2718 | CIP 70.70 | | type material | 2718 | Cardiobacterium hominis | | scientific name | 2718 | Cardiobacterium hominis Slotnick and Dougherty 1964 | | authority | 2718 | DSM 8339 | | type material | 2718 | LMG 3916 | | type material | 2718 | NCTC 10426 | | type material | 9606 | Homo sapiens | | scientific name | 9606 | Homo sapiens Linnaeus, 1758 | | authority | 9606 | human | | genbank common name | 9606 | man | | common name | 10090 | LK3 transgenic mice | | includes | 10090 | Mus muscaris | | misnomer | 10090 | Mus musculus | | scientific name | 10090 | Mus musculus Linnaeus, 1758 | | authority | 10090 | Mus sp. 129SV | | includes | 10090 | house mouse | | genbank common name | 10090 | mice C57BL/6xCBA/CaJ hybrid | | misspelling | 10090 | mouse | | common name | 10090 | nude mice | | includes | 10090 | transgenic mice | | includes | 10372 | HHV-7 | | genbank acronym | 10372 | Herpes simplex virus 7 | | synonym | 10372 | Human herpesvirus 7 | | scientific name | 10372 | Human herpesvirus type 7 | | synonym | 10372 | human herpesvirus 7 HHV-7 | | synonym | 10685 | Bacillus phage SP01 | | acronym | 10685 | Bacillus phage SPO1 | | scientific name | 10685 | Bacillus subtilis bacteriophage SPO1 | | synonym | 10685 | Bacteriophage SPO1 | | synonym | 10685 | Bacteriophage sp01 | | synonym | 10685 | phage SPO1 | | synonym | 10845 | Bacteriophage St-1 | | synonym | 10845 | Enterobacteria phage St-1 | | scientific name | 10845 | phage St-1 | | synonym | 10849 | Bacteriophage alpha-3 | | synonym | 10849 | Bacteriophage alpha3 | | synonym | 10849 | Coliphage alpha3 | | synonym | 10849 | Enterobacteria phage alpha3 | | scientific name | 10849 | phage alpha-3 | | synonym | 13690 | ATCC 51230 | | type material | 13690 | Beijerinckia B1 | | includes | 13690 | Beijerinckia sp. B1 | | includes | 13690 | CCUG 28380 | | type material | 13690 | CCUG 31205 | | type material | 13690 | CIP 106726 | | type material | 13690 | DSM 7462 | | type material | 13690 | GIFU 9882 | | type material | 13690 | HAMBI 1842 | | type material | 13690 | IFO 15102 | | type material | 13690 | JCM 7371 | | type material | 13690 | LMG 11252 | | type material | 13690 | NBRC 15102 | | type material | 13690 | Sphingobium yanoikuyae | | scientific name | 13690 | Sphingobium yanoikuyae (Yabuuchi et al. 1990) Takeuchi et al. 2001 | | synonym | 13690 | Sphingomonas yanoikuyae | | genbank synonym | 13690 | Sphingomonas yanoikuyae Yabuuchi et al. 1990 | | synonym | 28035 | ATCC 43809 | | type material | 28035 | CCUG 25348 | | type material | 28035 | CIP 103642 | | type material | 28035 | DSM 4804 | | type material | 28035 | LMG 13346 | | type material | 28035 | NCTC 12217 | | type material | 28035 | NRRL B-14774 | | type material | 28035 | Staphylococcus lugdunensis | | scientific name | 28035 | Staphylococcus lugdunensis Freney et al. 1988 | | authority | 28035 | strain N860297 | | type material | 28080 | ATCC 43954 | | type material | 28080 | CCUG 14913 | | type material | 28080 | CIP 103681 | | type material | 28080 | CNW group | | synonym | 28080 | Campylobacter upsaliensis | | scientific name | 28080 | Campylobacter upsaliensis Sandstedt and Ursing 1991 | | authority | 28080 | DSM 5365 | | type material | 28080 | NCTC 11541 | | type material | 28080 | catalase-negative or weak group of campylobacteria | | synonym | 28090 | "Acinetobacter lwoffi" (sic) (Audureau 1940) Brisou and Prevot 1954 | | authority | 28090 | "Moraxella lwoffi" (sic) Audureau 1940 | | authority | 28090 | ATCC 15309 | | type material | 28090 | Acinetobacter genomosp. 8 | | synonym | 28090 | Acinetobacter genomosp. 9 | | synonym | 28090 | Acinetobacter genomospecies 8 | | synonym | 28090 | Acinetobacter genomospecies 9 | | synonym | 28090 | Acinetobacter lwoff | | misspelling | 28090 | Acinetobacter lwoffi | | misspelling | 28090 | Acinetobacter lwoffii | | scientific name | 28090 | Acinetobacter lwoffii (Audureau 1940) Brisou and Prevot 1954 (Approved Lists 1980) emend. Bouvet and Grimont 1986 | | authority | 28090 | CCUG 33984 | | type material | 28090 | CIP 64.10 | | type material | 28090 | DSM 2403 | | type material | 28090 | JCM 6840 | | type material | 28090 | LMG 1029 | | type material | 28090 | Moraxella lwoffi | | synonym | 28090 | NCAIM B.01101 | | type material | 28090 | NCCB 73001 | | type material | 28090 | NCTC 5866 | | type material | 28111 | ATCC 27754 | | type material | 28111 | Bacteroides eggerthii | | scientific name | 28111 | Bacteroides eggerthii Holdeman and Moore 1974 | | authority | 28111 | CCUG 9559 | | type material | 28111 | CIP 104285 | | type material | 28111 | DSM 20697 | | type material | 28111 | JCM 12986 | | type material | 28111 | NCTC 11155 | | type material | 28117 | "Bacillus putredinis" Weinberg et al. 1937 | | authority | 28117 | "Pseudobacterium putredinis" (Weinberg et al. 1937) Krasil'nikov 1949 | | authority | 28117 | "Ristella putredinis" (Weinberg et al. 1937) Prevot 1938 | | authority | 28117 | ATCC 29800 | | type material | 28117 | Alistipes putredinis | | scientific name | 28117 | Alistipes putredinis (Weinberg et al. 1937) Rautio et al. 2003 | | authority | 28117 | Bacillus putredinis | | synonym | 28117 | Bacteroides putredenis | | misspelling | 28117 | Bacteroides putredinis | | synonym | 28117 | Bacteroides putredinis (Weinberg et al. 1937) Kelly 1957 (Approved Lists 1980) | | authority | 28117 | CCUG 45780 | | type material | 28117 | CIP 104286 | | type material | 28117 | DSM 17216 | | type material | 28117 | JCM 16772 | | type material | 28117 | Pseudobacterium putredinis | | synonym | 28117 | Ristella putredinis | | synonym | 28126 | ATCC 33574 | | type material | 28126 | Bacteroides buccae | | synonym | 28126 | Bacteroides buccae Holdeman et al. 1982 | | authority | 28126 | Bacteroides capillus | | synonym | 28126 | Bacteroides capillus Kornman and Holt 1982 | | authority | 28126 | Bacteroides pentosaceus | | synonym | 28126 | Bacteroides pentosaceus Shah and Collins 1982 | | authority | 28126 | CCUG 15401 | | type material | 28126 | CIP 105106 | | type material | 28126 | DSM 19025 | | type material | 28126 | JCM 12245 | | type material | 28126 | Prevotella buccae | | scientific name | 28126 | Prevotella buccae (Holdeman et al. 1982) Shah and Collins 1990 | | authority | 28126 | VPI D3A-6 | | type material | 28127 | ATCC 35310 | | type material | 28127 | Bacteroides buccalis | | synonym | 28127 | Bacteroides buccalis Shah and Collins 1982 | | synonym | 28127 | CCUG 15557 | | type material | 28127 | DSM 20616 | | type material | 28127 | JCM 12246 | | type material | 28127 | NCDO 2354 | | type material | 28127 | NCTC 13064 | | type material | 28127 | Prevotella buccalis | | scientific name | 28127 | Prevotella buccalis (Shah and Collins 1982) Shah and Collins 1990 | | synonym | 28133 | ATCC 33563 | | type material | 28133 | CCUG 9560 | | type material | 28133 | CIP 105552 | | type material | 28133 | DSM 13386 | | type material | 28133 | JCM 12250 | | type material | 28133 | JCM 6322 | | type material | 28133 | NCTC 9336 | | type material | 28133 | Prevotella nigrescens | | scientific name | 28133 | Prevotella nigrescens Shah and Gharbia 1992 | | authority | 28133 | VPI 8944 | | type material | 28133 | strain Lambe 729-74 | | type material | 28134 | "Ristella oralis" (Loesche et al. 1964) Prevot et al. 1967 | | authority | 28134 | ATCC 33269 | | type material | 28134 | Bacteroides oralis | | synonym | 28134 | Bacteroides oralis Loesche et al. 1964 (Approved Lists 1980) | | authority | 28134 | CCUG 15408 | | type material | 28134 | DSM 20702 | | type material | 28134 | JCM 12251 | | type material | 28134 | NCTC 11459 | | type material | 28134 | Prevotella oralis | | scientific name | 28134 | Prevotella oralis (Loesche et al. 1964) Shah and Collins 1990 | | authority | 28134 | Ristella oralis | | synonym | 28134 | VPI D27B-24 | | type material | 28135 | ATCC 33573 | | type material | 28135 | Bacteroides oris | | synonym | 28135 | Bacteroides oris Holdeman et al. 1982 | | authority | 28135 | CCUG 15405 | | type material | 28135 | CIP 104480 | | type material | 28135 | DSM 18711 | | type material | 28135 | JCM 12252 | | type material | 28135 | JCM 8540 | | type material | 28135 | NCTC 13071 | | type material | 28135 | Prevotella oris | | scientific name | 28135 | Prevotella oris (Holdeman et al. 1982) Shah and Collins 1990 | | authority | 28135 | VPI D1A-1A | | type material | 28197 | ATCC 49616 | | type material | 28197 | Arcibacter butzleri | | equivalent name | 28197 | Arcobacter butzleri | | scientific name | 28197 | Arcobacter butzleri (Kiehlbauch et al. 1991) Vandamme et al. 1992 | | authority | 28197 | Arcobacter butzlerii | | misspelling | 28197 | Arquibacter butzleri | | equivalent name | 28197 | CCUG 30485 | | type material | 28197 | CDC D2686 | | type material | 28197 | CIP 103493 | | type material | 28197 | CIP 103537 | | type material | 28197 | Campylobacter butzleri | | synonym | 28197 | Campylobacter butzleri Kiehlbauch et al. 1991 | | authority | 28197 | DSM 8739 | | type material | 28197 | LMG 10828 | | type material | 28197 | NCTC 12481 | | type material | 28197 | strain D2686 | | type material | 28211 | "Alphabacteria" Cavalier-Smith 1992 | | authority | 28211 | Alphabacteria | | synonym | 28211 | Alphabacteria Cavalier-Smith 2002 | | authority | 28211 | Alphaproteobacteria | | scientific name | 28211 | Alphaproteobacteria Garrity et al. 2006 | | authority | 28211 | Proteobacteria alpha subdivision | | synonym | 28211 | Purple bacteria, alpha subdivision | | synonym | 28211 | a-proteobacteria | alpha proteos | blast name | 28211 | alpha proteobacteria | | synonym | 28211 | alpha subdivision | | synonym | 28211 | alpha subgroup | | synonym | 28449 | "Micrococcus subflavus" Flugge 1886 | | authority | 28449 | ATCC 49275 | | type material | 28449 | CCUG 23930 | | type material | 28449 | CIP 103343 | | type material | 28449 | DSM 17610 | | type material | 28449 | LMG 5313 | | type material | 28449 | Micrococcus subflavus | | synonym | 28449 | NRL 30,017 | | type material | 28449 | Neisseria subflava | | scientific name | 28449 | Neisseria subflava (Flugge 1886) Trevisan 1889 | | authority | 28449 | strain U37 | | type material | 29321 | ATCC 51513 | | type material | 29321 | CCUG 32254 | | type material | 29321 | CDC coryneform group ANF-1 like | | synonym | 29321 | CIP 104075 | | type material | 29321 | Corynebacterium otitidis | | synonym | 29321 | DSM 8821 | | type material | 29321 | JCM 12146 | | type material | 29321 | LMG 19071 | | type material | 29321 | Turicella otitidis | | scientific name | 29321 | Turicella otitidis Funke et al. 1994 | | authority | 29321 | strain 234/92 | | type material | 29348 | ATCC 29900 | | type material | 29348 | CCUG 46510 | | type material | 29348 | CIP 106966 | | type material | 29348 | Clostridium spiroforme | | equivalent name | 29348 | Clostridium spiroforme Kaneuchi et al. 1979 | | authority | 29348 | DSM 1552 | | type material | 29348 | JCM 1432 | | type material | 29348 | NCTC 11211 | | type material | 29348 | VPI C28-23-1A | | type material | 29348 | [Clostridium] spiroforme | | scientific name | 29430 | "Achromobacter haemolyticus" Stenzel and Mannheim 1963 | | authority | 29430 | ATCC 17906 | | type material | 29430 | Achromobacter haemolyticus | | synonym | 29430 | Acinetobacter genomosp. 4 | | synonym | 29430 | Acinetobacter genomospecies 4 | | synonym | 29430 | Acinetobacter haematolyticus | | synonym | 29430 | Acinetobacter haemolyticus | | scientific name | 29430 | Acinetobacter haemolyticus (ex Stenzel and Mannheim 1963) Bouvet and Grimont 1986 | | authority | 29430 | CCUG 888 | | type material | 29430 | CIP 64.3 | | type material | 29430 | DSM 6962 | | type material | 29430 | LMG 996 | | type material | 29430 | NCCB 85026 | | type material | 29430 | NCTC 12155 | | type material | 29430 | strain B40 | | type material | 29430 | strain Mannheim 2446/60 | | type material | 29466 | "Micrococcus gazogenes alcalescens anaerobius" Lewkowicz 1901 | | authority | 29466 | "Micrococcus gazogenes" Hall and Howitt 1925 | | authority | 29466 | "Micrococcus lactilyticus" Foubert and Douglas 1948 | | authority | 29466 | "Staphylococcus parvulus" Veillon and Zuber 1898 | | authority | 29466 | "Veillonella gazogenes" (Hall and Howitt 1925) Murray 1939 | | authority | 29466 | ATCC 10790 | | type material | 29466 | CCUG 5123 | | type material | 29466 | DSM 2008 | | type material | 29466 | JCM 12972 | | type material | 29466 | Micrococcus gazogenes | | synonym | 29466 | Micrococcus gazogenes alcalescens anaerobius | | synonym | 29466 | Micrococcus lactilyticus | | synonym | 29466 | NCTC 11810 | | type material | 29466 | Staphylococcus parvulus | | synonym | 29466 | Veillonella alcalescens | | synonym | 29466 | Veillonella alcalescens Prevot 1933 | | authority | 29466 | Veillonella gazogenes | | synonym | 29466 | Veillonella parvula | | scientific name | 29466 | Veillonella parvula (Veillon and Zuber 1898) Prevot 1933 (AL 1980) emend. Mays et al. 1982 | | authority | 29466 | not "Micrococcus gazogenes" Choukevitch 1911 | | authority | 33007 | ATCC 51847 | | type material | 33007 | Actinomyces neuii | | scientific name | 33007 | Actinomyces neuii Funke et al. 1994 | | synonym | 33007 | CCUG 32252 | | type material | 33007 | CIP 104015 | | type material | 33007 | DSM 8576 | | type material | 33007 | strain 97/90 | | type material | 33010 | "Bacteroides avidus" Eggerth 1935 | | authority | 33010 | "Corynebacterium avidum" (Eggerth 1935) Prevot 1938 | | authority | 33010 | "Mycobacterium avidum" (Eggerth 1935) Krasil'nikov 1949 | | authority | 33010 | ATCC 25577 | | type material | 33010 | Bacteroides avidus | | synonym | 33010 | CCUG 36754 | | type material | 33010 | CIP 103261 | | type material | 33010 | Corynebacterium avidum | | synonym | 33010 | DSM 4901 | | type material | 33010 | IFO 15671 | | type material | 33010 | Mycobacterium avidum | | synonym | 33010 | NBRC 15671 | | type material | 33010 | NCTC 11864 | | type material | 33010 | Propionibacterium avidum | | scientific name | 33010 | Propionibacterium avidum (Eggerth 1935) Moore and Holdeman 1969 | | authority | 33010 | Propionicibacterium avidum | | equivalent name | 33032 | ATCC 51172 | | type material | 33032 | Anaerococcus lactolyticus | | scientific name | 33032 | Anaerococcus lactolyticus (Li et al. 1992) Ezaki et al. 2001 | | authority | 33032 | CCUG 31351 | | type material | 33032 | CIP 103725 | | type material | 33032 | DSM 7456 | | type material | 33032 | GIFU 8586 | | type material | 33032 | JCM 8140 | | type material | 33032 | Peptostreptococcus lactolyticus | | synonym | 33032 | Peptostreptococcus lactolyticus Li et al. 1992 | | authority | 33038 | ATCC 29149 | | type material | 33038 | Ruminococcus gnavus | | equivalent name | 33038 | Ruminococcus gnavus Moore et al. 1976 | | authority | 33038 | Ruminococcus gravus | | misspelling | 33038 | VPI C7-9 | | type material | 33038 | [Ruminococcus] gnavus | | scientific name | 36834 | ATCC 27791 | | type material | 36834 | CIP 104316 | | type material | 36834 | Clostridium celatum | | scientific name | 36834 | Clostridium celatum Hauschild and Holdeman 1974 | | synonym | 36834 | DSM 1785 | | type material | 36834 | JCM 1394 | | type material | 36834 | NCTC 12746 | | type material | 37734 | "Streptococcus casseliflavus" Vaughan et al. 1979 | | authority | 37734 | ATCC 25788 | | type material | 37734 | CCUG 18657 | | type material | 37734 | CIP 103018 | | type material | 37734 | DSM 20680 | | type material | 37734 | Enterococcus casseliflavus | | scientific name | 37734 | Enterococcus casseliflavus (ex Vaughan et al. 1979) Collins et al. 1984 | | authority | 37734 | Enterococcus flavescens | | synonym | 37734 | Enterococcus flavescens Pompei et al. 1992 | | authority | 37734 | JCM 8723 | | type material | 37734 | LMG 10745 | | type material | 37734 | MUTK 20 | | type material | 37734 | NBRC 100478 | | type material | 37734 | NCDO 2372 | | type material | 37734 | NCIMB 11449 | | type material | 37734 | NCTC 12361 | | type material | 37734 | NRRL B-3502 | | type material | 37734 | Streptococcus casseliflavus | | synonym | 37734 | Streptococcus faecium subsp. casseliflavus | | synonym | 37734 | Streptococcus faecium var. casseliflavus | | synonym | 38284 | ATCC 49725 | | type material | 38284 | CCUG 28779 | | type material | 38284 | CDC coryneform group G-1 | | synonym | 38284 | CIP 104783 | | type material | 38284 | CNCTC Th1/57 | | type material | 38284 | Corynebacterium accolens | | scientific name | 38284 | Corynebacterium accolens Neubauer et al. 1991 | | synonym | 38284 | DSM 44278 | | type material | 38284 | JCM 8331 | | type material | 38289 | ATCC 43734 | | type material | 38289 | CCUG 27192 | | type material | 38289 | CDC coryneform group JK | | synonym | 38289 | CIP 103337 | | type material | 38289 | Corynebacterium jeikeium | | scientific name | 38289 | Corynebacterium jeikeium Jackman et al. 1988 | | synonym | 38289 | DSM 7171 | | type material | 38289 | JCM 9384 | | type material | 38289 | NCTC 11913 | | type material | 39492 | ATCC 29066 | | type material | 39492 | DSM 3996 | | type material | 39492 | Eubacterium siraeum | | scientific name | 39492 | Eubacterium siraeum Moore et al. 1976 | | authority | 39492 | [Eubacterium] siraeum | | equivalent name | 39496 | "Bacillus ventriosus" Tissier 1908 | | authority | 39496 | "Bacteroides ventriosus" (Tissier 1908) Eggerth 1935 | | authority | 39496 | "Pseudobacterium ventriosum" (Tissier 1908) Krasil'nikov 1949 | | authority | 39496 | ATCC 27560 | | type material | 39496 | Bacillus ventriosus | | synonym | 39496 | Bacteroides ventriosus | | synonym | 39496 | DSM 3988 | | type material | 39496 | Eubacterium ventriosum | | scientific name | 39496 | Eubacterium ventriosum (Tissier 1908) Prevot 1938 | | authority | 39496 | Pseudobacterium ventriosum | | synonym | 39496 | [Eubacterium] ventriosum | | equivalent name | 39778 | ATCC 17748 | | type material | 39778 | DSM 20735 | | type material | 39778 | NCTC 11831 | | type material | 39778 | Veillonella alcalescens subsp. dispar | | synonym | 39778 | Veillonella dispar | | scientific name | 39778 | Veillonella dispar (Rogosa 1965) Mays et al. 1982 | | synonym | 40214 | ATCC 17909 | | type material | 40214 | Acinetobacter genomosp. 7 | | synonym | 40214 | Acinetobacter genomospecies 7 | | synonym | 40214 | Acinetobacter johnsonii | | scientific name | 40214 | Acinetobacter johnsonii Bouvet and Grimont 1986 | | authority | 40214 | CCUG 19095 | | type material | 40214 | CIP 64.6 | | type material | 40214 | DSM 6963 | | type material | 40214 | HAMBI 1969 | | type material | 40214 | HAMBI 1971 | | type material | 40214 | LMG 999 | | type material | 40214 | NCIMB 12460 | | type material | 40214 | NCTC 12154 | | type material | 40214 | strain Mannheim 3865/60 | | type material | 40215 | ATCC 17908 | | type material | 40215 | Acinetobacter genomosp. 5 | | synonym | 40215 | Acinetobacter genomospecies 5 | | synonym | 40215 | Acinetobacter grimontii | | genbank synonym | 40215 | Acinetobacter grimontii Carr et al. 2003 | | authority | 40215 | Acinetobacter junii | | scientific name | 40215 | Acinetobacter junii Bouvet and Grimont 1986 | | authority | 40215 | CCUG 889 | | type material | 40215 | CIP 64.5 | | type material | 40215 | DSM 6964 | | type material | 40215 | LMG 998 | | type material | 40215 | NCTC 12153 | | type material | 40215 | strain Mannheim 2723/59 | | type material | 40216 | ATCC 43998 | | type material | 40216 | Acinetobacter genomosp. 12 | | synonym | 40216 | Acinetobacter genomospecies 12 | | synonym | 40216 | Acinetobacter radiiresistens | | misspelling | 40216 | Acinetobacter radioresistens | | scientific name | 40216 | Acinetobacter radioresistens Nishimura et al. 1988 | | authority | 40216 | CIP 103788 | | type material | 40216 | DSM 6976 | | type material | 40216 | IAM 13186 | | type material | 40216 | JCM 9326 | | type material | 40216 | LMG 10613 | | type material | 40216 | NBRC 102413 | | type material | 40216 | strain FO-1 | | type material | 42631 | BStV | | acronym | 42631 | Brome streak mosaic potyvirus | | synonym | 42631 | Brome streak mosaic rymovirus | | synonym | 42631 | Brome streak mosaic virus | | scientific name | 42631 | Brome streak virus | | synonym | 43765 | 'Corynebacterium asperum' | | synonym | 43765 | ATCC 49368 | | type material | 43765 | CCUG 35685 | | type material | 43765 | CDC coryneform group F-2 | | includes | 43765 | CDC coryneform group I-2 | | includes | 43765 | CIP 103452 | | type material | 43765 | Corynebacterium amycolatum | | scientific name | 43765 | Corynebacterium amycolatum Collins et al. 1988 | | synonym | 43765 | Corynebacterium asperum | | synonym | 43765 | DSM 6922 | | type material | 43765 | IFO 15207 | | type material | 43765 | JCM 7447 | | type material | 43765 | NBRC 15207 | | type material | 43765 | NCFB 2768 | | type material | 43765 | NCIMB 13130 | | type material | 43765 | strain S160 | | type material | 43767 | "Bacillus hoagii" Morse 1912 | | authority | 43767 | "Corynebacterium (pyogenes) equi roseum" Lutje 1923 | | authority | 43767 | "Corynebacterium magnusson-holth" Plum 1940 | | authority | 43767 | "Corynebacterium purulentus" (sic) Holtman 1945 | | authority | 43767 | "Corynebacterium pyogenes (equi)" Miessner and Wetzel 1923 | | authority | 43767 | "Mycobacterium equi" (Magnusson 1923) Jensen 1934 | | authority | 43767 | "Mycobacterium restrictum" (Turfitt 1944) Krasil'nikov 1949 | | authority | 43767 | "Prescottia equi" Jones et al. 2013 | | authority | 43767 | "Proactinomyces restrictus" Turfitt 1944 | | authority | 43767 | ATCC 25729 | | type material | 43767 | ATCC 6939 | | type material | 43767 | Bacillus hoagii | | synonym | 43767 | CCUG 892 | | type material | 43767 | CIP 54.72 | | type material | 43767 | Corynebacterium (pyogenes) equi roseum | | synonym | 43767 | Corynebacterium equi | | genbank synonym | 43767 | Corynebacterium equi Magnusson 1923 (Approved Lists 1980) | | authority | 43767 | Corynebacterium equii | | misspelling | 43767 | Corynebacterium hoagii | | synonym | 43767 | Corynebacterium hoagii (Morse 1912) Eberson 1918 | | authority | 43767 | Corynebacterium magnusson-holth | | synonym | 43767 | Corynebacterium purulentus | | synonym | 43767 | Corynebacterium pyogenes (equi) | | synonym | 43767 | DSM 20307 | | type material | 43767 | HAMBI 2061 | | type material | 43767 | IFO 14956 | | type material | 43767 | JCM 1311 | | type material | 43767 | JCM 3209 | | type material | 43767 | LMG 18452 | | type material | 43767 | Mycobacterium equi | | synonym | 43767 | Mycobacterium restrictum | | synonym | 43767 | NBRC 101255 | | type material | 43767 | NBRC 14956 | | type material | 43767 | NCTC 1621 | | type material | 43767 | NRRL B-16538 | | type material | 43767 | Nocardia restrica | | misspelling | 43767 | Nocardia restricta | | synonym | 43767 | Nocardia restricta (Turfitt 1944) McClung 1974 (Approved Lists 1980) | | authority | 43767 | Prescottia equi | | synonym | 43767 | Proactinomyces restrictus | | synonym | 43767 | Rhodococcus equi | | scientific name | 43767 | Rhodococcus equi (Magnusson 1923) Goodfellow and Alderson 1977 | | authority | 43767 | Rhodococcus equi (Magnusson 1923) Goodfellow and Alderson 1979 (sic) | | authority | 43767 | VKM Ac-953 | | type material | 43768 | "Actinomyces matruchoti" (Mendel 1919) Nannizzi 1934 | | synonym | 43768 | "Cladothrix matruchoti" (sic) Mendel 1919 | | synonym | 43768 | "Oospora matruchoti" (Mendel 1919) Sartory 1930 | | synonym | 43768 | ATCC 14266 | | type material | 43768 | Actinomyces matruchoti | | synonym | 43768 | Bacterionema matruchotii | | synonym | 43768 | Bacterionema matruchotii (Mendel 1919) Gilmour et al. 1961 (Approved Lists 1980) | | synonym | 43768 | CCUG 27545 | | type material | 43768 | CCUG 46620 | | type material | 43768 | CIP 81.82 | | type material | 43768 | Cladothrix matruchoti | | synonym | 43768 | Corynebacterium matruchotii | | scientific name | 43768 | Corynebacterium matruchotii (Mendel 1919) Collins 1983 | | synonym | 43768 | DSM 20635 | | type material | 43768 | IFO 15360 | | type material | 43768 | JCM 9386 | | type material | 43768 | NBRC 15360 | | type material | 43768 | NCTC 10254 | | type material | 43768 | Oospora matruchoti | | synonym | 46503 | ATCC 43184 | | type material | 46503 | Bacteroides merdae | | synonym | 46503 | Bacteroides merdae Johnson et al. 1986 | | authority | 46503 | CCUG 38734 | | type material | 46503 | CIP 104202 | | type material | 46503 | JCM 9497 | | type material | 46503 | NCTC 13052 | | type material | 46503 | Parabacteroides merdae | | scientific name | 46503 | Parabacteroides merdae (Johnson et al. 1986) Sakamoto and Benno 2006 | | authority | 46503 | VPI T4-1 | | type material | 47229 | CCUG 45783 | | type material | 47229 | CIP 105350 | | type material | 47229 | Janthinobacterium sp. R2-11 | | includes | 47229 | Massilia timonae | | scientific name | 47229 | Massilia timonae La Scola et al. 2000 emend. Lindquist et al. 2003 | | authority | 47229 | Timone isolate | | synonym | 47229 | strain UR/MT95 | | type material | 47671 | ATCC 51599 | | type material | 47671 | CCUG 34794 | | type material | 47671 | CIP 106317 | | type material | 47671 | DSM 11362 | | type material | 47671 | Lautropia mirabilis | | scientific name | 47671 | Lautropia mirabilis Gerner-Smidt et al. 1995 | | authority | 47671 | NCTC 12852 | | type material | 47671 | strain AB2188 | | type material | 47715 | ATCC 7469 | | type material | 47715 | CCUG 21452 | | type material | 47715 | CIP A157 | | type material | 47715 | DSM 20021 | | type material | 47715 | IFO 3425 | | type material | 47715 | JCM 1136 | | type material | 47715 | LMG 6400 | | type material | 47715 | Lactobacillus casei rhamnosus | | synonym | 47715 | Lactobacillus casei subsp. rhamnosus | | synonym | 47715 | Lactobacillus casei subsp. rhamnosus Hansen 1968 (Approved Lists 1980) | | authority | 47715 | Lactobacillus rhamnosus | | scientific name | 47715 | Lactobacillus rhamnosus (Hansen 1968) Collins et al. 1989 | | authority | 47715 | Lactobacillus sp. W6 | | includes | 47715 | Lactobacillus sp. X9 | | includes | 47715 | NBRC 3425 | | type material | 47715 | NCAIM B.01147 | | type material | 47715 | NCCB 46033 | | type material | 47715 | NCDO 243 | | type material | 47715 | NCIMB 6375 | | type material | 47715 | NCTC 12953 | | type material | 47715 | NRRL B-442 | | type material | 47715 | VKM B-574 | | type material | 49338 | DSM 10664 | | type material | 49338 | Desulfitobacterium frappieri | | synonym | 49338 | Desulfitobacterium frappieri Bouchard et al. 1996 | | authority | 49338 | Desulfitobacterium hafniense | | scientific name | 49338 | Desulfitobacterium hafniense Christiansen and Ahring 1996 emend. Niggemyer et al. 2001 | | authority | 49338 | anaerobic eubacterium PCP-1 | | includes | 49338 | strain DCB-2 | | type material | 50290 | Aotine herpesvirus 1 | | scientific name | 50290 | Herpesvirus aotus 1 | | synonym | 53443 | Blautia hydrogenotrophica | | scientific name | 53443 | Blautia hydrogenotrophica (Bernalier et al. 1997) Liu et al. 2008 | | authority | 53443 | DSM 10507 | | type material | 53443 | JCM 14656 | | type material | 53443 | Ruminococcus hydrogenotrophicus | | synonym | 53443 | Ruminococcus hydrogenotrophicus Bernalier et al. 1997 | | authority | 53443 | strain S5a33 | | type material | 56774 | Eubacterium infirmum | | equivalent name | 56774 | Eubacterium infirmum Cheeseman et al. 1996 | | authority | 56774 | Eubacterium sp. (strain W 1417) | | includes | 56774 | NCTC 12940 | | type material | 56774 | [Eubacterium] infirmum | | scientific name | 56946 | ATCC 49717 | | type material | 56946 | Afipia broomae | | misspelling | 56946 | Afipia broomeae | | scientific name | 56946 | Afipia broomeae Brenner et al. 1992 | | authority | 56946 | CCUG 30458 | | type material | 56946 | CIP 103517 | | type material | 56946 | DSM 7327 | | type material | 56946 | NCTC 12720 | | type material | 56946 | strain B-91-007286 | | type material | 69218 | ATCC 33241 | | type material | 69218 | CCUG 25231 | | type material | 69218 | CDC Enteric Group 19 | | synonym | 69218 | CFBP 4167 | | type material | 69218 | CIP 103787 | | type material | 69218 | DSM 17580 | | type material | 69218 | Enterobacter cancerogenus | | scientific name | 69218 | Enterobacter cancerogenus (Urosevic 1966) Dickey and Zumoff 1988 | | authority | 69218 | Enterobacter taylorae | | synonym | 69218 | Enterobacter taylorae Farmer et al. 1985 | | authority | 69218 | Erwinia cancerogena | | synonym | 69218 | Erwinia cancerogena Urosevic 1966 (Approved Lists 1980) | | authority | 69218 | ICMP 5706 | | type material | 69218 | LMG 2693 | | type material | 69218 | NCPPB 2176 | | type material | 71421 | Haemophilus influenzae KW20 | | equivalent name | 71421 | Haemophilus influenzae Rd | | equivalent name | 71421 | Haemophilus influenzae Rd KW20 | | scientific name | 72556 | ATCC 43552 | | type material | 72556 | Achromobacter piechaudii | | scientific name | 72556 | Achromobacter piechaudii (Kiredjian et al. 1986) Yabuuchi et al. 1998 | | authority | 72556 | Alcaligenes piechaudii | | synonym | 72556 | Alcaligenes piechaudii Kiredjian et al. 1986 | | authority | 72556 | CCUG 724 | | type material | 72556 | CIP 60.75 | | type material | 72556 | DSM 10342 | | type material | 72556 | IAM 12591 | | type material | 72556 | JCM 20668 | | type material | 72556 | LMG 1873 | | type material | 72556 | NBRC 102461 | | type material | 72556 | NCTC 11970 | | type material | 72556 | strain Hugh 366-5 | | type material | 76122 | 'Alloprevotella tannerae' | | synonym | 76122 | ATCC 51259 | | type material | 76122 | Alloprevotella tannerae | | scientific name | 76122 | CCUG 34292 | | type material | 76122 | CIP 104476 | | type material | 76122 | NCTC 13073 | | type material | 76122 | Prevotella tannerae | | synonym | 76122 | Prevotella tannerae Moore et al. 1994 | | authority | 76122 | Prevotella tanneriae | | misspelling | 76122 | VPI N14B-15 | | type material | 76832 | CCUG 39352 | | type material | 76832 | CIP 105170 | | type material | 76832 | JCM 7460 | | type material | 76832 | LMG 4029 | | type material | 76832 | Myroides odoratimimus | | scientific name | 76832 | Myroides odoratimimus Vancanneyt et al. 1996 | | authority | 76832 | NCTC 11180 | | type material | 78258 | AS 1.2280 | | type material | 78258 | Bifidobacterium denticolens | | synonym | 78258 | Bifidobacterium denticolens Crociani et al. 1996 | | authority | 78258 | CCUG 35728 | | type material | 78258 | CCUG 36886 | | type material | 78258 | DSM 10105 | | type material | 78258 | JCM 12538 | | type material | 78258 | NCTC 12936 | | type material | 78258 | Parascardovia denticolens | | scientific name | 78258 | Parascardovia denticolens (Crociani et al. 1996) Jian and Dong 2002 | | authority | 78258 | strain B3028 | | type material | 80840 | 'Burkholderiales' | | synonym | 80840 | Burkholderia/Oxalobacter/Ralstonia group | | synonym | 80840 | Burkholderiales | | scientific name | 82203 | ATCC 35019 | | type material | 82203 | CCUG 44586 | | type material | 82203 | CIP 105322 | | type material | 82203 | Centipeda periodontii | | scientific name | 82203 | Centipeda periodontii Lai et al. 1983 | | authority | 82203 | DSM 2778 | | type material | 82203 | strain LL2383 | | type material | 85698 | "Achromobacter xylosoxidans" Yabuuchi and Ohyama 1971 | | authority | 85698 | ATCC 27061 | | type material | 85698 | Achromobacter xylosoxidans | | scientific name | 85698 | Achromobacter xylosoxidans (ex Yabuuchi and Ohyama 1971) Yabuuchi and Yano 1981 | | authority | 85698 | Achromobacter xylosoxidans KF701 | | includes | 85698 | Achromobacter xylosoxidans subsp. xylosoxidans | | includes | 85698 | Achromobacter xylosoxidans subsp. xylosoxidans (ex Yabuuchi & Ohyama 1971) Yabuuchi & Yano 1981 | | authority | 85698 | Achromobacter xylosoxydans | | equivalent name | 85698 | Alcaligenes denitrificans subsp. xylosoxydans | | includes | 85698 | Alcaligenes denitrificans subsp. xylosoxydans (Yabuuchi and Yano 1981) Kersters and De Ley 1984 | | authority | 85698 | Alcaligenes denitrificans xylosoxydans | | includes | 85698 | Alcaligenes xylosoxidans | | synonym | 85698 | Alcaligenes xylosoxidans (Yabuuchi and Yano 1981) Kiredjian et al. 1986 | | authority | 85698 | Alcaligenes xylosoxidans subsp. xylosoxidans | | includes | 85698 | Alcaligenes xylosoxidans subsp. xylosoxidans (Yabuuchi and Yano 1981) Kiredjian et al. 1986 | | authority | 85698 | Alcaligenes xylosoxydans | | equivalent name | 85698 | Alcaligenes xylosoxydans xylosoxydans | | includes | 85698 | CCUG 12689 | | type material | 85698 | CIP 71.32 | | type material | 85698 | DSM 10346 | | type material | 85698 | DSM 2402 | | type material | 85698 | Flavobacterium sp. 650 | | includes | 85698 | IFO 15126 | | type material | 85698 | JCM 9659 | | type material | 85698 | LMG 1863 | | type material | 85698 | NBRC 15126 | | type material | 85698 | NCTC 10807 | | type material | 85698 | NRRL B-4082 | | type material | 85698 | strain Hugh 2838 | | type material | 85698 | strain KM 543 | | type material | 85698 | strain Yabuuchi KM 543 | | type material | 100886 | CCUG 48821 A | | type material | 100886 | CCUG 48821 B | | type material | 100886 | CIP 106738 | | type material | 100886 | Catenabacterium mitsuokai | | misspelling | 100886 | Catenibacterium mitsuokai | | scientific name | 100886 | Catenibacterium mitsuokai Kageyama and Benno 2000 | | synonym | 100886 | JCM 10609 | | type material | 100886 | strain RCA 14-39 | | type material | 102862 | ATCC 33519 | | type material | 102862 | CCUG 15722 | | type material | 102862 | CDC 1808-73 | | type material | 102862 | CIP 103030 | | type material | 102862 | DSM 4544 | | type material | 102862 | JCM 3948 | | type material | 102862 | NCTC 12737 | | type material | 102862 | Proteus genomosp. 1 | | synonym | 102862 | Proteus genomospecies 1 | | synonym | 102862 | Proteus penneri | | scientific name | 102862 | Proteus penneri Hickman et al. 1983 | | synonym | 102862 | Proteus vulgaris biogroup 1 | | synonym | 102862 | Proteus vulgaris indole negative | | synonym | 103621 | Actinomyces sp. CCUG 28744 | | includes | 103621 | Actinomyces sp. CCUG 42029 | | equivalent name | 103621 | Actinomyces urogenitalis | | scientific name | 103621 | Actinomyces urogenitalis Nikolaitchouk et al. 2000 | | synonym | 103621 | CCUG 38702 | | type material | 103621 | CIP 106421 | | type material | 103621 | DSM 15434 | | type material | 109790 | ATCC 25258 | | type material | 109790 | CCUG 21961 | | type material | 109790 | CCUG 35572 | | type material | 109790 | CIP 69.17 | | type material | 109790 | DSM 20557 | | type material | 109790 | JCM 1146 | | type material | 109790 | JCM 15953 | | type material | 109790 | LMG 6414 | | type material | 109790 | Lactobacillus jensenii | | scientific name | 109790 | Lactobacillus jensenii Gasser et al. 1970 | | synonym | 109790 | NRRL B-4550 | | type material | 113287 | "Ramibacterium alactolyticum" Prevot and Taffanel 1942 | | authority | 113287 | "Ramibacterium dentium" Vinzent and Reynes 1947 | | authority | 113287 | "Ramibacterium pleuriticum" Prevot et al. 1947 | | authority | 113287 | ATCC 23263 | | type material | 113287 | CIP 106365 | | type material | 113287 | DSM 3980 | | type material | 113287 | Eubacterium alactolyticum | | synonym | 113287 | Eubacterium alactolyticum (Prevot and Taffanel 1942) Holdeman and Moore 1970 (Approved Lists 1980) | | authority | 113287 | JCM 6480 | | type material | 113287 | Pseudoramibacter alactolyticus | | scientific name | 113287 | Pseudoramibacter alactolyticus (Prevot and Taffanel 1942) Willems and Collins 1996 | | authority | 113287 | Ramibacterium alactolyticum | | synonym | 113287 | Ramibacterium dentium | | synonym | 113287 | Ramibacterium pleuriticum | | synonym | 126385 | "Bacillus inconstans" Ornstein 1920 | | authority | 126385 | "Eberthella alcalifaciens" de Salles Gomes 1944 | | authority | 126385 | ATCC 9886 | | type material | 126385 | Bacillus inconstans | | synonym | 126385 | CCUG 6325 | | type material | 126385 | CIP 82.90 | | type material | 126385 | DSM 30120 | | type material | 126385 | Eberthella alcalifaciens | | synonym | 126385 | JCM 1673 | | type material | 126385 | NCTC 10286 | | type material | 126385 | Proteus inconstans (Ornstein 1920) Shaw and Clarke 1955 | | authority | 126385 | Providencia alcalifaciens | | scientific name | 126385 | Providencia alcalifaciens (de Salles Gomes 1944) Ewing 1962 | | authority | 133448 | ATCC 29935 | | type material | 133448 | CCUG 30791 | | type material | 133448 | CDC 460-61 | | type material | 133448 | CIP 105016 | | type material | 133448 | Citrobacter genomospecies 5 | | synonym | 133448 | Citrobacter youngae | | scientific name | 133448 | Citrobacter youngae Brenner et al. 1993 | | authority | 133448 | DSM 17578 | | type material | 133448 | GTC 1314 | | type material | 135080 | ATCC 43531 | | type material | 135080 | DSM 19720 | | type material | 135080 | JCM 8544 | | type material | 135080 | Selenomonas flueggei | | scientific name | 135080 | Selenomonas flueggei Moore et al. 1987 | | authority | 135082 | ATCC 43532 | | type material | 135082 | DSM 19666 | | type material | 135082 | JCM 8545 | | type material | 135082 | Selenomonas infelix | | scientific name | 135082 | Selenomonas infelix Moore et al. 1987 | | synonym | 135083 | ATCC 43541 | | type material | 135083 | DSM 19578 | | type material | 135083 | JCM 8546 | | type material | 135083 | Selenomonas noxia | | scientific name | 135083 | Selenomonas noxia Moore et al. 1987 | | authority | 135083 | VPI D9B-5 | | type material | 138119 | Desulfitobacterium hafniense Y51 | | scientific name | 138119 | Desulfitobacterium hafniense str. Y51 | | equivalent name | 138119 | Desulfitobacterium hafniense strain Y51 | | equivalent name | 138119 | Desulfitobacterium sp. Y51 | | equivalent name | 154046 | CCUG 43506 | | type material | 154046 | Clostridium hathewayi | | scientific name | 154046 | Clostridium hathewayi Steer et al. 2002 | | authority | 154046 | Clostridium sp. DSM 13479 | | includes | 154046 | DSM 13479 | | type material | 154046 | [Clostridium] hathewayi | | equivalent name | 154046 | strain 1313 | | type material | 155864 | Escherichia coli 0157:H7 EDL933 | | misspelling | 155864 | Escherichia coli O157:H7 EDL933 | | equivalent name | 155864 | Escherichia coli O157:H7 str. EDL 933 | | misspelling | 155864 | Escherichia coli O157:H7 str. EDL933 | | scientific name | 155864 | Escherichia coli O157:H7 strain EDL933 | | equivalent name | 157692 | CCUG 32286 | | type material | 157692 | CIP 107915 | | type material | 157692 | JCM 16774 | | type material | 157692 | Leptotrichia goodfellowii | | scientific name | 157692 | Leptotrichia goodfellowii Eribe et al. 2004 | | authority | 157692 | strain LB 57 | | type material | 158836 | ATCC 49162 | | type material | 158836 | CCUG 27126 | | type material | 158836 | CDC Enteric Group 75 | | synonym | 158836 | CIP 103441 | | type material | 158836 | Enterobacter hormaechei | | scientific name | 158836 | Enterobacter hormaechei O'Hara et al. 1990 | | authority | 158836 | strain 0992-77 | | type material | 158850 | ATCC 33673 | | type material | 158850 | CCUG 15723 | | type material | 158850 | CDC 0132-68 | | type material | 158850 | CIP 103032 | | type material | 158850 | DSM 4541 | | type material | 158850 | JCM 3953 | | type material | 158850 | NCTC 11802 | | type material | 158850 | Providencia alcalifaciens biogroup 3 | | synonym | 158850 | Providencia friedericiana | | synonym | 158850 | Providencia friedericiana Muller 1983 | | authority | 158850 | Providencia friederikeana | | synonym | 158850 | Providencia friederikeiana | | synonym | 158850 | Providencia rustigianii | | scientific name | 158850 | Providencia rustigianii Hickman-Brenner et al. 1983 | | authority | 158877 | ATCC 49455 | | type material | 158877 | BCRC 12225 | | type material | 158877 | CCRC 12225 | | type material | 158877 | CIP 105435 | | type material | 158877 | Enteric Group 45 | | synonym | 158877 | JCM 2403 | | type material | 158877 | Koserella trabulsii | | synonym | 158877 | Koserella trabulsii Hickman-Brenner et al. 1985 | | authority | 158877 | NBRC 102600 | | type material | 158877 | NCTC 11966 | | type material | 158877 | NIH 725-83 | | type material | 158877 | Yokenella regensburgei | | scientific name | 158877 | Yokenella regensburgei Kosako et al. 1985 | | authority | 161889 | ATCC 700352 | | type material | 161889 | CCUG 37336 | | type material | 161889 | CIP 105127 | | type material | 161889 | Corynebacterium lipophiloflavum | | scientific name | 161889 | Corynebacterium lipophiloflavum Funke et al. 1997 | | synonym | 161889 | Corynebacterium sp. 1944 | | includes | 161889 | DMMZ 1944 | | type material | 161889 | DSM 44291 | | type material | 161889 | JCM 10383 | | type material | 168384 | Bryantella formatexigens | | synonym | 168384 | Bryantella formatexigens Wolin et al. 2004 | | authority | 168384 | CCUG 46960 | | type material | 168384 | DSM 14469 | | type material | 168384 | Marvinbryantia formatexigens | | scientific name | 168384 | Marvinbryantia formatexigens (Wolin et al. 2004) Wolin et al. 2008 | | authority | 168384 | strain I-52 | | type material | 178214 | ATCC 700628 | | type material | 178214 | CCUG 36813 | | type material | 178214 | CIP 105962 | | type material | 178214 | Facklamia hominis | | scientific name | 178214 | Facklamia hominis Collins et al. 1997 | | synonym | 178214 | LMG 18980 | | type material | 194702 | ATCC BAA-694 | | type material | 194702 | CCUG 48245 | | type material | 194702 | Cardiobacterium valvarum | | scientific name | 194702 | Cardiobacterium valvarum Han et al. 2004 emend. Han and Falsen 2005 | | authority | 194702 | Cardiobacterium valvitidis | | misspelling | 194702 | DSM 17211 | | type material | 194702 | NCTC 13294 | | type material | 194702 | strain MDA3079 | | type material | 199310 | Escherichia coli CFT073 | | scientific name | 199310 | Escherichia coli str. CFT073 | | equivalent name | 199310 | Escherichia coli strain CFT073 | | equivalent name | 204525 | ATCC 49957 | | type material | 204525 | CIP 104027 | | type material | 204525 | Roseomonas cervicalis | | scientific name | 204525 | Roseomonas cervicalis Rihs et al. 1998 | | synonym | 204525 | strain E7107 | | type material | 207769 | unclassified Eubacteriaceae | | scientific name | 212035 | Acanthamoeba polyphaga mimivirus | | scientific name | 212035 | Acanthomoeba polyphaga mimivirus | | misspelling | 212035 | Mimi | | misnomer | 214851 | CCUG 47106 | | type material | 214851 | Clostridium sp. BI-114 | | includes | 214851 | DSM 15176 | | type material | 214851 | Subdoligranulum variabile | | scientific name | 214851 | Subdoligranulum variabile Holstrom et al. 2004 | | authority | 214851 | strain BI 114 | | type material | 218538 | CCUG 47026 | | type material | 218538 | DSM 15470 | | type material | 218538 | Dialister invisus | | scientific name | 218538 | Dialister invisus Downes et al. 2003 | | authority | 218538 | JCM 17566 | | type material | 218538 | strain E7.25 | | type material | 225324 | ATCC 27094 | | type material | 225324 | Enhydrobacter aerosaccus | | scientific name | 225324 | Enhydrobacter aerosaccus Staley et al. 1987 | | synonym | 225324 | LMG 21877 | | type material | 246144 | CCM 7220 [[Enterococcus saccharominimus]] | | type material | 246144 | CCUG 50447 | | type material | 246144 | DSM 15952 | | type material | 246144 | Enterococcus italicus | | scientific name | 246144 | Enterococcus italicus Fortina et al. 2004 | | authority | 246144 | Enterococcus saccharominimus | | synonym | 246144 | Enterococcus saccharominimus Vancanneyt et al. 2004 | | authority | 246144 | Enterococcus sp. CDC PNS-E1 | | includes | 246144 | Enterococcus sp. TP1.5 | | includes | 246144 | LMG 21727 [[Enterococcus saccharominimus]] | | type material | 246144 | LMG 22039 | | type material | 246144 | strain TP1.5 | | type material | 246787 | Bacteroides cellulosilyticus | | scientific name | 246787 | Bacteroides cellulosilyticus Robert et al. 2007 | | authority | 246787 | CCUG 44979 | | type material | 246787 | DSM 14838 | | type material | 246787 | JCM 15632 | | type material | 246787 | strain CRE21 | | type material | 249188 | CCUG 48703 | | type material | 249188 | DSM 17240 | | type material | 249188 | DSM 21203 | | type material | 249188 | Haemophilus pittmaniae | | scientific name | 249188 | Haemophilus pittmaniae Norskov-Lauritsen et al. 2005 | | authority | 249188 | Haemophilus pittmanii | | misspelling | 249188 | NCTC 13334 | | type material | 249188 | strain HK 85 | | type material | 272559 | Bacteroides fragilis ATCC 25285 | | synonym | 272559 | Bacteroides fragilis NCTC 9343 | | scientific name | 272559 | Bacteroides fragilis NCTC9343 | | misspelling | 272559 | Bacteroides fragilis str. NCTC 9343 | | equivalent name | 272559 | Bacteroides fragilis strain NCTC 9343 | | equivalent name | 291644 | ATCC BAA-997 | | type material | 291644 | Bacteroides salyersae | | synonym | 291644 | Bacteroides salyersiae | | scientific name | 291644 | Bacteroides salyersiae corrig. Song et al. 2005 | | authority | 291644 | Bacteroides sp. WAL 10018 | | includes | 291644 | CCUG 48945 | | type material | 291644 | DSM 18765 | | type material | 291644 | JCM 12988 | | type material | 291644 | WAL 10018 | | type material | 292800 | "Bacille de Plaut, Kritchevsky and Seguin 1921" | | authority | 292800 | "Bacillus plauti" (sic) Seguin 1928 | | authority | 292800 | "Fusocillus plauti" (sic) (Seguin 1928) Prevot 1938 | | authority | 292800 | "Zuberella plauti" (sic) (Seguin 1928) Sebald 1962 | | authority | 292800 | ATCC 29863 | | type material | 292800 | ATCC 49531 [[Clostridium orbiscindens]] | | type material | 292800 | Bacillus plauti | | synonym | 292800 | CCUG 28093 | | type material | 292800 | Clostridium orbiscindens | | synonym | 292800 | Clostridium orbiscindens Winter et al. 1991 | | authority | 292800 | DSM 4000 | | type material | 292800 | DSM 6740 [[Clostridium orbiscindens]] | | type material | 292800 | DSM 6749 [[Clostridium orbiscindens]] | | type material | 292800 | Eubacterium plautii | | synonym | 292800 | Eubacterium plautii (Seguin 1928) Hofstad and Aasjord 1982 | | authority | 292800 | Flavonifractor plautii | | scientific name | 292800 | Flavonifractor plautii (Seguin 1928) Carlier et al. 2010 | | authority | 292800 | Fusobacterium plautii | | synonym | 292800 | Fusobacterium plautii corrig. Seguin 1928 (Approved Lists 1980) | | authority | 292800 | Fusocillus plauti | | synonym | 292800 | Zuberella plauti | | synonym | 328812 | ATCC BAA-1180 | | type material | 328812 | Bacteroides goldsteinii | | synonym | 328812 | Bacteroides goldsteinii Song et al. 2006 | | authority | 328812 | Bacteroides sp. WAL 12034 | | includes | 328812 | CCUG 48944 | | type material | 328812 | DSM 19448 | | type material | 328812 | JCM 13446 | | type material | 328812 | Parabacteroides goldsteinii | | scientific name | 328812 | Parabacteroides goldsteinii (Song et al. 2006) Sakamoto and Benno 2006 | | authority | 328812 | WAL 12034 | | type material | 329854 | Bacteroides intestinalis | | scientific name | 329854 | Bacteroides intestinalis Bakir et al. 2006 | | authority | 329854 | DSM 17393 | | type material | 329854 | JCM 13265 | | type material | 329854 | strain 341 | | type material | 331111 | Escherichia coli E24377A | | scientific name | 331111 | Escherichia coli str. E24377A | | equivalent name | 331111 | Escherichia coli strain E24377A | | equivalent name | 331112 | Escherichia coli HS | | scientific name | 331112 | Escherichia coli str. HS | | equivalent name | 331112 | Escherichia coli strain HS | | equivalent name | 357276 | Bacteroides dorei | | scientific name | 357276 | Bacteroides dorei Bakir et al. 2006 | | authority | 357276 | Bacteroides sp. 175T | | includes | 357276 | Bacteroides sp. 219 | | includes | 357276 | DSM 17855 | | type material | 357276 | JCM 13471 | | type material | 357276 | strain 175 | | type material | 363265 | DSM 18206 | | type material | 363265 | JCM 13469 | | type material | 363265 | Prevotella sp. CB35 | | includes | 363265 | Prevotella stercorea | | scientific name | 363265 | Prevotella stercorea Hayashi et al. 2007 | | authority | 363265 | strain CB35 | | type material | 374840 | Enterobacteria phage phiX174 sensu lato | | scientific name | 374844 | Enterobacteria phage G4 sensu lato | | scientific name | 374844 | Enterobacteria phage G4-like viruses | | synonym | 375288 | Parabacteroides | | scientific name | 375288 | Parabacteroides Sakamoto and Benno 2006 | | authority | 387661 | DSM 18315 | | type material | 387661 | JCM 13406 | | type material | 387661 | Parabacteroides johnsonii | | scientific name | 387661 | Parabacteroides johnsonii Sakamoto et al. 2007 | | authority | 387661 | strain M-165 | | type material | 400667 | Acinetobacter baumannii ATCC 17978 | | scientific name | 400667 | Acinetobacter baumannii str. ATCC 17978 | | equivalent name | 400667 | Acinetobacter baumannii strain ATCC 17978 | | equivalent name | 405416 | Acinetobacter baumannii ACICU | | scientific name | 405416 | Acinetobacter baumannii ICU | | misspelling | 405416 | Acinetobacter baumannii str. ACICU | | equivalent name | 405416 | Acinetobacter baumannii strain ACICU | | equivalent name | 409438 | Escherichia coli SE11 | | scientific name | 409438 | Escherichia coli str. SE11 | | equivalent name | 409438 | Escherichia coli strain SE11 | | equivalent name | 435590 | Bacteroides vulgatus ATCC 8482 | | scientific name | 435590 | Bacteroides vulgatus str. ATCC 8482 | | equivalent name | 435590 | Bacteroides vulgatus strain ATCC 8482 | | equivalent name | 435591 | Parabacteroides distasonis ATCC 8503 | | scientific name | 435591 | Parabacteroides distasonis str. ATCC 8503 | | equivalent name | 435591 | Parabacteroides distasonis strain ATCC 8503 | | equivalent name | 437897 | DSM 19343 | | type material | 437897 | JCM 14723 | | type material | 437897 | Megamonas funiformis | | scientific name | 437897 | Megamonas funiformis Sakon et al. 2008 | | authority | 437897 | YIT 11815 | | type material | 437898 | DSM 19354 | | type material | 437898 | JCM 14724 | | type material | 437898 | Sutterella parvirubra | | scientific name | 437898 | Sutterella parvirubra Sakon et al. 2008 | | authority | 437898 | YIT 11816 | | type material | 439703 | CCUG 54766 | | type material | 439703 | DSM 19339 | | type material | 439703 | JCM 15638 | | type material | 439703 | Prevotella genomosp. T3 | | synonym | 439703 | Prevotella maculosa | | scientific name | 439703 | Prevotella maculosa Downes et al. 2007 | | authority | 439703 | strain W1609 | | type material | 444860 | Cyanophage 8017-1 | | synonym | 444860 | Synechococcus phage S-SM2 | | scientific name | 479436 | Veillonella parvula DSM 2008 | | scientific name | 479436 | Veillonella parvula str. DSM 2008 | | equivalent name | 479436 | Veillonella parvula strain DSM 2008 | | equivalent name | 480119 | Acinetobacter baumannii AB0057 | | scientific name | 480119 | Acinetobacter baumannii str. AB0057 | | equivalent name | 480119 | Acinetobacter baumannii strain AB0057 | | equivalent name | 481722 | DSM 19906 | | type material | 481722 | JCM 15041 | | type material | 481722 | Lactobacillus kisonensis | | scientific name | 481722 | Lactobacillus kisonensis Watanabe et al. 2009 | | authority | 481722 | Lactobacillus sp. YIT 11168 | | includes | 481722 | Lactobacillus sp. YIT 11510 | | includes | 481722 | Lactobacillus sp. YIT 11661 | | includes | 481722 | NRIC 0741 | | type material | 481722 | YIT 11168 | | type material | 487173 | DSM 21274 | | type material | 487173 | Dialister succinatiphilus | | scientific name | 487173 | Dialister succinatiphilus Morotomi et al. 2008 | | authority | 487173 | JCM 15077 | | type material | 487173 | YIT 11850 | | type material | 487174 | Barnesiella intestinihominis | | scientific name | 487174 | Barnesiella intestinihominis Morotomi et al. 2008 | | authority | 487174 | Barnesiella sp. YIT 11860 | | includes | 487174 | DSM 21032 | | type material | 487174 | JCM 15079 | | type material | 487174 | YIT 11860 | | type material | 487175 | DSM 21040 | | type material | 487175 | JCM 15078 | | type material | 487175 | Parasutterella excrementihominis | | scientific name | 487175 | Parasutterella excrementihominis Nagai et al. 2009 | | authority | 487175 | strain YIT 11859 | | type material | 489828 | Enterobacteria phage WA13 sensu lato | | scientific name | 489829 | Enterobacteria phage ID18 sensu lato | | scientific name | 497978 | Acinetobacter baumannii MDR-ZJ06 | | scientific name | 497978 | Acinetobacter baumannii str. MDR-ZJ06 | | equivalent name | 497978 | Acinetobacter baumannii strain MDR-ZJ06 | | equivalent name | 509170 | Acinetobacter baumannii SDF | | scientific name | 509170 | Acinetobacter baumannii str. SDF | | equivalent name | 509170 | Acinetobacter baumannii strain SDF | | equivalent name | 509173 | Acinetobacter baumannii AYE | | scientific name | 509173 | Acinetobacter baumannii str. AYE | | equivalent name | 509173 | Acinetobacter baumannii strain AYE | | equivalent name | 511969 | Enterobacteria phage ID2 Moscow/ID/2001 | | scientific name | 546271 | Selenomonas sputigena ATCC 35185 | | scientific name | 546271 | Selenomonas sputigena DSM 20758 | | synonym | 546271 | Selenomonas sputigena HMP_JCVI_SC0180 | | synonym | 546271 | Selenomonas sputigena str. ATCC 35185 | | equivalent name | 546271 | Selenomonas sputigena strain ATCC 35185 | | equivalent name | 585535 | Helicobacter pylori 35A | | scientific name | 585538 | Helicobacter pylori 83 | | scientific name | 607711 | CIP 109934 | | type material | 607711 | DSM 22247 | | type material | 607711 | Neisseria sp. WC 05-2507 | | includes | 607711 | Neisseria wadsworthii | | scientific name | 607711 | Neisseria wadsworthii Wolfgang et al. 2011 | | authority | 607711 | WC 05-9715 | | type material | 607711 | strain 9715 | | type material | 607712 | CIP 109933 | | type material | 607712 | DSM 22246 | | type material | 607712 | Neisseria shayeganii | | scientific name | 607712 | Neisseria shayeganii Wolfgang et al. 2011 | | authority | 607712 | Neisseria sp. WC 04-12337 | | includes | 607712 | WC 08-871 | | type material | 607712 | strain 871 | | type material | 626929 | Bacteroides clarus | | scientific name | 626929 | Bacteroides clarus Watanabe et al. 2010 | | authority | 626929 | DSM 22519 | | type material | 626929 | JCM 16067 | | type material | 626929 | YIT 12056 | | type material | 626931 | Bacteroides oleiciplenus | | scientific name | 626931 | Bacteroides oleiciplenus Watanabe et al. 2010 | | authority | 626931 | DSM 22535 | | type material | 626931 | JCM 16102 | | type material | 626931 | YIT 12058 | | type material | 626932 | Alistipes indistinctus | | scientific name | 626932 | Alistipes indistinctus Nagai et al. 2010 | | authority | 626932 | DSM 22520 | | type material | 626932 | JCM 16068 | | type material | 626932 | YIT 12060 | | type material | 626938 | 'Succinatimonas hippei' | | synonym | 626938 | DSM 22608 | | type material | 626938 | JCM 16073 | | type material | 626938 | Succinatimonas hippei | | scientific name | 626938 | YIT 12066 | | type material | 634176 | Aggregatibacter aphrophilus NJ8700 | | scientific name | 634176 | Aggregatibacter aphrophilus str. NJ8700 | | equivalent name | 634176 | Aggregatibacter aphrophilus strain NJ8700 | | equivalent name | 645687 | Astrovirus VA1 | | scientific name | 649756 | "Anaerostipes hadrus" Allen-Vercoe et al. 2012 | | authority | 649756 | ATCC 29173 | | type material | 649756 | Anaerostipes hadrus | | scientific name | 649756 | DSM 3319 | | type material | 649756 | Eubacterium hadrum | | synonym | 649756 | Eubacterium hadrum Moore et al. 1976 | | authority | 649756 | JCM 9980 | | type material | 649756 | VP 82-52 | | type material | 649756 | VPI B2-52 | | type material | 652103 | Rhodopseudomonas palustris DX-1 | | scientific name | 652103 | Rhodopseudomonas palustris str. DX-1 | | equivalent name | 652103 | Rhodopseudomonas palustris strain DX-1 | | equivalent name | 655817 | Escherichia coli ABU 83972 | | scientific name | 655817 | Escherichia coli str. ABU 83972 | | equivalent name | 655817 | Escherichia coli strain ABU 83972 | | equivalent name | 682382 | HMO Astrovirus A | | scientific name | 682382 | Human-Mink-Ovine like astrovirus A | | synonym | 683173 | Astrovirus VA2 | | scientific name | 683174 | Astrovirus VA3 | | scientific name | 685727 | Rhodococcus equi 103S | | scientific name | 685727 | Rhodococcus equi str. 103S | | equivalent name | 685727 | Rhodococcus equi strain 103S | | equivalent name | 693272 | Cafeteria roenbergensis virus BV-PW1 | | scientific name | 693272 | Cafeteria roenbergensis virus MGF-2008 | | synonym | 693272 | Cafeteria roenbergensis virus strain BV-PW1 | | synonym | 693272 | CroV | | acronym | 696749 | Acinetobacter baumannii 1656-2 | | scientific name | 696749 | Acinetobacter baumannii str. 1656-2 | | equivalent name | 696749 | Acinetobacter baumannii strain 1656-2 | | equivalent name | 759851 | 'Sporosarcina newyorkensis' | | synonym | 759851 | CCUG 59649 | | type material | 759851 | DSM 23544 | | type material | 759851 | LMG 26022 | | type material | 759851 | Sporosarcina newyorkensis | | scientific name | 759851 | Sporosarcina sp. 1655 | | includes | 759851 | Sporosarcina sp. 3418 | | includes | 759851 | Sporosarcina sp. 4331 | | includes | 759851 | Sporosarcina sp. 4469 | | includes | 759851 | Sporosarcina sp. 4974 | | includes | 759851 | Sporosarcina sp. 4984 | | includes | 759851 | Sporosarcina sp. 5353 | | includes | 759851 | Sporosarcina sp. 57 | | includes | 759851 | Sporosarcina sp. 5868 | | includes | 759851 | Sporosarcina sp. 6062 | | includes | 759851 | Sporosarcina sp. R-31323 | | includes | 759851 | strain 6062 | | type material | 760570 | Streptococcus parasanguinis ATCC 15912 | | scientific name | 760570 | Streptococcus parasanguinis CCUG 30417 | | synonym | 760570 | Streptococcus parasanguinis CIP 104372 | | synonym | 760570 | Streptococcus parasanguinis DSM 6778 | | synonym | 760570 | Streptococcus parasanguinis GIFU 12468 | | synonym | 760570 | Streptococcus parasanguinis GTC498 | | synonym | 760570 | Streptococcus parasanguinis LMG 14537 | | synonym | 760570 | Streptococcus parasanguinis str. ATCC 15912 | | equivalent name | 760570 | Streptococcus parasanguinis strain ATCC 15912 | | equivalent name | 767029 | Propionibacterium propionicum F0230a | | scientific name | 767029 | Propionibacterium propionicum str. F0230a | | equivalent name | 767029 | Propionibacterium propionicum strain F0230a | | equivalent name | 796939 | Eubacteriaceae bacterium CM2 | | scientific name | 796942 | 'Stomatobaculum longum' | | synonym | 796942 | Lachnospiraceae bacterium ACC2 | | includes | 796942 | Stomatobaculum longum | | scientific name | 885276 | Escherichia coli clone D i2 | | misspelling | 885276 | Escherichia coli str. 'clone D i2' | | scientific name | 885276 | Escherichia coli strain 'clone D i2' | | equivalent name | 908937 | Prevotella dentalis ATCC 49559 | | synonym | 908937 | Prevotella dentalis DSM 3688 | | scientific name | 908937 | Prevotella dentalis JCM 13448 | | synonym | 908937 | Prevotella dentalis str. DSM 3688 | | equivalent name | 908937 | Prevotella dentalis strain DSM 3688 | | equivalent name | 935897 | Haemophilus influenzae F3047 | | scientific name | 935897 | Haemophilus influenzae str. F3047 | | equivalent name | 935897 | Haemophilus influenzae strain F3047 | | equivalent name | 1049283 | Acinetobacter phage ZZ1 | | scientific name | 1094892 | Megavirus chiliensis | | scientific name | 1157951 | Providencia stuartii MRSN 2154 | | scientific name | 1157951 | Providencia stuartii str. MRSN 2154 | | equivalent name | 1157951 | Providencia stuartii strain MRSN 2154 | | equivalent name | 1235314 | Megavirus lba | | scientific name | 1239574 | Mamastrovirus 10 | | scientific name | 1239574 | Mink astrovirus | | synonym | 1239577 | Mamastrovirus 13 | | scientific name | 1239577 | Ovine astrovirus | | synonym | 1239577 | sheep astrovirus | | synonym | 1247113 | Astrovirus VA4 | | scientific name | 1254425 | Porcine astrovirus 3 | | scientific name | 1269028 | Acanthamoeba polyphaga moumouvirus | | scientific name | metaMix/inst/doc/0000755000176200001440000000000013427050664013407 5ustar liggesusersmetaMix/inst/doc/guide.Rnw0000644000176200001440000004067113427050477015206 0ustar liggesusers%\VignetteEngine{knitr::knitr} %\VignetteIndexEntry{metaMix User Guide} \documentclass[a4paper]{article} \usepackage[margin=1.5cm,includefoot,footskip=30pt]{geometry} \usepackage[colorlinks=true]{hyperref} \usepackage{fullpage} \title{metaMix user guide} \author{Sofia Morfopoulou} \date{\today} \begin{document} \maketitle %\tableofcontents %\newpage <>= options(tidy=TRUE, width=80) @ \section{What is new} \textbf{Version 0.2:} Added Bayes Factor computation. \textbf{Version 0.3:} Allow user to specify number of MCMC iterations (Step 3) and Burn-in percentage (Step 4). Due to NCBI phasing out GI numbers, added support for protein accession identifier file for mapping to taxon (STEP1). Fixed bug in step4 for Bayes Factor calculation when only one species is present, that is only human and unknown. Also fixed bug with semi-colon separated taxonids in custom BLAST format, as well as NAs (STEP 1). Replaced deprecated cBind function with cbind. \section{Installation} You will need to have openMPI (Message Passage Interface) installed to be able to install the R package \verb!Rmpi!, which provides the interface to openMPI. \verb!Rmpi! is one of the package dependencies, along with \verb!data.table!, \verb!Matrix!, \verb!gtools! and \verb!ggplot2!. You can check whether you have openMPI installed using the command \verb!mpirun! and you can find more information here:\\ \url{http://www.open-mpi.org/software/ompi} \section{Introduction} metaMix is a tool designed to identify the set of species most likely to be present in a metagenomic community. metaMix also estimates their relative abundances and resolves ambiguous assignments by considering all reads simultaneously. metaMix considers the competing models that could accommodate our observed data, i.e the BLASTx results and compares them. The different mixture models represent different sets of species being present in the sample. The method is structured in the following manner: in the first instance we assume that a set of species is present in the sample and we estimate the parameters given the data. At the next step, we randomly add or remove a species and fit this new model. The process is iterated in order to explore the model state space and we record the MCMC choices over time. Additionally we parallelise the process, running $n$ (usually 12) parallel chains, allowing exchange of information between them. Using this Bayesian Mixture Model framework, we finally perform model averaging in order to account for model uncertainty. The initial motivation for developing metaMix was the analysis of deep transcriptome sequencing datasets, with a particular focus on viral pathogen detection. However the ideas are applicable more generally to all types of metagenomics mixtures. Some bionformatics processing is required prior to using metaMix. This is usually filtering out the low quality, duplicate and host reads. The user may wish to attempt some assembly step as well prior to resolving the mixture; however this step is not necessary. More importantly, the similarities between the short reads (and/or contigs) and a reference database must be provided. At the end of the analysis, the user will obtain a probabilistic summary of present species and some supporting plots. The implementation of the ideas described here is computationally intensive and requires a supercomputer. However for the purposes of this tutorial, we demonstrate the usage on a toy example and all the steps can be performed on a single machine. %\newpage \section{Tutorial} \subsection*{Step1} The work described here is similarity-based, therefore the starting point is to obtain the sequence similarity between a query and a target sequence. The obvious choice for this is BLAST. Both nucleotide and amino acid similarities are supported. We demonstrate the use of metaMix working with the latter, i.e we have used BLASTx. \begin{description} \item[Default BLAST output] The default output tabular file is supported, obtained using \verb!-outfmt 6! in the BLAST command. <>= blastx -db referenceDB -query input.fa -outfmt 6 -max_target_seqs 10 @ The default output file has the following fields:\\ \verb!Query ID!, \verb!Subject ID!, \verb!% Identity!, \verb!Alignment Length!, \verb!Mismatches!, \verb!Gap Openings!, \verb!Query Start!, \verb!Query End!, \verb!Subject Start!, \verb!Subject End!, \verb!E-value!, \verb!Bit Score!. <>= library(metaMix) ###Location of input files. datapath <- system.file("extdata", package="metaMix") blastOut.default<-file.path(datapath, "blastOut_default.tab") read.table(blastOut.default, nrows=2, sep="\t") @ metaMix needs information on the read lengths as well as a file mapping the gi identifiers to the taxon identifiers. These are not included in the default output of BLAST, therefore should be provided as additional arguments. <>= read.lengths<-file.path(datapath, "read_lengths.tab") read.weights<-file.path(datapath, "read_weights.tab") taxon.file<-file.path(datapath, "gi_taxid_prot_example.dmp") read.table(read.lengths, nrows=2, sep="\t") read.table(read.weights, nrows=2, sep="\t") read.table(taxon.file, nrows=2, sep="\t") @ \item[Custom BLAST output] Alternatively, metaMix accepts a custom BLAST output file that has already incorporated the read lengths and the taxon identifiers. At the moment, only the output that is produced by the following command is supported: <>= blastx -db referenceDB -query input.fa -max_target_seqs 10 -outfmt "6 qacc qlen sacc slen mismatch bitscore length pident evalue staxids" @ Therefore the fields are \\ \verb!Query ID!, \verb!Query Length!, \verb!Subject ID!, \verb!Subject Length!, \verb!Mismatches!, \verb!Bit Score!, \verb!Alignment Length!, \verb!%Identity!, \verb!E-value!, \verb!Taxon ID!. <>= blastOut.custom<-file.path(datapath, "blastOut_custom.tab") read.table(blastOut.custom, nrows=2, sep="\t") @ \end{description} \vspace{5mm} The first step in the analysis is to compute the read-species generative probabilities based on the BLASTx data. We achieve this by using the \verb!generative.prob()! function. In this instance we will work with the custom BLAST output file. <>= step1 <-generative.prob(blast.output.file = blastOut.custom, contig.weight.file=read.weights, blast.default=FALSE, outDir=NULL) @ where \verb!blast.default! denotes whether we are working with the BLAST default output (TRUE) or with the specified above custom output (FALSE). \verb!blast.output.file! is the tabular BLASTx output file. If we are working with unassembled reads, we can omit the argument \verb!contig.weight.file! as the weight is set by default to be 1, same for all reads. However if an assembly step has been performed, as in this example, we need to provide information on the number of reads that make up each contig. This will be a two column tab-separated file, where the first column is the contig identifier and the second the number of reads. Finally \verb!outDir! is the directory where the results are written and where an object from each step is saved. When it is set to NULL no objects will be saved. \vspace{3mm} \emph{NOTE}: If we were using the default BLAST output the command would look like so: <>= step1 <-generative.prob(blast.output.file = blastOut.default, read.length.file=read.lengths, contig.weight.file=read.weights, gi.taxon.file = taxon.file, blast.default=TRUE, outDir=NULL) @ The information missing from the BLAST file is now provided with two extra arguments: \verb!read.length.file! can be either the file mapping each read to its sequence length or a numerical value, representing the average read length (default value=100). \verb!'gi_taxid_prot.dmp'! is a taxonomy file, mapping each protein gi identifier to the corresponding taxon identifier. It can be downloaded from \\ \url{ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_prot.dmp.gz} \\ The function \verb!generative.prob! creates a list of five elements. One of these is a sparse matrix \verb!pij.sparse.mat! where each row corresponds to one read and each column to a species. The value of the cell is the generative probability $p_{ij}$. Additionally a \verb!data.frame! with all the species that correspond to the proteins in the BLASTx output file. Finally the \verb!read.weights!, \verb!gen.prob.unknown! and \verb!outDir! are the other three elements of the list \verb!step1!, carried forward to be used in the second step. <>= ###The resulting list consists of five elements names(step1) ### The sparse matrix of generative probs. step1$pij.sparse.mat[1:5,c("374840", "258", "unknown")] ### There are that many potential species in the sample: nrow(step1$ordered.species) @ \subsection*{Step2} Having the generative probabilities from the previous step (generative.prob), we could proceed directly with the PT MCMC to explore the state space. However, typically the number of all potential species $S$ is large. We are therefore interested in reducing the size of the species pool, from the thousands to the low hundreds. In this simple example we have only 224 organisms but still we attempt to reduce it for demonstrating the usage of the function. We achieve this by fitting a mixture model with 224 categories, considering all 224 potential species simultaneously. Post fitting, we retain only the species categories that are not empty, that is the categories that have at least one read assigned to them. The required argument is simply the list created in the first step, i.e using the \verb!generative.prob! function. <>= step2 <- reduce.space(step1=step1) @ Alternatively, if the list created in the first step was saved in a ``step1.RData'' file, a character string containing the path to the file could be provided, i.e <>= step2 <- reduce.space(step1="/pathtoFile/step1.RData") @ To speed up computations, we have already performed step2 and saved the output which we will now load: <>= data(step2) @ <>= ##These are the elements of the step2 list. names(step2) ## After this approximating step, there are now that many potential species in ##the sample: nrow(step2$ordered.species) ## And these are: step2$ordered.species @ We see that even though we started with 224 potential organisms, we reduced the species space to 7. Bear in mind that this a simple example and the usual scenario is to move from thousands of species to hundreds. \subsection*{Step3} In this step, the different models are considered and compared. The space exploration by the parallel tempering MCMC is implemented by the function \verb!parallel.temper!: <>= step3<-parallel.temper(step2=step2) @ The required argument is simply the list created in the second step (or the character string containing the path to the respective .RData file where the step2 list was saved to), i.e using the \verb!reduce.space! function. An important optional argument of this function is \verb!readSupport!. For the type of data we analyse (i.e from mostly sterile human tissues) we expect that parsimonious models with a limited number of species are more likely. Therefore our default model prior uses a penalty limiting the number of species in the model. We approximate this penalty factor based on \verb!readSupport!, which represents the species read support required from the user in order to believe in the presence of a species in the sample. The default value is 10 and it is suitable for when we want to detect rare signal. We have found this value to work well in most human RNA-seq datasets. Same as before, we have already performed step3 and saved the output which we now load: <>= data(step3) @ <>= ##These are the elements of the step3 list. names(step3) @ <>= ## Steps MCMC took during some iterations. step3$result$slave1$record[10:15,] @ For each parallel chain, the MCMC trajectory has been recorded. There is information on what steps were proposed, which were accepted or rejected throughout the iterations. For example at iteration 10, removing species 645687 was proposed but not accepted, as denoted by the 1 in the column 645687. We can also see that between iterations 13 and 14 an exchange of the sets of species between Chain 1 and Chain 2 occurred. At iter. 13 species 2 was present, while at the next one, it no longer is there. That means that the attempt at swapping the values of the two neighboring chains was successful. This information is also recorded, i.e how many swaps were attempted and how many accepted. Each chain will produce a log file that will be printed in your working directory. \subsection*{Step4} Having explored the different possible models, the final step is to perform model averaging. We study the MCMC choices for Chain 1 and produce a probabilistic summary for the presence of the species. <>= ## Location of the taxonomy names file. taxon.file<-file.path(datapath, "names_example.dmp") step4<-bayes.model.aver(step2=step2, step3=step3, taxon.name.map=taxon.file) @ The required arguments are the lists created in the second and third steps, i.e using the \verb!reduce.space! and the \verb!parallel.temper! functions. Additionally the taxonomy names file 'names.dmp', which can be downloaded and extracted from \url{ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz} <>= ##These are the elements of the step4 list. names(step4) ##This is the species summary print(step4$presentSpecies.allInfo) @ We find four species with a posterior probability greater than 0.9 (default value), plus the unknown category. Finally we also produce log-likelihood traceplots for Chain 1. We discard the first 20\% of the iterations as burn-in and we look at the mixing of the chain. Due to having very few iterations for this toy example, the produced traceplot would not be representative or insightful. Instead we present below the log-likelihood traceplot from a real dataset. <>= PTastro<-file.path(datapath, "PT_plots.RData") load(PTastro) nIter<- length(PTresult$result$slave1$record[,'logL']) plot(PTresult$result$slave1$record[(nIter/5):nIter,'logL'], type='l', col='dodgerblue', xlab='Last 80% of iterations', ylab='Log-likelihood', main='Parallel Tempering - Coldest Chain', lwd=1.5) @ \section{Submit jobs on cluster compute servers} In order to run steps 1, 2 and 4 of metaMix (i.e \verb!generative.prob!, \verb!reduce.space!, \verb!bayes.model.aver!) efficiently, these should be submitted as jobs to a compute cluster. In our experience, 4G of memory, 1 hour of wall clock time and 1 processor should be plenty. In order to run the parallel tempering efficiently (step3), we need at least 12 parallel chains. I usually request 6 or 12 threads, each with 2G of RAM. The wall clock time depends on how many iterations will be performed. A larger number of reads mean that the computations will become slower. We typically submit all 4 steps in one go using one submission script. I usually assess the size of the dataset, but 12 hours for all 4 steps should be safe. This is a sample submission script, it requests 6 processors on 1 node for 12 hours (more processors, less time necessary). \begin{verbatim} #!/bin/bash #$ -S /bin/bash #$ -o cluster/out #$ -e cluster/error #$ -cwd #$ -pe smp 6 #$ -l tmem=2G,h_vmem=2G #$ -l h_rt=12:00:00 #$ -V #$ -R y mpirun -np 1 R-3.0.1/bin/R --slave CMD BATCH --no-save --no-restore allsteps.R \end{verbatim} an example allsteps.R looks like this: \begin{verbatim} library(metaMix) step1<-generative.prob(blast.output.file="sample_diamond.tab", read.length.file="read_lengths.tab", contig.weight.file="contig_weights.tab", outDir="./", gi.taxon.file="gi_taxid_prot.dmp", blast.default=TRUE, gi.or.prot="gi") step2<-reduce.space(step1="step1.RData") step3<-parallel.temper(step2="step2.RData") step4<-bayes.model.aver(step2="step2.RData", step3="step3.RData", taxon.name.map="names.dmp") \end{verbatim} \section{Technical information about the R session} <>= sessionInfo() @ \end{document} metaMix/inst/doc/guide.R0000644000176200001440000001014213427050664014625 0ustar liggesusers## ----setup, echo=FALSE-------------------------------------------------------- options(tidy=TRUE, width=80) ## ----echo=TRUE, eval=TRUE----------------------------------------------------- library(metaMix) ###Location of input files. datapath <- system.file("extdata", package="metaMix") blastOut.default<-file.path(datapath, "blastOut_default.tab") read.table(blastOut.default, nrows=2, sep="\t") ## ----echo=TRUE, eval=TRUE----------------------------------------------------- read.lengths<-file.path(datapath, "read_lengths.tab") read.weights<-file.path(datapath, "read_weights.tab") taxon.file<-file.path(datapath, "gi_taxid_prot_example.dmp") read.table(read.lengths, nrows=2, sep="\t") read.table(read.weights, nrows=2, sep="\t") read.table(taxon.file, nrows=2, sep="\t") ## ----echo=TRUE, eval=TRUE----------------------------------------------------- blastOut.custom<-file.path(datapath, "blastOut_custom.tab") read.table(blastOut.custom, nrows=2, sep="\t") ## ----echo=TRUE---------------------------------------------------------------- step1 <-generative.prob(blast.output.file = blastOut.custom, contig.weight.file=read.weights, blast.default=FALSE, outDir=NULL) ## ----echo=TRUE, eval=FALSE---------------------------------------------------- # step1 <-generative.prob(blast.output.file = blastOut.default, # read.length.file=read.lengths, # contig.weight.file=read.weights, # gi.taxon.file = taxon.file, # blast.default=TRUE, # outDir=NULL) ## ----echo=TRUE---------------------------------------------------------------- ###The resulting list consists of five elements names(step1) ### The sparse matrix of generative probs. step1$pij.sparse.mat[1:5,c("374840", "258", "unknown")] ### There are that many potential species in the sample: nrow(step1$ordered.species) ## ----echo=TRUE, eval=FALSE---------------------------------------------------- # step2 <- reduce.space(step1=step1) ## ----echo=TRUE, eval=FALSE---------------------------------------------------- # step2 <- reduce.space(step1="/pathtoFile/step1.RData") ## ----echo=FALSE, eval=TRUE---------------------------------------------------- data(step2) ## ----echo=TRUE---------------------------------------------------------------- ##These are the elements of the step2 list. names(step2) ## After this approximating step, there are now that many potential species in ##the sample: nrow(step2$ordered.species) ## And these are: step2$ordered.species ## ----echo=TRUE, eval=FALSE---------------------------------------------------- # step3<-parallel.temper(step2=step2) ## ----echo=FALSE, eval= TRUE--------------------------------------------------- data(step3) ## ----echo=TRUE---------------------------------------------------------------- ##These are the elements of the step3 list. names(step3) ## ----echo=TRUE---------------------------------------------------------------- ## Steps MCMC took during some iterations. step3$result$slave1$record[10:15,] ## ----echo=TRUE---------------------------------------------------------------- ## Location of the taxonomy names file. taxon.file<-file.path(datapath, "names_example.dmp") step4<-bayes.model.aver(step2=step2, step3=step3, taxon.name.map=taxon.file) ## ----echo=TRUE---------------------------------------------------------------- ##These are the elements of the step4 list. names(step4) ##This is the species summary print(step4$presentSpecies.allInfo) ## ----echo=FALSE, eval=TRUE, out.width='.6\\linewidth', out.height='.6\\linewidth', fig.align='center'---- PTastro<-file.path(datapath, "PT_plots.RData") load(PTastro) nIter<- length(PTresult$result$slave1$record[,'logL']) plot(PTresult$result$slave1$record[(nIter/5):nIter,'logL'], type='l', col='dodgerblue', xlab='Last 80% of iterations', ylab='Log-likelihood', main='Parallel Tempering - 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Two types of moves are implemented: a mutation step (within chain) and an exchange step (between neighboring chains). If working with BLASTx data, use parallel.temper(). #' @param step2 list. The output from reduce.space(). Alternatively, it can be a character string containing the path name of the ".RData" file where step2 list was saved. #' @param readSupport The number of reads the user requires in order to believe in the presence of the species. It is used to compute the penalty factor. The default value is 30. We compute the logarithmic penalty value as the log-likelihood difference between two models: one where all N reads belong to the "unknown" category and one where r reads have a perfect match to some unspecified species and the remaining reads belong to the "unknown" category. #' @param noChains The number of parallel chains to run. The default value is 12. #' @param seed Optional argument that sets the random seed (default is 1) to make results reproducible. #' @param median.genome.length To use in the penalty computation. #' @return step3: A list with two elements. The first one (result) is a list that records MCMC information from each parallel chain. The second one (duration) records how much time the MCMC exploration took. #' @seealso \code{\link{parallel.temper}} This function should be used when working with BLASTx data. #' @keywords parallel.temper.nucl #' @export parallel.temper.nucl #' @import Rmpi Matrix #' @importFrom gtools rdirichlet #' @importFrom stats runif ###################################################################################################################### parallel.temper.nucl = function(step2, readSupport=30, noChains=12, seed=1, median.genome.length=284332){ if (is.character(step2)) { load(step2) } should.be.in.the.list <- c("pij.sparse.mat", "ordered.species", "read.weights", "outDir", "gen.prob.unknown") if (sum (!( should.be.in.the.list %in% names(step2)) ) > 0) { message('Missing the following arguments') print(names(step2)[!(should.be.in.the.list %in% names(step2))] ) stop() } else { parallel.temper.nucl.wrapped<-function(readSupport.internal=readSupport, noChains.internal=noChains, pij.sparse.mat=step2$pij.sparse.mat, read.weights=step2$read.weights, ordered.species=step2$ordered.species, gen.prob.unknown=step2$gen.prob.unknown, outDir=step2$outDir, seed.internal=seed, median.genome.length.internal=median.genome.length){ set.seed(seed.internal); #print(warnings()) StartTime<-Sys.time() sieve <- function(n) { n <- as.integer(n) if(n > 1e6) stop("n too large") primes <- rep(TRUE, n) primes[1] <- FALSE last.prime <- 2L for(i in last.prime:floor(sqrt(n))) { primes[seq.int(2L*last.prime, n, last.prime)] <- FALSE last.prime <- last.prime + min(which(primes[(last.prime+1):n])) } which(primes) } list.integers <- sieve(1000) node.ids <- list.integers[ 1:noChains.internal ] mpi.spawn.Rslaves(nslaves = noChains.internal) #number of slaves to spawn, should be equal to individual chains # In case R exits unexpectedly, have it automatically clean up # resources taken up by Rmpi (slaves, memory, etc...) .Last <- function(){ if (is.loaded("mpi_initialize")){ if (mpi.comm.size(1) > 0){ print("Please use mpi.close.Rslaves() to close slaves.") mpi.close.Rslaves() } print("Please use mpi.quit() to quit R") .Call("mpi_finalize", PACKAGE='metaMix') } } pij.sparse.mat<-cbind(pij.sparse.mat, "unknown"=gen.prob.unknown) gc() allSpecies<-ordered.species[,c("taxonID", "samplingWeight")] lenSp<-nrow(allSpecies) lpenalty<-computePenalty.nucl(readSupport=readSupport.internal, readWeights=read.weights, pUnknown=gen.prob.unknown, median.genome.length=median.genome.length) ### penalty for accepting a new species ~ Use pij for the r readSupport perfect reads (=1/median(protein length)). ### EMiter EMiter<-10 ### PT parameters exchangeInterval<-1 ###leave chains run in parallel for that many iterations ExternIter<-5*(nrow(ordered.species)) ### make chains communicate 1 times TotalIter<-exchangeInterval * ExternIter ##Tempering Vector --Power Decay temper<-vector() K<-0.001 a<-3/2 for (n in 2:noChains.internal){ temper[1]<-1 temper[n]<-(temper[n-1]-K)^a } for (i in 1:noChains.internal) {names(temper)[i]<- paste("slave",i, sep="")} ###names ### flag for adding /removing species stepAdd<-vector(mode = "logical") #### broadcast necessary objects/functions to slaves mpi.bcast.Robj2slave(exchangeInterval) mpi.bcast.Robj2slave(ExternIter) mpi.bcast.Robj2slave(TotalIter) mpi.bcast.Robj2slave(list.integers) mpi.bcast.Robj2slave(node.ids) mpi.bcast.Robj2slave(ordered.species) mpi.bcast.Robj2slave(read.weights) mpi.bcast.Robj2slave(pij.sparse.mat) mpi.bcast.Robj2slave(lpenalty) mpi.bcast.Robj2slave(EM) mpi.bcast.Robj2slave(allSpecies) mpi.bcast.Robj2slave(lenSp) mpi.bcast.Robj2slave(EMiter) mpi.bcast.Robj2slave(noChains.internal) mpi.bcast.Robj2slave(temper) mpi.bcast.Robj2slave(gen.prob.unknown) ##########################---------------------------------------SINGLE CHAIN FUNCTION -----------------------------------------------------------------------------------------------####################### singleChain <- function(TotalIter, exchangeInterval){ if (file.exists('~/.Rprofile')) source('~/.Rprofile') print(.libPaths()) ind <- mpi.comm.rank() # Each slave gets its own copy of ind and chain based on mpi process rank print(ind) estimNew<-matrix(0, nrow=TotalIter, ncol=1) ### Create matrix that will hold the estimator of the log-likelihood estimNew[1,]<- sum(read.weights[,"weight"])*log(gen.prob.unknown)*temper[ind] print(estimNew[1,]) presentSpecies<-"unknown" ## create object that receives the species deemed as present, from previous (swapInterv*j) iteration. abundUsedSp<-c("unknown"=1) ### Create 2 lists. One that holds species names and one with their abundances. Each list has 2 elements. Element1: present species and Element2: tentative species being explored in current iteration. speciestoUse<-list("presentSp"=presentSpecies, "tentativeSp"=NULL) abundUsedSpecies<-list("presentSp"= abundUsedSp, "tentativeSp"=NULL) message("\nThis is the temperature for this slave") print(temper[ind]) ### create matrix to hold info on which species was added or removed, which species were present and logL , through iterations record<-matrix(0, ncol=(5+lenSp), nrow=(TotalIter)) record<-as.data.frame(record) colnames(record)<-c("Iter", "Move", "Candidate Species", allSpecies[,1], "unknown", "logL") record[,1]=1:(TotalIter) record[1, presentSpecies]<-1 record[1,(5+lenSp)]<-estimNew[1,] ###last colum is logL swaps.attempted<-0 swaps.accepted<-0 oddFlag<-0 ################ ----------------------------------- Begin MCMC (within single chain) ------------------------------------------------------------------------------------------############ for (i in 2:TotalIter) { cat('\n',i,'\n') ### temporary - debugging purposes #### Create 3 functions to use repeatedly in adding/removing species steps. ######################### 1a. For add step: species I sample my candidate species from. potentialSpecies<-function() { toChooseFrom <- allSpecies[,1][!(allSpecies[,1] %in% speciestoUse[[1]])] ### Species remaining after omitting "present species" toChooseFrom<-as.character(toChooseFrom) potentialSp<- allSpecies[allSpecies$taxonID %in% toChooseFrom,] resultPS<-list("potentialSp"=potentialSp, "toChooseFrom"=toChooseFrom) return(resultPS) } ######################## 1b. For add step, sample candidate organism to add and create object for tentative species moveAdd<-function() { randSp <- sample(as.character(potentialSp[,1]),1, prob=potentialSp[,2]) ### choose random species, weights need not sum to one. Here weights are based on intial read counts. cat('Add species', randSp, '\n') ### temporary - debugging purposes speciestoUse[[2]]<-c(randSp, speciestoUse[[1]]) ### tentative present species, to use in Gibbs below. record[i, 2]<- "Add" ### record info on species we are adding record[i,3]<- randSp result<-list("record"=record, "speciestoUse"=speciestoUse) return(result) } ######################## 2. For remove step, sample candidate organism to remove and create object for tentative species moveRemove<-function() { toremoveFrom <- speciestoUse[[1]][!(speciestoUse[[1]]%in%"unknown")] ### species set from which to remove (i.e present ones bar unknown) toremoveFrom<-as.character(toremoveFrom) removeProb<-(1/abundUsedSpecies[[1]][toremoveFrom])/sum(1/abundUsedSpecies[[1]][toremoveFrom]) ###### sampling weight inversely proportional to assigned read counts. ###Flatten removal probabilities percentiles<-quantile(removeProb, probs=c(0.2, 0.8)) removeProb[which(removeProb >= percentiles["80%"])] <- percentiles["80%"] removeProb[which(removeProb <= percentiles["20%"])] <- percentiles["20%"] ### sample candidate species to remove randSp<-sample(toremoveFrom, 1, prob=removeProb ) ### weights need not sum to one cat('Remove species', randSp, '\n') ### temporary - debugging purposes speciestoUse[[2]] <- speciestoUse[[1]][!(speciestoUse[[1]] %in% randSp)] ### tentative present species, to use in Gibbs below. record[i, 2]<- "Remove" ### record info on species we are adding record[i,3]<- randSp result<-list("record"=record, "speciestoUse"=speciestoUse) return(result) } addStep <-0.5 ####proability of doing add step ######################################################## Add species ######################################## if (runif(1)<= addStep) { resultPS<-potentialSpecies() potentialSp<-as.data.frame(resultPS$potentialSp) toChooseFrom<-as.character(resultPS$toChooseFrom) if (length(toChooseFrom) != 0L){ result<-moveAdd() speciestoUse<-result$speciestoUse record<-result$record } else { ################## ### If pool of species to add empty, go to remove step message("No more species to choose from, all are kept as present.") result<-moveRemove() speciestoUse<-result$speciestoUse record<-result$record addStep<-0 ### so do remove step with prob=1 } } ###close if runif(1)<=addStep else { ################################################### Remove species ################################################# toremoveFrom <- speciestoUse[[1]][!(speciestoUse[[1]]%in%"unknown")] ### species set from which to remove (i.e present ones bar unknown) toremoveFrom<-as.character(toremoveFrom) #### First check that more than 1 species are present, so don't risk of remaining only with X bin and wasting iteration. if (length(toremoveFrom) > 1) { result<-moveRemove() speciestoUse<-result$speciestoUse record<-result$record } else if (length(speciestoUse[[1]])==1) { #### speciestoUse[[1]]==1 when only unknown bin is there / We can only add message("We cannot remove, we only have unknown bin") potentialSp<-allSpecies result<-moveAdd() speciestoUse<-result$speciestoUse record<-result$record addStep <- 1 ### so do add step with prob=1 } else { ### we are adding species instead. Removing would leave us just with X-bin again. message("\nCannot remove a species, so instead we add\n") ### temporary resultPS<-potentialSpecies() potentialSp<-as.data.frame(resultPS$potentialSp) toChooseFrom<-as.character(resultPS$toChooseFrom) result<-moveAdd() speciestoUse<-result$speciestoUse record<-result$record addStep <- 1 } } ###close else (remove species) noSpecies<-length(speciestoUse[[2]]) print(noSpecies) hyperP<-rep(1, noSpecies) startW<-rdirichlet(1, hyperP) output100Tent<-EM(pij=pij.sparse.mat, iter=EMiter, species=speciestoUse[[2]], abund=startW, readWeights = read.weights) ### EM function estimator <- output100Tent$logL[EMiter,2] + (noSpecies * lpenalty) #### penalise likelihood message("EM took: ", output100Tent$RunningTime) mean1<-as.numeric(output100Tent$abundances[EMiter,2:(noSpecies+1)]) names(mean1)<-names(output100Tent$abundances[EMiter,2:(noSpecies+1)]) abundUsedSpecies[[2]]<-mean1 estimNew[i,]<-estimator*temper[ind] ###tempered likelihood message('\n', estimNew[i,] , ' ', estimNew[i-1,]) ### temporary print - which values am I comparing? ####### flag of adding/removing if (record[i,2]=="Add") { stepAdd<-TRUE } else {stepAdd<-FALSE} removeStep <- 1 - addStep ##remove step if (stepAdd) { candidateAdd<-allSpecies[allSpecies[,1]==(as.character(record[i,3])),2] removeProba<-(1/abundUsedSpecies[[2]])/sum(1/abundUsedSpecies[[2]]) ###### sampling weight inversely proportional to size. Tentative Species ###Flattening the sampling probabilities percentiles<-quantile(removeProba, probs=c(0.2, 0.8)) removeProba[which(removeProba >= percentiles["80%"])] <- percentiles["80%"] removeProba[which(removeProba <= percentiles["20%"])] <- percentiles["20%"] candidateRemove<-removeProba[as.character(record[i,3])] print(candidateRemove) print(candidateAdd) if (runif(1) < min( 1, exp(estimNew[i] - estimNew[i-1] + log(removeStep) - log(addStep) + log(candidateRemove) - log(candidateAdd) ))) { ### accept "add species" with prob min{1, P(D|i)*P(removeSpecies)*P(remove Specific Species)/P(D|i-1)*P(addSpecies)*P(add specific species) ######## Accept move ####### estimNew[i,]<-estimNew[i,] ### if move is accepted, record new logL speciestoUse[[1]]<-speciestoUse[[2]] ### if move is accepted, tentative species becomes present species. abundUsedSpecies[[1]]<-abundUsedSpecies[[2]] ### -->>-->>-- , abundances of new set of species are kept cat('Present species become:', speciestoUse[[1]], '\n') } else { ######### Reject Move ######## estimNew[i,]<-estimNew[i-1,] ### if move is rejected, record previous logL speciestoUse[[1]]<-speciestoUse[[1]] ### if move is rejected, keep present species as it is. abundUsedSpecies[[1]]<-abundUsedSpecies[[1]] cat('Present species remain:', speciestoUse[[1]], '\n') ### temporary } } ### close if(stepAdd==TRUE) else { ######################################## type of move was to remove species ############## removeProba<-(1/abundUsedSpecies[[1]])/sum(1/abundUsedSpecies[[1]]) ###### sampling weight inversely proportional to size. Do this for present Species candidateRemove<-removeProba[as.character(record[i,3])] candidateAdd<-allSpecies[allSpecies[,1]==(as.character(record[i,3])),2] if (runif(1) < min( 1, exp(estimNew[i] - estimNew[i-1] + log(addStep) - log(removeStep) + log(candidateAdd) - log(candidateRemove) ))) {############# Accept "remove species" estimNew[i,]<-estimNew[i,] speciestoUse[[1]]<-speciestoUse[[2]] ### tentative species becomes present species. abundUsedSpecies[[1]]<-abundUsedSpecies[[2]] cat('Present species become:', speciestoUse[[1]], '\n') } else { ######## Reject Move ########### estimNew[i,]<-estimNew[i-1,] speciestoUse[[1]]<-speciestoUse[[1]] abundUsedSpecies[[1]]<-abundUsedSpecies[[1]] cat('Present species remain:', speciestoUse[[1]], '\n') } } ###close else (i.e (stepAdd==FALSE)) #################################edw tha kanw attempt to direct swap between slaves, without going through master if( i%%exchangeInterval == 0 ){ ### every nth (2nd for now) iteration message("\n\nTime to attempt an exchange") oddFlag<-oddFlag+1 swap<-0 estim.current<-estimNew[i,]/temper[ind] ######### need untempered logL ########################################### CREATE prime tags for object to send around allowedLength<-175 Nsubobjects<-round(length(abundUsedSpecies[[1]])/allowedLength)+1 object.ids <- list.integers[ (noChains.internal+1):(noChains.internal + 4 + Nsubobjects) ] ### 4 objcts for logL, swap message, untempered , species PLUS as many as necessary for abundances if (ind%%2 == oddFlag%%2) { ###when oddFlag zero , the following code concerns even-numbered slaves. For oddFlag 1, it concerns odd-numbered slaves. ind.partner<-ind+1 if (0 1e6) stop("n too large") primes <- rep(TRUE, n) primes[1] <- FALSE last.prime <- 2L for(i in last.prime:floor(sqrt(n))) { primes[seq.int(2L*last.prime, n, last.prime)] <- FALSE last.prime <- last.prime + min(which(primes[(last.prime+1):n])) } which(primes) } list.integers <- sieve(1000) node.ids <- list.integers[ 1:noChains ] mpi.spawn.Rslaves(nslaves = noChains) #number of slaves to spawn, should be equal to individual chains # In case R exits unexpectedly, have it automatically clean up # resources taken up by Rmpi (slaves, memory, etc...) .Last <- function(){ if (is.loaded("mpi_initialize")){ if (mpi.comm.size(1) > 0){ print("Please use mpi.close.Rslaves() to close slaves.") mpi.close.Rslaves() } print("Please use mpi.quit() to quit R") .Call("mpi_finalize", PACKAGE='metaMix') } } pij.sparse.mat<-cbind(pij.sparse.mat, "unknown"=gen.prob.unknown) gc() allSpecies<-ordered.species[,c("taxonID", "samplingWeight")] lenSp<-nrow(allSpecies) lpenalty<-computePenalty.nucl(readSupport=readSupport, readWeights=read.weights, pUnknown=gen.prob.unknown, median.genome.length=median.genome.length) ### penalty for accepting a new species ~ Use pij for the r readSupport perfect reads (=1/median(protein length)). ### EMiter EMiter<-10 ### PT parameters exchangeInterval<-1 ###leave chains run in parallel for that many iterations ExternIter<-5*(nrow(ordered.species)) ### make chains communicate 1 times TotalIter<-exchangeInterval * ExternIter ##Tempering Vector --Power Decay temper<-vector() K<-0.001 a<-3/2 for (n in 2:noChains){ temper[1]<-1 temper[n]<-(temper[n-1]-K)^a } for (i in 1:noChains) {names(temper)[i]<- paste("slave",i, sep="")} ###names ### flag for adding /removing species stepAdd<-vector(mode = "logical") #### broadcast necessary objects/functions to slaves mpi.bcast.Robj2slave(exchangeInterval) mpi.bcast.Robj2slave(ExternIter) mpi.bcast.Robj2slave(TotalIter) mpi.bcast.Robj2slave(list.integers) mpi.bcast.Robj2slave(node.ids) mpi.bcast.Robj2slave(ordered.species) mpi.bcast.Robj2slave(read.weights) mpi.bcast.Robj2slave(pij.sparse.mat) mpi.bcast.Robj2slave(lpenalty) mpi.bcast.Robj2slave(EM) mpi.bcast.Robj2slave(allSpecies) mpi.bcast.Robj2slave(lenSp) mpi.bcast.Robj2slave(EMiter) mpi.bcast.Robj2slave(noChains) mpi.bcast.Robj2slave(temper) mpi.bcast.Robj2slave(gen.prob.unknown) ##########################---------------------------------------SINGLE CHAIN FUNCTION -----------------------------------------------------------------------------------------------####################### singleChain <- function(TotalIter, exchangeInterval){ if (file.exists('~/.Rprofile')) source('~/.Rprofile') print(.libPaths()) ind <- mpi.comm.rank() # Each slave gets its own copy of ind and chain based on mpi process rank print(ind) estimNew<-matrix(0, nrow=TotalIter, ncol=1) ### Create matrix that will hold the estimator of the log-likelihood estimNew[1,]<- sum(read.weights[,"weight"])*log(gen.prob.unknown)*temper[ind] print(estimNew[1,]) presentSpecies<-"unknown" ## create object that receives the species deemed as present, from previous (swapInterv*j) iteration. abundUsedSp<-c("unknown"=1) ### Create 2 lists. One that holds species names and one with their abundances. Each list has 2 elements. Element1: present species and Element2: tentative species being explored in current iteration. speciestoUse<-list("presentSp"=presentSpecies, "tentativeSp"=NULL) abundUsedSpecies<-list("presentSp"= abundUsedSp, "tentativeSp"=NULL) message("\nThis is the temperature for this slave") print(temper[ind]) ### create matrix to hold info on which species was added or removed, which species were present and logL , through iterations record<-matrix(0, ncol=(5+lenSp), nrow=(TotalIter)) record<-as.data.frame(record) colnames(record)<-c("Iter", "Move", "Candidate Species", allSpecies[,1], "unknown", "logL") record[,1]=1:(TotalIter) record[1, presentSpecies]<-1 record[1,(5+lenSp)]<-estimNew[1,] ###last colum is logL swaps.attempted<-0 swaps.accepted<-0 oddFlag<-0 ################ ----------------------------------- Begin MCMC (within single chain) ------------------------------------------------------------------------------------------############ for (i in 2:TotalIter) { cat('\n',i,'\n') ### temporary - debugging purposes #### Create 3 functions to use repeatedly in adding/removing species steps. ######################### 1a. For add step: species I sample my candidate species from. potentialSpecies<-function() { toChooseFrom <- allSpecies[,1][!(allSpecies[,1] %in% speciestoUse[[1]])] ### Species remaining after omitting "present species" toChooseFrom<-as.character(toChooseFrom) potentialSp<- allSpecies[allSpecies$taxonID %in% toChooseFrom,] resultPS<-list("potentialSp"=potentialSp, "toChooseFrom"=toChooseFrom) return(resultPS) } ######################## 1b. For add step, sample candidate organism to add and create object for tentative species moveAdd<-function() { randSp <- sample(as.character(potentialSp[,1]),1, prob=potentialSp[,2]) ### choose random species, weights need not sum to one. Here weights are based on intial read counts. cat('Add species', randSp, '\n') ### temporary - debugging purposes speciestoUse[[2]]<-c(randSp, speciestoUse[[1]]) ### tentative present species, to use in Gibbs below. record[i, 2]<- "Add" ### record info on species we are adding record[i,3]<- randSp result<-list("record"=record, "speciestoUse"=speciestoUse) return(result) } ######################## 2. For remove step, sample candidate organism to remove and create object for tentative species moveRemove<-function() { toremoveFrom <- speciestoUse[[1]][!(speciestoUse[[1]]%in%"unknown")] ### species set from which to remove (i.e present ones bar unknown) toremoveFrom<-as.character(toremoveFrom) removeProb<-(1/abundUsedSpecies[[1]][toremoveFrom])/sum(1/abundUsedSpecies[[1]][toremoveFrom]) ###### sampling weight inversely proportional to assigned read counts. ###Flatten removal probabilities percentiles<-quantile(removeProb, probs=c(0.2, 0.8)) removeProb[which(removeProb >= percentiles["80%"])] <- percentiles["80%"] removeProb[which(removeProb <= percentiles["20%"])] <- percentiles["20%"] ### sample candidate species to remove randSp<-sample(toremoveFrom, 1, prob=removeProb ) ### weights need not sum to one cat('Remove species', randSp, '\n') ### temporary - debugging purposes speciestoUse[[2]] <- speciestoUse[[1]][!(speciestoUse[[1]] %in% randSp)] ### tentative present species, to use in Gibbs below. record[i, 2]<- "Remove" ### record info on species we are adding record[i,3]<- randSp result<-list("record"=record, "speciestoUse"=speciestoUse) return(result) } addStep <-0.5 ####proability of doing add step ######################################################## Add species ######################################## if (runif(1)<= addStep) { resultPS<-potentialSpecies() potentialSp<-as.data.frame(resultPS$potentialSp) toChooseFrom<-as.character(resultPS$toChooseFrom) if (length(toChooseFrom) != 0L){ result<-moveAdd() speciestoUse<-result$speciestoUse record<-result$record } else { ################## ### If pool of species to add empty, go to remove step message("No more species to choose from, all are kept as present.") result<-moveRemove() speciestoUse<-result$speciestoUse record<-result$record addStep<-0 ### so do remove step with prob=1 } } ###close if runif(1)<=addStep else { ################################################### Remove species ################################################# toremoveFrom <- speciestoUse[[1]][!(speciestoUse[[1]]%in%"unknown")] ### species set from which to remove (i.e present ones bar unknown) toremoveFrom<-as.character(toremoveFrom) #### First check that more than 1 species are present, so don't risk of remaining only with X bin and wasting iteration. if (length(toremoveFrom) > 1) { result<-moveRemove() speciestoUse<-result$speciestoUse record<-result$record } else if (length(speciestoUse[[1]])==1) { #### speciestoUse[[1]]==1 when only unknown bin is there / We can only add message("We cannot remove, we only have unknown bin") potentialSp<-allSpecies result<-moveAdd() speciestoUse<-result$speciestoUse record<-result$record addStep <- 1 ### so do add step with prob=1 } else { ### we are adding species instead. Removing would leave us just with X-bin again. message("\nCannot remove a species, so instead we add\n") ### temporary resultPS<-potentialSpecies() potentialSp<-as.data.frame(resultPS$potentialSp) toChooseFrom<-as.character(resultPS$toChooseFrom) result<-moveAdd() speciestoUse<-result$speciestoUse record<-result$record addStep <- 1 } } ###close else (remove species) noSpecies<-length(speciestoUse[[2]]) print(noSpecies) hyperP<-rep(1, noSpecies) startW<-rdirichlet(1, hyperP) output100Tent<-EM(pij=pij.sparse.mat, iter=EMiter, species=speciestoUse[[2]], abund=startW, readWeights = read.weights) ### EM function estimator <- output100Tent$logL[EMiter,2] + (noSpecies * lpenalty) #### penalise likelihood message("EM took: ", output100Tent$RunningTime) mean1<-as.numeric(output100Tent$abundances[EMiter,2:(noSpecies+1)]) names(mean1)<-names(output100Tent$abundances[EMiter,2:(noSpecies+1)]) abundUsedSpecies[[2]]<-mean1 estimNew[i,]<-estimator*temper[ind] ###tempered likelihood message('\n', estimNew[i,] , ' ', estimNew[i-1,]) ### temporary print - which values am I comparing? ####### flag of adding/removing if (record[i,2]=="Add") { stepAdd<-TRUE } else {stepAdd<-FALSE} removeStep <- 1 - addStep ##remove step if (stepAdd) { candidateAdd<-allSpecies[allSpecies[,1]==(as.character(record[i,3])),2] removeProba<-(1/abundUsedSpecies[[2]])/sum(1/abundUsedSpecies[[2]]) ###### sampling weight inversely proportional to size. Tentative Species ###Flattening the sampling probabilities percentiles<-quantile(removeProba, probs=c(0.2, 0.8)) removeProba[which(removeProba >= percentiles["80%"])] <- percentiles["80%"] removeProba[which(removeProba <= percentiles["20%"])] <- percentiles["20%"] candidateRemove<-removeProba[as.character(record[i,3])] print(candidateRemove) print(candidateAdd) if (runif(1) < min( 1, exp(estimNew[i] - estimNew[i-1] + log(removeStep) - log(addStep) + log(candidateRemove) - log(candidateAdd) ))) { ### accept "add species" with prob min{1, P(D|i)*P(removeSpecies)*P(remove Specific Species)/P(D|i-1)*P(addSpecies)*P(add specific species) ######## Accept move ####### estimNew[i,]<-estimNew[i,] ### if move is accepted, record new logL speciestoUse[[1]]<-speciestoUse[[2]] ### if move is accepted, tentative species becomes present species. abundUsedSpecies[[1]]<-abundUsedSpecies[[2]] ### -->>-->>-- , abundances of new set of species are kept cat('Present species become:', speciestoUse[[1]], '\n') } else { ######### Reject Move ######## estimNew[i,]<-estimNew[i-1,] ### if move is rejected, record previous logL speciestoUse[[1]]<-speciestoUse[[1]] ### if move is rejected, keep present species as it is. abundUsedSpecies[[1]]<-abundUsedSpecies[[1]] cat('Present species remain:', speciestoUse[[1]], '\n') ### temporary } } ### close if(stepAdd==TRUE) else { ######################################## type of move was to remove species ############## removeProba<-(1/abundUsedSpecies[[1]])/sum(1/abundUsedSpecies[[1]]) ###### sampling weight inversely proportional to size. Do this for present Species candidateRemove<-removeProba[as.character(record[i,3])] candidateAdd<-allSpecies[allSpecies[,1]==(as.character(record[i,3])),2] if (runif(1) < min( 1, exp(estimNew[i] - estimNew[i-1] + log(addStep) - log(removeStep) + log(candidateAdd) - log(candidateRemove) ))) {############# Accept "remove species" estimNew[i,]<-estimNew[i,] speciestoUse[[1]]<-speciestoUse[[2]] ### tentative species becomes present species. abundUsedSpecies[[1]]<-abundUsedSpecies[[2]] cat('Present species become:', speciestoUse[[1]], '\n') } else { ######## Reject Move ########### estimNew[i,]<-estimNew[i-1,] speciestoUse[[1]]<-speciestoUse[[1]] abundUsedSpecies[[1]]<-abundUsedSpecies[[1]] cat('Present species remain:', speciestoUse[[1]], '\n') } } ###close else (i.e (stepAdd==FALSE)) #################################edw tha kanw attempt to direct swap between slaves, without going through master if( i%%exchangeInterval == 0 ){ ### every nth (2nd for now) iteration message("\n\nTime to attempt an exchange") oddFlag<-oddFlag+1 swap<-0 estim.current<-estimNew[i,]/temper[ind] ######### need untempered logL ########################################### CREATE prime tags for object to send around allowedLength<-175 Nsubobjects<-round(length(abundUsedSpecies[[1]])/allowedLength)+1 object.ids <- list.integers[ (noChains+1):(noChains + 4 + Nsubobjects) ] ### 4 objcts for logL, swap message, untempered , species PLUS as many as necessary for abundances if (ind%%2 == oddFlag%%2) { ###when oddFlag zero , the following code concerns even-numbered slaves. For oddFlag 1, it concerns odd-numbered slaves. ind.partner<-ind+1 if (0 0) { message('Missing the following arguments') print(names(step1)[!(should.be.in.the.list %in% names(step1))] ) stop() } else { reduce.space.wrapped = function(pij.sparse.mat=step1$pij.sparse.mat, ordered.species=step1$ordered.species, read.weights=step1$read.weights, outDir=step1$outDir, gen.prob.unknown=step1$gen.prob.unknown, read.cutoff.internal=read.cutoff, EMiter.internal=EMiter, seed.internal=seed){ set.seed(seed.internal); tentative.species<-colnames(pij.sparse.mat) noSpecies<-length(tentative.species) hyperP<-rep(1, noSpecies) startW<-rdirichlet(1, hyperP) outputEM<-EM(pij = pij.sparse.mat, iter = EMiter.internal, species = tentative.species, abund = startW, readWeights = read.weights) ### EM function message("EM done") approxSpecies0<-names(which(round(colMeans(outputEM$abundances[EMiter.internal,])*sum(read.weights[,"weight"]))>0)) approxSpecies0<-approxSpecies0[-1] approxPij<-pij.sparse.mat[, approxSpecies0] approxSpecies.with.counts<-round(colMeans(outputEM$abundances[EMiter.internal,2:length(colnames(outputEM$abundances))])*sum(read.weights[,"weight"])) ordered.approx.species<-cbind(approxSpecies.with.counts, approxSpecies.with.counts/sum(approxSpecies.with.counts)) colnames(ordered.approx.species)<-c( "countReads", "samplingWeight") ordered.approx.species<- data.frame("taxonID"=rownames(ordered.approx.species), ordered.approx.species, stringsAsFactors=FALSE) ordered.species<-ordered.approx.species[order(-ordered.approx.species[,2]) , ] #### order them by read count ordered.species<-ordered.species[which(ordered.species$countReads>=read.cutoff.internal),] ###potential species are the ones that have at least one read assigned to them if (!("unknown" %in% ordered.species$taxonID)==T){ordered.species<-rbind(ordered.species, c("unknown", 0, 0))} ordered.species$countReads<- as.numeric(ordered.species$countReads) ordered.species$samplingWeight<- as.numeric(ordered.species$samplingWeight) ordered.species<- ordered.species[-which(ordered.species$taxonID=="unknown"),] approxSpecies<-ordered.species$taxonID pij.sparse.mat<-pij.sparse.mat[,approxSpecies] ## ###Flattening the sampling probabilities percentiles<-quantile(ordered.species$samplingWeight, probs=c(0.2, 0.8)) ordered.species$samplingWeight[which(ordered.species$samplingWeight >= percentiles["80%"])] <- percentiles["80%"] ordered.species$samplingWeight[which(ordered.species$samplingWeight <= percentiles["20%"])] <- percentiles["20%"] ### remove objects step2<-list("outputEM"=outputEM, "pij.sparse.mat"=pij.sparse.mat, "ordered.species"=ordered.species, "read.weights"=read.weights, "outDir"=outDir, "gen.prob.unknown"=gen.prob.unknown) if (!is.null(outDir)) { step2.name <- paste(outDir, "/step2.RData", sep = "") save(step2, file=step2.name) rm(list= ls()[!ls() %in% c("step2")]) gc() } else { rm(list= ls()[!ls() %in% c("step2")]) gc() } return(step2) } reduce.space.wrapped() } } #' @rdname reduce.space #' @title reduce.space.explicit #' @description reduce.space.explicit is the same function as reduce.space but with more involved syntax. #' @param pij.sparse.mat sparse Matrix of generative probabilities computed by generative.prob() / generative.prob.nucl(). #' @param ordered.species data.frame with potential species ordered by numbers of reads matching them. Computed by generative.prob(). #' @param read.weights data.frame mapping each read identifier to a weight. For contigs the weight is the number of reads that were used to assemble it. For unassembled reads the weight is equal to one. #' @param outDir character vector holding the path to the output directory where the results are written. #' @param gen.prob.unknown numeric vector. This is the generative probability for the unknown category. Default value for BLASTx-analysis is 1e-06 while for BLASTn-analysis is 1e-20. #' @keywords reduce.space.explicit #' @export reduce.space.explicit #' @import Matrix data.table #' @importFrom gtools rdirichlet ##############################################################################################################################################################) reduce.space.explicit = function(pij.sparse.mat, ordered.species, read.weights, outDir, gen.prob.unknown, read.cutoff=1, EMiter=500, seed=1){ set.seed(seed); tentative.species<-colnames(pij.sparse.mat) noSpecies<-length(tentative.species) hyperP<-rep(1, noSpecies) startW<-rdirichlet(1, hyperP) outputEM<-EM(pij = pij.sparse.mat, iter = EMiter, species = tentative.species, abund = startW, readWeights = read.weights) ### EM function message("EM done") approxSpecies0<-names(which(round(colMeans(outputEM$abundances[EMiter,])*sum(read.weights[,"weight"]))>0)) approxSpecies0<-approxSpecies0[-1] approxPij<-pij.sparse.mat[, approxSpecies0] approxSpecies.with.counts<-round(colMeans(outputEM$abundances[EMiter,2:length(colnames(outputEM$abundances))])*sum(read.weights[,"weight"])) ordered.approx.species<-cbind(approxSpecies.with.counts, approxSpecies.with.counts/sum(approxSpecies.with.counts)) colnames(ordered.approx.species)<-c( "countReads", "samplingWeight") ordered.approx.species<- data.frame("taxonID"=rownames(ordered.approx.species), ordered.approx.species, stringsAsFactors=FALSE) ordered.species<-ordered.approx.species[order(-ordered.approx.species[,2]) , ] #### order them by read count ordered.species<-ordered.species[which(ordered.species$countReads>=read.cutoff),] ###potential species are the ones that have at least one read assigned to them if (!("unknown" %in% ordered.species$taxonID)==T){ordered.species<-rbind(ordered.species, c("unknown", 0, 0))} ordered.species$countReads<- as.numeric(ordered.species$countReads) ordered.species$samplingWeight<- as.numeric(ordered.species$samplingWeight) ordered.species<- ordered.species[-which(ordered.species$taxonID=="unknown"),] approxSpecies<-ordered.species$taxonID pij.sparse.mat<-pij.sparse.mat[,approxSpecies] ## ###Flattening the sampling probabilities percentiles<-quantile(ordered.species$samplingWeight, probs=c(0.2, 0.8)) ordered.species$samplingWeight[which(ordered.species$samplingWeight >= percentiles["80%"])] <- percentiles["80%"] ordered.species$samplingWeight[which(ordered.species$samplingWeight <= percentiles["20%"])] <- percentiles["20%"] ### remove objects step2<-list("outputEM"=outputEM, "pij.sparse.mat"=pij.sparse.mat, "ordered.species"=ordered.species, "read.weights"=read.weights, "outDir"=outDir, "gen.prob.unknown"=gen.prob.unknown) if (!is.null(outDir)) { step2.name <- paste(outDir, "/step2.RData", sep = "") save(step2, file=step2.name) rm(list= ls()[!ls() %in% c("step2")]) gc() } else { rm(list= ls()[!ls() %in% c("step2")]) gc() } return(step2) } metaMix/R/step1_preprocess.R0000644000176200001440000010720113427027250015506 0ustar liggesusers################################################ CALCULATE pij: PROBABILITY READ IS GENERATED BY CERTAIN SPECIES ###############################################Use Poisson probabilities to incorporate quality of match. #' @name generative.prob #' @aliases generative.prob #' @aliases generative.prob.nucl #' @title Compute generative probabilities from BLAST output NULL #' @rdname generative.prob #' @title generative.prob #' @description generative.prob() computes the probability for a read to be generated by a certain species, given that it originates from this species. The input for this function is the tabular BLAST output format, either default or custom. The function uses the recorded mismatches to produce a Poisson probability. #' @param blast.output.file This is the tabular BLASTx output format for generative.prob(), while it is the tabular BLASTn output format for generative.prob.nucl(). It can either be the default output format or a specific custom output format, incorporating read length and taxon identifier. Please see the vignette for column order and the exact BLAST command to use. You can also use DIAMOND instead of BLASTx which is much faster and produces default format according to BLAST default output specifications. #' @param read.length.file This argument can either be a file mapping each read to its length or a numerical value, representing the average read length. #' @param contig.weight.file This argument can either be a file where weights are assigned to reads and contigs. For unassembled reads the weight is equal to 1 while for contigs the weight should reflect the number of reads that assembled it. #' @param gi.taxon.file For generative.prob() this would be the 'gi_taxid_prot.dmp' taxonomy file, mapping each protein gi identifier to the corresponding taxon identifier. It can be downloaded from \url{ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_prot.dmp.gz} . For generative.prob.nucl() this would be the 'gi_taxid_nucl.dmp' taxonomy file, mapping each nucleotide gi identifier to the corresponding taxon identifier. It can be downloaded from \url{ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp.gz}. #' @param protaccession.taxon.file This parameter has been added as NCBI is phasing out the usage of GI identifiers. For generative.prob() this would be the prot.accession2taxid taxonomy file, mapping each protein accession identifier to the corresponding taxon identifier. It can be downloaded from \url{ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz}. I have found that it is useful to concatenate it with \url{ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/dead_prot.accession2taxid.gz} so you can search in both files for the protein identifier (sometimes obsolete sequences can still be present in latest RefSeq releases but not in taxonomy files and vice versa and these mismatches can cause loss of information). TODO add support for nucleotides as well. #' @param gi.or.prot This parameter specifies whether the user is using the GI identifiers or protein accession identifiers to map to taxon identifiers. Values are 'gi' or 'prot'. The default value is 'prot'. #' @param gen.prob.unknown User-defined generative probability for unknown category. Default value for generative.prob() is 1e-06, while for generative.prob.nucl() is 1e-20. #' @param outDir Output directory. #' @param blast.default logical. Is the input the default blast output tabular format? Default value is TRUE. That means that the BLAST output file needs to have the following fields:Query id, Subject id, percent identity, alignment length, mismatches, gap openings, query start, query end, subject start, subject end, e-value, bit score. Alternatively we can use the 'blast.default=FALSE' option, providing a custom blast output that has been produced using the option -outfmt '6 qacc qlen sacc slen stitle bitscore length pident evalue staxids'. #' @return step1: A list with five elements. The first one (pij.sparse.mat) is a sparse matrix with the generative probability between each read and each species. The second (ordered.species) is matrix containing all the potential species as recorded by BLAST, ordered by the number of reads. The third one (read.weights) is a data.frame mapping each contig to a weight which is essentially the number of reads that were used to assemble it. For unassembled reads the weight is equal to one. The fourth one is the generative probability for the unknown category (gen.prob.unknown), to be used in all subsequent steps. Finally we also record the output directory (outDir) where the results will be stored. #' @keywords generative.prob #' @export generative.prob #' @import Matrix data.table #' @importFrom stats ppois #' @importFrom stats quantile #' @examples #' # See vignette for more details #' #' \dontrun{ #' # When using custom BLAST output file #' step1 <-generative.prob(blast.output.file = "pathtoFile/blastOut.custom", blast.default=FALSE) #' #' # When using default BLAST output file #' step1 <-generative.prob(blast.output.file = "pathtoFile/blastOut.default", #' read.length.file="pathtoFile/read.lengths", #' contig.weight.file="pathtoFile/read.weights", #' gi.taxon.file = "pathtoFile/taxon.file") #' } ############################################################################################################################################################## generative.prob = function(blast.output.file=NULL, read.length.file=80, contig.weight.file=1, gi.taxon.file=NULL, protaccession.taxon.file=NULL, gi.or.prot="prot", gen.prob.unknown=1e-06, outDir=NULL, blast.default=TRUE){ if (blast.default){ if (gi.or.prot=="gi") { if (is.null(gi.taxon.file)) { stop("Please provide the 'gi_taxid_prot.dmp' file. This can be downloaded from ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_prot.dmp.gz") } else { taxon.prot<-fread(input=gi.taxon.file, sep="\t", header=F) setnames(x=taxon.prot, old=c("proteinID","taxonID" )) } } if (gi.or.prot=="prot") { if (is.null(protaccession.taxon.file)) { stop("Please provide the 'prot.accession2taxid' file. This can be downloaded from ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz . I have found that it is useful to concatenate it with ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/dead_prot.accession2taxid.gz so you can search in both for the protein identifier, since obsolete sequences can still be present in RefSeq releases. However due to its size you need to increase the memory requirements quite a bit, more than 20G.") } else { taxon.prot<-fread(input=protaccession.taxon.file, sep="\t", header=T, select=c(2,3)) setnames(x=taxon.prot, old=c("proteinID", "taxonID")) } } if (!is.null(blast.output.file)) { check.output<-fread(input=blast.output.file, sep="\t", header=F) if (ncol(check.output)!=12) { ###quick check for format stop("Please check your BLAST output file. You have used the 'blast.default=TRUE' option, therefore your file needs to have the following fields:'Query id, Subject id, % identity, alignment length, mismatches, gap openings, query start, query end, subject start, subject end, e-value, bit score'. \n Alternatively you can use the 'blast.default=FALSE' option, providing a custom blast output that has been produced using the option -outfmt '6 qacc qlen sacc slen stitle bitscore length pident evalue staxids' ") } else if (ncol(check.output)==12){ blast.output<-fread(input=blast.output.file, sep="\t", header=F, select=c(1,3, 4, 12)) setnames(x=blast.output, old=c("read", "ident", "aln", "bit.score")) if (gi.or.prot=="prot"){ protID<-fread(input=blast.output.file, sep="|", header=F, select=c(4)) } else { protID<-fread(input=blast.output.file, sep="|", header=F, select=c(2)) } setnames(x=protID, old="proteinID") blast.out.gi<-cbind.data.frame(blast.output, protID) } else { stop("Please provide the output file from BLASTx. The default tabular format is accepted, using the -m6 flag in the BLASTx command.") } } if (is.character(read.length.file)) { read.length<-fread(input=read.length.file, sep="\t", header=F) setnames(x=read.length, old=c("read", "length")) } else if (is.numeric(read.length.file)) { read.length<-cbind.data.frame("read"=unique(blast.output[["read"]]), "length"=read.length.file) } else { stop("Please provide either a file containing the sequence lengths for reads and contigs or, assuming you haven't assembled contigs enter an average read length value.") } if (is.character(contig.weight.file)) { contig.weights<-fread(input=contig.weight.file, sep="\t", header=F) setnames(x=contig.weights, old=c("read", "weight")) rownames(contig.weights)<-contig.weights[["read"]] } else if (is.numeric(contig.weight.file)) { contig.weights<-cbind.data.frame("read"=unique(blast.output[["read"]]), "weight"=contig.weight.file) rownames(contig.weights)<-contig.weights[,"read"] } else { stop("Please provide either a file containing the weights for reads (=1) and contigs (>1) or, assuming you haven't assembled contigs enter contig.weight.file=1.") } rm(blast.output) gc() blast.length<-merge(blast.out.gi, read.length, by="read") rm(blast.out.gi) gc() blast.length$mismatch <- (blast.length[["length"]]/3)-(blast.length[["ident"]]* blast.length[["aln"]])/100 ## the mismatches throughout read length not hsp length blast.length.weight<-merge(blast.length, contig.weights, by ="read", all.x=T) rm(blast.length) gc() indx<-which(is.na(blast.length.weight[["weight"]])) blast.length.weight$weight[indx]<-1 read.weights<- unique(blast.length.weight[,c("read","weight"), with=FALSE]) rownames(read.weights)<-read.weights[["read"]] allInfo.temp<-merge(blast.length.weight, taxon.prot, by="proteinID", all.x=T) if (length(unique(allInfo.temp[which(is.na(allInfo.temp[["taxonID"]])), get('proteinID')]))!=0){ message("Some of the proteins in your reference database are not in the 'gi_taxon_prot.dmp' or the 'prot.accession2taxid' file (depends on which you used. If you used the latter 'prot.accession2taxid' it may be worth adding to it dead_prot.accession2taxid.gz, see help to see download details). Therefore these cannot be assigned a taxon identifier. \n We will remove these hits from subsequent analyses. \n For reference the respective gis are: ") print(unique(allInfo.temp[which(is.na(allInfo.temp[["taxonID"]])),get('proteinID')])) allInfo<-merge(blast.length.weight, taxon.prot, by="proteinID") } else { allInfo<-allInfo.temp } probPois<-ppois(allInfo[["mismatch"]] - 1, lambda=0.09*((allInfo[["length"]])/3), lower.tail=FALSE) ### at least that many mismatches could be observed by chance. Divide by 3 for translated read length data_0.03<-cbind.data.frame(allInfo, "pij"=probPois) ### combine Poisson prob with other read info. data.dt<- data.table(data_0.03) data.grouped<-data.dt[,list(pij=max(pij)),by=c("read", "weight", "taxonID")] ### one hit per taxonid (best one) pij<-as.data.frame(data.grouped) taxonID<-NULL ############use Sparse Matrix "reshape" long -> wide fromat pij.sparse<-with(pij, sparseMatrix(i = as.numeric(factor(get('read'))), j=as.numeric((factor(taxonID))), x=pij, dimnames=list(levels(factor(get('read'))), levels(factor(taxonID))))) pij.dt<-data.table(pij) allspecies.dt<-pij.dt[,list(count.reads=sum(get('weight'))), by="taxonID"] allspecies<-as.data.frame(allspecies.dt) ordered.species<-allspecies[order(-allspecies[,2]) , ] #### order them by read count ### add unknown bin and assign a pij pij.sparse.mat<-cbind(pij.sparse, gen.prob.unknown) colnames(pij.sparse.mat)<-c(colnames(pij.sparse), "unknown") if (length(which(!(rownames(read.weights)%in%rownames(pij.sparse.mat))))!=0) { message("The following reads match only proteins that are no longer supported, i.e their gis are not in 'gi_taxon_prot.dmp' or their protein accession not in 'prot.accession2taxid' (depends on which you used. If you used the latter 'prot.accession2taxid' it may be worth adding to it dead_prot.accession2taxid.gz, see help to see download details). \n Therefore the reads were removed from subsequent analyses as these could be misclassified.") print(rownames(read.weights[which(!(rownames(read.weights)%in%rownames(pij.sparse.mat))),])) read.weights<-read.weights[which(rownames(read.weights)%in%rownames(pij.sparse.mat)),] read.weights<-data.frame(read.weights, row.names=read.weights[["read"]] ) } else { read.weights<-data.frame(read.weights, row.names=read.weights[["read"]] ) } ### sampling weight to use when choosing which species to add during MCMC uniqReads<-dim(pij.sparse.mat)[[1]] ordered.species$sampling.weight<-ordered.species[,2]/uniqReads ###Flattening the sampling probabilities percentiles<-quantile(ordered.species$sampling.weight, probs=c(0.2, 0.8)) ordered.species$sampling.weight[which(ordered.species$sampling.weight >= percentiles["80%"])] <- percentiles["80%"] ordered.species$sampling.weight[which(ordered.species$sampling.weight <= percentiles["20%"])] <- percentiles["20%"] colnames(ordered.species)<-c("taxonID", "count.reads", "sampling.weight") ### remove objects step1<-list("ordered.species"=ordered.species,"pij.sparse.mat"=pij.sparse.mat, "read.weights"=read.weights, "outDir"=outDir, "gen.prob.unknown"=gen.prob.unknown) if (!is.null(outDir)) { step1.name <- paste(outDir, "/step1.RData", sep = "") save(step1, file=step1.name) rm(list= ls()[!ls() %in% c("step1")]) gc() } else { rm(list= ls()[!ls() %in% c("step1")]) gc() } return(step1) } else { ###if we are not dealing with default format, but rather with custom blast output that has incorporated the query length and the taxon id) if (!is.null(blast.output.file)) { check.output<-fread(input=blast.output.file, sep="\t", header=F) if (ncol(check.output)!=10) { ###quick check for format stop("Please check your blast output file. The custom blast tabular format we accept as input has the following 10 columns 'qacc qlen sacc slen stitle bitscore length pident evalue staxids'. Alternatively you can use the default blast tabular output and use it along with 'blast.default=TRUE' option. You will need also to provide the 'gi_taxid_prot.dmp' or the ' prot.accession2taxid' file. The first can be downloaded from ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_prot.dmp.gz and the latter from ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz") } else if (ncol(check.output==10)) { blast.output.length.temp<-fread(input=blast.output.file, sep="\t", header=F, select=c(1,2, 7, 8, 10)) setnames(x=blast.output.length.temp, old=c("read", "length", "aln", "ident", "taxonID")) } else { stop("Please provide the output file from BLASTx. The default tabular format is accepted, using the '-outfmt 6' flag in the BLASTx command.") } } taxonID<-NULL read<-NULL length<-NULL aln<-NULL ident<-NULL if ( is.character(blast.output.length.temp[,taxonID])){ blast.output.length.temp2 <- blast.output.length.temp[, list(taxonID = as.integer(unlist(strsplit(taxonID, ";")))), by=list(read, length, aln, ident)] ## handle comma separated taxonIDS and NAs blast.output.length<- blast.output.length.temp2[which(!is.na(blast.output.length.temp2[,taxonID])),] } else { blast.output.length<-blast.output.length.temp } if (!is.integer(blast.output.length[["taxonID"]])) { stop("Your blast output does not have correctly formatted taxon identifiers. Please use the 'blast.default=TRUE' option, providing the default blast tabular format (using the blast option '-outfmt 6' and provide seperately the 'gi_taxid_prot.dmp' file.") } if (is.character(contig.weight.file)) { contig.weights<-fread(input=contig.weight.file, sep="\t", header=F) setnames(x=contig.weights, old=c("read", "weight")) rownames(contig.weights)<-contig.weights[["read"]] } else if (is.numeric(contig.weight.file)) { contig.weights<-cbind.data.frame("read"=unique(blast.output.length[["read"]]), "weight"=contig.weight.file) rownames(contig.weights)<-contig.weights[,"read"] } else { stop("Please provide either a file containing the weights for reads (=1) and contigs (>1) or, assuming you haven't assembled contigs enter contig.weight.file=1") } blast.output.length$mismatch <- (blast.output.length[["length"]]/3)-(blast.output.length[["ident"]]* blast.output.length[["aln"]])/100 ## the mismatches throughout read length not hsp length blast.length.weight<-merge(blast.output.length, contig.weights, by ="read", all.x=T) rm(blast.length) gc() indx<-which(is.na(blast.length.weight[["weight"]])) blast.length.weight$weight[indx]<-1 read.weights<- unique(blast.length.weight[,c("read","weight"), with=FALSE]) rownames(read.weights)<-read.weights[["read"]] allInfo<-blast.length.weight probPois<-ppois(allInfo[["mismatch"]] - 1, lambda=0.09*((allInfo[["length"]])/3), lower.tail=FALSE) ### at least that many mismatches could be observed by chance. Divide by 3 for translated read length data_0.03<-cbind.data.frame(allInfo, "pij"=probPois) ### combine Poisson prob with other read info. data.dt<- data.table(data_0.03) data.grouped<-data.dt[,list(pij=max(pij)),by=c("read", "weight", "taxonID")] ### one hit per taxonid (best one) pij<-as.data.frame(data.grouped) ############use Sparse Matrix "reshape" long -> wide fromat pij.sparse<-with(pij, sparseMatrix(i = as.numeric(factor(get('read'))), j=as.numeric((factor(taxonID))), x=pij, dimnames=list(levels(factor(get('read'))), levels(factor(taxonID))))) pij.dt<-data.table(pij) allspecies.dt<-pij.dt[,list(count.reads=sum(get('weight'))), by="taxonID"] allspecies<-as.data.frame(allspecies.dt) ordered.species<-allspecies[order(-allspecies[,2]) , ] #### order them by read count ### add unknown bin and assign a pij pij.sparse.mat<-cbind(pij.sparse, gen.prob.unknown) colnames(pij.sparse.mat)<-c(colnames(pij.sparse), "unknown") if (length(which(!(rownames(read.weights)%in%rownames(pij.sparse.mat))))!=0) { # message("The following reads match only proteins that are no longer supported, i.e their gis are not in 'gi_taxon_prot.dmp'. \n Therefore the reads were removed from subsequent analyses.") print(rownames(read.weights[which(!(rownames(read.weights)%in%rownames(pij.sparse.mat))),])) read.weights<-read.weights[which(rownames(read.weights)%in%rownames(pij.sparse.mat)),] read.weights<-data.frame(read.weights, row.names=read.weights[["read"]] ) } else { read.weights<-data.frame(read.weights, row.names=read.weights[["read"]] ) } ### sampling weight to use when choosing which species to add during MCMC uniqReads<-dim(pij.sparse.mat)[[1]] ordered.species$sampling.weight<-ordered.species[,2]/uniqReads ###Flattening the sampling probabilities percentiles<-quantile(ordered.species$sampling.weight, probs=c(0.2, 0.8)) ordered.species$sampling.weight[which(ordered.species$sampling.weight >= percentiles["80%"])] <- percentiles["80%"] ordered.species$sampling.weight[which(ordered.species$sampling.weight <= percentiles["20%"])] <- percentiles["20%"] colnames(ordered.species)<-c("taxonID", "count.reads", "sampling.weight") ### remove objects step1<-list("ordered.species"=ordered.species,"pij.sparse.mat"=pij.sparse.mat, "read.weights"=read.weights, "outDir"=outDir, "gen.prob.unknown"=gen.prob.unknown) if (!is.null(outDir)) { step1.name <- paste(outDir, "/step1.RData", sep = "") save(step1, file=step1.name) rm(list= ls()[!ls() %in% c("step1")]) gc() } else { rm(list= ls()[!ls() %in% c("step1")]) gc() } return(step1) } } #' @rdname generative.prob #' @title generative.prob.nucl #' @description generative.prob.nucl() for when we have nucleotide similarity, i.e we have performed BLASTn. #' @param genomeLength This is applicable only for generative.prob.nucl() . It is a file mapping each genome/nucleotide to its respective length. The file must be tab seperated and the first column the nucleotide gi identifier (integer) and the second the corresponding sequence length (integer). It will be used to correct the Poisson probabilities between each read and genome. #' @keywords generative.prob.nucl #' @export generative.prob.nucl #' @import Matrix data.table ############################################################################################################################################################## generative.prob.nucl = function(blast.output.file=NULL, read.length.file=80, contig.weight.file=1, gi.taxon.file, gen.prob.unknown=1e-20, outDir=NULL, genomeLength=NULL, blast.default=TRUE){ if (blast.default){ if (!is.null(blast.output.file)) { check.output<-fread(input=blast.output.file, sep="\t", header=F) if (ncol(check.output)!=12) { ###quick check for format stop("Please check your BLAST output file. You have used the 'blast.default=TRUE' option, therefore your file needs to have the following fields:'Query id, Subject id, % identity, alignment length, mismatches, gap openings, query start, query end, subject start, subject end, e-value, bit score'. \n Alternatively you can use the 'blast.default=FALSE' option, providing a custom blast output that has been produced using the option -outfmt '6 qacc qlen sacc slen stitle bitscore length pident evalue staxids' ") } else if (ncol(check.output)==12){ blast.output<-fread(input=blast.output.file, sep="\t", header=F, select=c(1,3, 4, 5)) setnames(x=blast.output, old=c("read", "ident", "aln", "mismatch")) nuclID<-fread(input=blast.output.file, sep="|", header=F, select=c(2)) setnames(x=nuclID, old="nucleotideID") blast.out.gi<-cbind.data.frame(blast.output, nuclID) } else { stop("Please provide the output file from BLASTx. The default tabular format is accepted, using the -m6 flag in the BLASTx command.") } } if (is.character(read.length.file)) { read.length<-fread(input=read.length.file, sep="\t", header=F) setnames(x=read.length, old=c("read", "length")) } else if (is.numeric(read.length.file)) { read.length<-cbind.data.frame("read"=unique(blast.output[["read"]]), "length"=read.length.file) } else { stop("Please provide either a file containing the sequence lengths for reads and contigs or, assuming you haven't assembled contigs enter an average read length value.") } if (is.character(contig.weight.file)) { contig.weights<-fread(input=contig.weight.file, sep="\t", header=F) setnames(x=contig.weights, old=c("read", "weight")) rownames(contig.weights)<-contig.weights[["read"]] } else if (is.numeric(contig.weight.file)) { contig.weights<-cbind.data.frame("read"=unique(blast.output[["read"]]), "weight"=contig.weight.file) rownames(contig.weights)<-contig.weights[,"read"] } else { stop("Please provide either a file containing the weights for reads (=1) and contigs (>1) or, assuming you haven't assembled contigs enter contig.weight=1.") } message("Map nucleotide gi identifiers to taxon identifiers. This could take a couple of minutes.") if (is.null(gi.taxon.file)) { stop("Please provide the 'gi_taxid_nucl.dmp' file. It can be downloaded from ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp.gz") } else { taxon.nucl<-fread(input=gi.taxon.file, sep="\t", header=F) setnames(x=taxon.nucl, old=c("nucleotideID","taxonID" )) } if (is.null(genomeLength)) { stop("Please provide the file of genomes lengths. The first column should be the gi nucleotide identifier and the second column the sequence length") } else { genome.length<-fread(input=genomeLength, sep="\t", header=F) setnames(x=genome.length, old=c("nucleotideID","genome.length" )) genome.length$genome.length<-as.integer(genome.length$genome.length) genome.length$nucleotideID<-as.integer(genome.length$nucleotideID) genome.length<-unique(genome.length) } ################### poisson prob with lambda=3 mismatches per 100 nucleotides blast.length<-merge(blast.out.gi, read.length, by="read") mismatchNew<-ifelse(blast.length[["length"]]>=200, blast.length[["mismatch"]], blast.length[["length"]]-(blast.length[["ident"]]* blast.length[["aln"]])/100) blast.length$mismatch<-mismatchNew blast.length.weight<-merge(blast.length, contig.weights, by ="read", all.x=T) indx<-which(is.na(blast.length.weight[["weight"]])) blast.length.weight$weight[indx]<-1 read.weights<- unique(blast.length.weight[,c("read","weight"), with=FALSE]) rownames(read.weights)<-read.weights[["read"]] allInfo.temp<-merge(blast.length.weight, taxon.nucl, by="nucleotideID", all.x=T) if (length(unique(allInfo.temp[which(is.na(allInfo.temp[["taxonID"]])),get('nucleotideID')]))!=0){ message("Some of the nucleotides in your reference database are not in the 'gi_taxon_nucl.dmp' file. Therefore these cannot be assigned a taxon identifier. \n We will remove these hits from subsequent analyses. \n For reference the respective gis are: ") print(unique(allInfo.temp[which(is.na(allInfo.temp[["taxonID"]])),get('nucleotideID')])) allInfo<-merge(blast.length.weight, taxon.nucl, by="nucleotideID") ######Just corrected it } else { allInfo<-allInfo.temp } probPois<-ppois(allInfo[["mismatch"]] - 1, lambda=0.03*(allInfo[["length"]]), lower.tail=FALSE) ### at least that many mismatches could be observed by chance. Divide by 3 for translated read length data_0.03<-cbind.data.frame(allInfo, "pois"=probPois) ### combine Poisson prob with other read info. data_0.03.dt<- data.table(data_0.03) data.dt<-merge(data_0.03.dt, genome.length, by="nucleotideID") data.dt$pij<-data.dt[["pois"]]/data.dt[["genome.length"]] data.grouped<-data.dt[,list(pij=max(pij)),by=c("read", "weight", "taxonID")] ### one hit per taxonid (best one) pij<-as.data.frame(data.grouped) taxonID<-NULL ############use Sparse Matrix "reshape" long -> wide fromat pij.sparse<-with(pij, sparseMatrix(i = as.numeric(factor(get('read'))), j=as.numeric((factor(taxonID))), x=pij, dimnames=list(levels(factor(get('read'))), levels(factor(taxonID))))) pij.dt<-data.table(pij) allspecies.dt<-pij.dt[,list(count.reads=length(get('read'))), by="taxonID"] allspecies<-as.data.frame(allspecies.dt) ordered.species<-allspecies[order(-allspecies[,2]) , ] #### order them by read count ### add unknown bin and assign a pij pij.sparse.mat<-cbind(pij.sparse, gen.prob.unknown) colnames(pij.sparse.mat)<-c(colnames(pij.sparse), "unknown") if (length(which(!(rownames(read.weights)%in%rownames(pij.sparse.mat))))!=0) { # message("The following reads match only nucleotides that are no longer supported, i.e their gis are not in", gi.taxon.file, "\n Therefore the reads were removed from subsequent analyses.") print(rownames(read.weights[which(!(rownames(read.weights)%in%rownames(pij.sparse.mat))),])) read.weights<-read.weights[which(rownames(read.weights)%in%rownames(pij.sparse.mat)),] read.weights<-data.frame(read.weights, row.names=read.weights[["read"]] ) } else { read.weights<-data.frame(read.weights, row.names=read.weights[["read"]] ) } ### sampling weight to use when choosing which species to add during MCMC uniqReads<-dim(pij.sparse.mat)[[1]] ordered.species$sampling.weight<-ordered.species[,2]/uniqReads ###Flattening the sampling probabilities percentiles<-quantile(ordered.species$sampling.weight, probs=c(0.2, 0.8)) ordered.species$sampling.weight[which(ordered.species$sampling.weight >= percentiles["80%"])] <- percentiles["80%"] ordered.species$sampling.weight[which(ordered.species$sampling.weight <= percentiles["20%"])] <- percentiles["20%"] colnames(ordered.species)<-c("taxonID", "count.reads", "sampling.weight") ### remove objects step1<-list("ordered.species"=ordered.species,"pij.sparse.mat"=pij.sparse.mat, "read.weights"=read.weights, "outDir"=outDir, "gen.prob.unknown"=gen.prob.unknown) if (!is.null(outDir)) { step1.name <- paste(outDir, "/step1.RData", sep = "") save(step1, file=step1.name) rm(list= ls()[!ls() %in% c("step1")]) gc() } else { rm(list= ls()[!ls() %in% c("step1")]) gc() } return(step1) } else { ################ if we are not dealing with default format, but rather with custom blast output that has incorporated the query length and the taxon id) if (!is.null(blast.output.file)) { check.output<-fread(input=blast.output.file, sep="\t", header=F) if (ncol(check.output)!=10) { ###quick check for format stop("Please check your blast output file. The custom blast tabular format we accept as input has the following 10 columns 'qacc qlen sacc slen stitle bitscore length pident evalue staxids'. Alternatively you can use the default blast tabular output and use it along with 'blast.default=TRUE' option. You will need also to provide the 'gi_taxid_prot.dmp' file, which can be downloaded from ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_prot.dmp.gz") } else if (ncol(check.output)==10){ blast.output.length.temp<-fread(input=blast.output.file, sep="\t", header=F, select=c(1,2, 4, 7, 8, 10)) setnames(x=blast.output.length.temp, old=c("read", "length", "genome.length", "aln", "ident", "taxonID")) } else { stop("Please provide the output file from BLASTx. The default tabular format is accepted, using the '-outfmt 6' flag in the BLASTx command.") } } taxonID<-NULL read<-NULL length<-NULL aln<-NULL ident<-NULL genome.length<-NULL if ( is.character(blast.output.length.temp[,taxonID])){ blast.output.length.temp2 <- blast.output.length.temp[, list(taxonID = as.integer(unlist(strsplit(taxonID, ";")))), by=list(read, length, genome.length, aln, ident)] ## handle comma separated taxonIDS and NAs blast.output.length<- blast.output.length.temp2[which(!is.na(blast.output.length.temp2[,taxonID])),] } else { blast.output.length<-blast.output.length.temp } if (!is.integer(blast.output.length[["taxonID"]])) { stop("Your blast output does not have correctly formatted taxon identifiers. Please use the 'blast.default=TRUE' option, providing the default blast tabular format (using the blast option '-outfmt 6' and provide seperately the 'gi_taxid_prot.dmp' file.") } if (is.character(contig.weight.file)) { contig.weights<-fread(input=contig.weight.file, sep="\t", header=F) setnames(x=contig.weights, old=c("read", "weight")) rownames(contig.weights)<-contig.weights[["read"]] } else if (is.numeric(contig.weight.file)) { contig.weights<-cbind.data.frame("read"=unique(blast.output.length[["read"]]), "weight"=contig.weight.file) rownames(contig.weights)<-contig.weights[,"read"] } else { stop("Please provide either a file containing the weights for reads (=1) and contigs (>1) or, assuming you haven't assembled contigs enter contig.weight.file=1.") } blast.output.length$mismatch<-ifelse(blast.output.length[["length"]]>=200, (1-blast.output.length[["ident"]]/100)*blast.output.length[["aln"]], blast.output.length[["length"]]-(blast.output.length[["ident"]]* blast.output.length[["aln"]])/100) # blast.output.length$mismatch<-mismatchNew blast.length.weight<-merge(blast.output.length, contig.weights, by ="read", all.x=T) indx<-which(is.na(blast.length.weight[["weight"]])) blast.length.weight$weight[indx]<-1 read.weights<- unique(blast.length.weight[,c("read","weight"), with=FALSE]) rownames(read.weights)<-read.weights[["read"]] ################### poisson prob with lambda=3 mismatches per 100 nucleotides allInfo<-blast.length.weight probPois<-ppois(allInfo[["mismatch"]] - 1, lambda=0.03*(allInfo[["length"]]), lower.tail=FALSE) ### at least that many mismatches could be observed by chance. Divide by 3 for translated read length data_0.03<-cbind.data.frame(allInfo, "pois"=probPois) ### combine Poisson prob with other read info. data.dt<- data.table(data_0.03) # data.dt<-merge(data_0.03.dt, genome.length, by="nucleotideID") data.dt$pij<-data.dt[["pois"]]/data.dt[["genome.length"]] data.grouped<-data.dt[,list(pij=max(pij)),by=c("read", "weight", "taxonID")] ### one hit per taxonid (best one) pij<-as.data.frame(data.grouped) ############use Sparse Matrix "reshape" long -> wide fromat pij.sparse<-with(pij, sparseMatrix(i = as.numeric(factor(get('read'))), j=as.numeric((factor(taxonID))), x=pij, dimnames=list(levels(factor(get('read'))), levels(factor(taxonID))))) pij.dt<-data.table(pij) allspecies.dt<-pij.dt[,list(count.reads=length(get('read'))), by="taxonID"] allspecies<-as.data.frame(allspecies.dt) ordered.species<-allspecies[order(-allspecies[,2]) , ] #### order them by read count ### add unknown bin and assign a pij pij.sparse.mat<-cbind(pij.sparse, gen.prob.unknown) colnames(pij.sparse.mat)<-c(colnames(pij.sparse), "unknown") if (length(which(!(rownames(read.weights)%in%rownames(pij.sparse.mat))))!=0) { # message("The following reads match only nucleotides that are no longer supported, i.e their gis are not in", gi.taxon.file, "\n Therefore the reads were removed from subsequent analyses.") print(rownames(read.weights[which(!(rownames(read.weights)%in%rownames(pij.sparse.mat))),])) read.weights<-read.weights[which(rownames(read.weights)%in%rownames(pij.sparse.mat)),] read.weights<-data.frame(read.weights, row.names=read.weights[["read"]] ) } else { read.weights<-data.frame(read.weights, row.names=read.weights[["read"]] ) } ### sampling weight to use when choosing which species to add during MCMC uniqReads<-dim(pij.sparse.mat)[[1]] ordered.species$sampling.weight<-ordered.species[,2]/uniqReads ###Flattening the sampling probabilities percentiles<-quantile(ordered.species$sampling.weight, probs=c(0.2, 0.8)) ordered.species$sampling.weight[which(ordered.species$sampling.weight >= percentiles["80%"])] <- percentiles["80%"] ordered.species$sampling.weight[which(ordered.species$sampling.weight <= percentiles["20%"])] <- percentiles["20%"] colnames(ordered.species)<-c("taxonID", "count.reads", "sampling.weight") ### remove objects step1<-list("ordered.species"=ordered.species,"pij.sparse.mat"=pij.sparse.mat, "read.weights"=read.weights, "outDir"=outDir, "gen.prob.unknown"=gen.prob.unknown) if (!is.null(outDir)) { step1.name <- paste(outDir, "/step1.RData", sep = "") save(step1, file=step1.name) rm(list= ls()[!ls() %in% c("step1")]) gc() } else { rm(list= ls()[!ls() %in% c("step1")]) gc() } return(step1) } } metaMix/R/getArgs.R0000644000176200001440000000034713403500106013572 0ustar liggesusersgetArgs <- function() { myargs.list <- strsplit(grep("=",gsub("--","",commandArgs()),value=TRUE),"=") myargs <- lapply(myargs.list,function(x) x[2] ) names(myargs) <- lapply(myargs.list,function(x) x[1]) return (myargs) } metaMix/R/step4_bayesModelAver.R0000644000176200001440000005356413427027343016245 0ustar liggesusers################################################ Perform Bayesian Model Averaging ############################################### #' @name bayes.model.aver #' @title Bayesian Model Averaging NULL #' @rdname bayes.model.aver #' @title bayes.model.aver #' @description Perform Bayesian Model Averaging. We concentrate on the chain with temperature=1 , i.e the untempered posterior, to study the distribution over the model choices and perform model averaging. We consider as present the species that have a posterior probability greater than 0.9. We then fit the mixture model with these species in order to obtain relative abundances and read classification probabilities. A tab seperated file that has a species summary is produced, as well as log-likelihood traceplots and cumulative histogram plots. #' @param step3 list. The output from parallel.temper(), i.e the third step of the pipeline. Alternatively, it can be a character string containing the path name of the ".RData" file where step3 list was saved. #' @param step2 list. The output from reduce.space(), i.e the second step of the pipeline. Alternatively, it can be a character string containing the path name of the ".RData" file where step2 list was saved. #' @param taxon.name.map The 'names.dmp' taxonomy names file, mapping each taxon identifier to the corresponding scientific name. It can be downloaded from \url{ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz} #' @param poster.prob.thr Posterior probability of presence of species threshold for reporting in the species summary. #' @param burnin Percentage of burn in iterations, default value is 0.4 #' @keywords bayes.model.aver #' @export bayes.model.aver #' @import Matrix ggplot2 data.table #' @importFrom gtools rdirichlet #' @importFrom grDevices dev.off #' @importFrom grDevices pdf #' @importFrom graphics plot #' @importFrom utils write.table #' @useDynLib metaMix #' @examples #' ## See vignette for more details #' #' \dontrun{ #' # Either load the object created by previous steps #' data(step2) ## example output of step2, i.e reduce.space() #' data(step3) ## example ouput of step3, i.e parallel.temper() #' step4<-bayes.model.aver(step2=step2, step3=step3, taxon.name.map="pathtoFile/taxon.file") #' #' # or alternatively point to the location of the step2.RData and step3.RData objects #' step4<-bayes.model.aver(step2="pathtoFile/step2.RData", step3="pathtoFile/step3.RData", #' taxon.name.map="pathtoFile/taxon.file") #' #' } ###################################################################################################################### bayes.model.aver = function(step2, step3, taxon.name.map=NULL, poster.prob.thr=0.9, burnin=0.4){ if (is.character(step2)) { load(step2) } if (is.character(step3)) { load(step3) } should.be.in.step3 <- c("duration", "result") should.be.in.the.list <- c("pij.sparse.mat", "read.weights", "outDir", "gen.prob.unknown") if (sum (!( should.be.in.step3 %in% names(step3))) > 0) { message('Missing the following arguments') print(names(step3)[!(should.be.in.step3 %in% names(step3))] ) stop() } else if (sum (!( should.be.in.the.list %in% names(step2)) ) > 0) { message('Missing the following arguments') print(names(step2)[!(should.be.in.the.list %in% names(step2))] ) stop() } else { bayes.model.aver.wrapped<-function(result=step3$result, pij.sparse.mat=step2$pij.sparse.mat, read.weights=step2$read.weights, outDir=step2$outDir, gen.prob.unknown=step2$gen.prob.unknown, taxon.name.map.internal=taxon.name.map, poster.prob.thr.internal=poster.prob.thr){ fast.rmultinom.weight <- function(proba.matrix, z.matrix, seed, weights) { return( .Call("C_rmultinom_weight", proba.matrix, z.matrix, weights, PACKAGE='metaMix') ) } ..count..<-NULL if (is.null(taxon.name.map.internal)) { stop("Please provide the 'names.dmp' file. It can be downloaded from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz") } nIter<- nrow(result$slave1$record) pijSparseUnknown<-cbind(pij.sparse.mat, "unknown"=gen.prob.unknown) # message("Associate taxonIDs with scientific names: reading \"names.dmp\" can take a few minutes") names.dmp<-fread(input=taxon.name.map.internal, header=F, sep="|", select=c(1,2,4)) testTaxon<- as.data.table(lapply(names.dmp, function(x) {gsub("\t", "", x)})) taxonNames<-testTaxon[which(grepl("scientific", testTaxon[["V4"]])),1:2, with=FALSE] setnames(x=taxonNames, old=c("taxonID", "scientName")) taxonNames<-as.data.frame(taxonNames) ofInterest<-result$slave1$record[round(nIter*burnin):nIter,4:(ncol(result$slave1$record)-1)] ##burn-in 40% present.probabilities<- round(apply(ofInterest, MARGIN=2, function(x) sum(x)/length(x)), digits=2) poster.prob.all<-present.probabilities[present.probabilities>0] if (length(present.probabilities[present.probabilities>=poster.prob.thr.internal])>1) { ###default poster.prob<-present.probabilities[present.probabilities>=poster.prob.thr.internal] ###default } else if (length(present.probabilities[present.probabilities>=poster.prob.thr.internal])==1) { message("Only the unknown category has posterior probability>=",poster.prob.thr.internal, ". Try post.prob>=", poster.prob.thr.internal-0.1) if (length(present.probabilities[present.probabilities>=(poster.prob.thr.internal-0.1)])>1) { poster.prob<-present.probabilities[present.probabilities>=(poster.prob.thr.internal-0.1)] } else { message("Only the unknown category has posterior probability>=",poster.prob.thr.internal-0.1 ,". Try post.prob>=0.5 but be careful with the interpretation of the results") poster.prob<-present.probabilities[present.probabilities>=0.5] } } if (length(present.probabilities[present.probabilities>0.5])==1) { stop("The method did not find any present organisms in this dataset, defined as present species with posterior probability greater than 0.5. Maybe you used the wrong reference database to annotate your sequences?") } poster.probM<-as.data.frame(poster.prob) poster.probM$taxonID<-rownames(poster.probM) poster.prob.final<-merge(taxonNames, poster.probM, by.y="taxonID", by.x="taxonID", all.y=T) ### compute Bayes Factor namesBF<-rownames(poster.probM)[!(rownames(poster.probM)%in%"unknown")] ofInterestBF<-result$slave1$record[round(nIter*burnin):nIter,c(namesBF, "logL")] ##burn-in 20% BayesFactor<-matrix(0, ncol=2, nrow=(length(colnames(ofInterestBF))-1) ) BayesFactor<-as.data.frame(BayesFactor) colnames(BayesFactor)<-c("taxonID", "log10BF") EMiter<-10 pij.sparse.unknown<-cbind(pij.sparse.mat, "unknown"=gen.prob.unknown) for ( i in 1:(length(colnames(ofInterestBF))-1) ){ BayesFactor[i,"taxonID"]<-colnames(ofInterestBF)[i] if (length(colnames(ofInterestBF))-1==1) { onlyUnknown.logL<- sum(read.weights[,"weight"])*log(gen.prob.unknown) BayesFactor[i,"log10BF"]<-logmean(ofInterestBF[which(ofInterestBF[,colnames(ofInterestBF)[i]]==1),"logL"])/log(10) - onlyUnknown.logL } else { if (!all(ofInterestBF[,colnames(ofInterestBF)[i]]==1)) { BayesFactor[i,"log10BF"]<-logmean(ofInterestBF[which(ofInterestBF[,colnames(ofInterestBF)[i]]==1),"logL"])/log(10) - logmean(ofInterestBF[which(ofInterestBF[,colnames(ofInterestBF)[i]]==0),"logL"])/log(10) } else { maxLog<- ofInterestBF[which(ofInterestBF[,"logL"]==max(ofInterestBF[which(ofInterestBF[,i]==1),"logL"]))[1],] namesSp<-colnames(maxLog[which(maxLog==1)]) tempSet<- namesSp[!(namesSp %in% BayesFactor[i, "taxonID"])] tentSet<- c(tempSet,"unknown") noSpecies<-length(tentSet) hyperP<-rep(1, noSpecies) startW<-rdirichlet(1, hyperP) output10Tent<-EM(pij=pij.sparse.unknown, iter=EMiter, species=tentSet, abund=startW, readWeights = read.weights) #lpenalty<-(computePenalty(readSupport=result$readSupport, readWeights=read.weights, pUnknown=gen.prob.unknown))/log(10) lpenalty<-(result$slave1$lpenalty)/log(10) estimator <- (output10Tent$logL[EMiter,2])/log(10) + (noSpecies * lpenalty) BayesFactor[i,"log10BF"]<-(maxLog[,"logL"])/log(10) - estimator } } } poster.prob.final[which(poster.prob.final[,"taxonID"]=="unknown"),"scientName"]<-"unknown" poster.prob<-poster.prob.final[order(-poster.prob.final[,"poster.prob"]),] finalSpecies<-poster.prob[,"taxonID"] noSpecies<-length(finalSpecies) ###parameters for gibbs hyperP<-rep(1, noSpecies) startW<-rdirichlet(1, hyperP) BurnIn<-50 GibbsCycles<-100 # message("Running final longer chain") output100<-Gibbs(pij=pijSparseUnknown, iter=GibbsCycles, species=finalSpecies, abund=startW, hyperParam=hyperP, fast.rmultinom.weight=fast.rmultinom.weight, readWeights=read.weights) finalAssignments<-matrix(output100$assignments[GibbsCycles,], ncol=1, dimnames=list(colnames(output100$assignments[GibbsCycles,]))) finalAssignmentsDF <- data.frame(taxonID=rownames(finalAssignments), finalAssignments=unlist(finalAssignments)) finalAssignmentsDF<- finalAssignmentsDF[which(finalAssignmentsDF$taxonID!="Iter"),] presentSpecies<-merge(taxonNames, finalAssignmentsDF, by.y="taxonID", by.x="taxonID" ,all.y=T) presentSpecies[presentSpecies[,"taxonID"]=="unknown",][,"scientName"]<-"unknown" presentSpecies<-presentSpecies[as.numeric(order(presentSpecies[,"finalAssignments"]), decreasing=TRUE),] presentSpecies.allInfo.temp<-merge(presentSpecies, poster.probM, by.y="taxonID", by.x="taxonID", all.y=T) presentSpecies.allInfo<- merge(presentSpecies.allInfo.temp, BayesFactor, by.x ="taxonID", all.x=T) presentSpecies.allInfo<-presentSpecies.allInfo[order(as.numeric(presentSpecies.allInfo[,"finalAssignments"]), decreasing=TRUE),] summary.name <- paste(outDir, "/presentSpecies_assignedReads.tsv", sep="") ###Classification Probability noSpecies<-nrow(presentSpecies) mean1000<-output100$abundances[GibbsCycles,2:(noSpecies+1)] zij<-output100$pijs %*% diag(mean1000) sumProd<-rowSums(zij) zijFinal <- as.matrix(zij / sumProd) colnames(zijFinal)<-colnames(output100$pijs) zijFinal<-zijFinal[,presentSpecies[,"taxonID"]] assignedReads<-list() classProb<-list() for (i in presentSpecies[,"taxonID"]){ assignedReads[[i]]<-rownames(output100$assignedReads[output100$assignedReads[,i]>0,]) classProb[[i]]<-zijFinal[assignedReads[[i]], i] } scientNames<-vector() for (i in names(classProb)) { scN<-presentSpecies[presentSpecies[,"taxonID"]==i, "scientName"] scientNames<-append(scientNames, scN) } names(classProb)<-scientNames step4<-list("result"=result, "pij.sparse.mat"=pijSparseUnknown, "presentSpecies.allInfo"=presentSpecies.allInfo, "output100"=output100, "assignedReads"=assignedReads, "classProb"=classProb) if (!is.null(outDir)) { histograms.name<-paste(outDir, "/histograms_cdf.pdf", sep="") pdf(histograms.name) for (i in names(classProb)) { if ( length(classProb[[i]])>1 ){ temp<-data.frame(read=names(classProb[[i]]), prob=classProb[[i]], stringsAsFactors=F) temp2<-merge(temp, read.weights, by= "read", all.x=T ) temp3<-temp2[rep(seq_len(nrow(temp2)), temp2$weight),c("read", "prob")] ### edw einai to provlima sth vignette ploti<-ggplot(temp3, aes(x=get('prob'))) + stat_bin(aes(y=..count../sum(..count..), fill = ..count../sum(..count..)), breaks=c(0,0.1, 0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1) ) + stat_ecdf() + labs(list(title = paste(nrow(temp3),"reads assigned to ", i), x = "Classification probability", y = "Percentage of reads")) + guides(fill=guide_legend(title="Percentage of reads")) + scale_x_continuous(breaks=c(0,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1) ) + theme(plot.title = element_text(size = 12)) #print(ploti) #suppressMessages(print(ploti)) suppressMessages(suppressWarnings(print(ploti))) } } dev.off() traceplot1<-paste(outDir, "/logLikelihood_traceplot_all.pdf" ,sep="") pdf(traceplot1) plot(result$slave1$record[1:nIter,"logL"], type="l", xlab="All iterations", ylab="Log-likelihood", main="Parallel Tempering - Coldest Chain", lwd=1.5) dev.off() traceplot2<-paste(outDir, "/logLikelihood_traceplot_60.pdf", sep="") pdf(traceplot2) plot(result$slave1$record[(nIter*burnin):nIter,"logL"], type="l", col="dodgerblue", xlab="Last 60% of iterations", ylab="Log-likelihood", main="Parallel Tempering - Coldest Chain", lwd=1.5) dev.off() # message("Results in ", summary.name) write.table(presentSpecies.allInfo, summary.name, sep="\t") step4.name <- paste(outDir, "/step4.RData", sep="") save(step4, file=step4.name) rm(list= ls()[!ls() %in% c("step4")]) gc() } else { rm(list= ls()[!ls() %in% c("step4")]) gc() } return(step4) } bayes.model.aver.wrapped() } } #' @rdname bayes.model.aver #' @title bayes.model.aver.explicit #' @description bayes.model.aver.explicit is the same function as bayes.model.aver with a more involved syntax. #' @param result The list produced by parallel.temper() (or paraller.temper.nucl()) . It holds a detailed record for each chain, what moves were proposed, which were accepted and which were rejected as well the log-likelihood through the iterations. #' @param pij.sparse.mat see ?reduce.space #' @param read.weights see ?reduce.space #' @param gen.prob.unknown see ?reduce.space #' @param outDir see ?reduce.space #' @keywords bayes.model.aver.explicit #' @export bayes.model.aver.explicit #' @import Matrix ggplot2 data.table #' @importFrom gtools rdirichlet #' @useDynLib metaMix ##########################-------------------------------------------- MAIN --------------------------------------------------------------------------------- bayes.model.aver.explicit<-function(result, pij.sparse.mat, read.weights, outDir, gen.prob.unknown, taxon.name.map=NULL, poster.prob.thr=0.9, burnin=0.4){ fast.rmultinom.weight <- function(proba.matrix, z.matrix, seed, weights) { return( .Call("C_rmultinom_weight", proba.matrix, z.matrix, weights, PACKAGE='metaMix') ) } ..count..<-NULL if (is.null(taxon.name.map)) { stop("Please provide the 'names.dmp' file. It can be downloaded from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz") } nIter<- nrow(result$slave1$record) pijSparseUnknown<-cbind(pij.sparse.mat, "unknown"=gen.prob.unknown) message("Associate taxonIDs with scientific names: reading \"names.dmp\" could take a couple of minutes") names.dmp<-fread(input=taxon.name.map, header=F, sep="|", select=c(1,2,4)) testTaxon<- as.data.table(lapply(names.dmp, function(x) {gsub("\t", "", x)})) taxonNames<-testTaxon[which(grepl("scientific", testTaxon[["V4"]])),1:2, with=FALSE] setnames(x=taxonNames, old=c("taxonID", "scientName")) taxonNames<-as.data.frame(taxonNames) ofInterest<-result$slave1$record[round(nIter*burnin):nIter,4:(ncol(result$slave1$record)-1)] ##burn-in 20% present.probabilities<- round(apply(ofInterest, MARGIN=2, function(x) sum(x)/length(x)), digits=2) poster.prob.all<-present.probabilities[present.probabilities>0] if (length(present.probabilities[present.probabilities>=poster.prob.thr])>1) { ###default poster.prob<-present.probabilities[present.probabilities>=poster.prob.thr] ###default } else if (length(present.probabilities[present.probabilities>=poster.prob.thr])==1) { message("Only the unknown category has posterior probability>=",poster.prob.thr, ". Try post.prob>=", poster.prob.thr-0.1) if (length(present.probabilities[present.probabilities>=(poster.prob.thr-0.1)])>1) { poster.prob<-present.probabilities[present.probabilities>=(poster.prob.thr-0.1)] } else { message("Only the unknown category has posterior probability>=",poster.prob.thr-0.1 ,". Try post.prob>=0.5 but be careful with the interpretation of the results") poster.prob<-present.probabilities[present.probabilities>=0.5] } } if (length(present.probabilities[present.probabilities>0.5])==1) { stop("The method did not find any present organisms in this dataset, defining as present species with posterior probability greater than 0.5. Maybe you used the wrong reference database to annotate your sequences?") } poster.probM<-as.data.frame(poster.prob) poster.probM$taxonID<-rownames(poster.probM) poster.prob.final<-merge(taxonNames, poster.probM, by.y="taxonID", by.x="taxonID", all.y=T) poster.prob.final[which(poster.prob.final[,"taxonID"]=="unknown"),"scientName"]<-"unknown" poster.prob<-poster.prob.final[order(-poster.prob.final[,"poster.prob"]),] finalSpecies<-poster.prob[,"taxonID"] noSpecies<-length(finalSpecies) ###parameters for gibbs hyperP<-rep(1, noSpecies) startW<-rdirichlet(1, hyperP) BurnIn<-50 GibbsCycles<-100 # message("Running final longer chain") output100<-Gibbs(pij=pijSparseUnknown, iter=GibbsCycles, species=finalSpecies, abund=startW, hyperParam=hyperP, fast.rmultinom.weight=fast.rmultinom.weight, readWeights=read.weights) finalAssignments<-matrix(output100$assignments[GibbsCycles,], ncol=1, dimnames=list(colnames(output100$assignments[GibbsCycles,]))) finalAssignmentsDF <- data.frame(taxonID=rownames(finalAssignments), finalAssignments=unlist(finalAssignments)) finalAssignmentsDF<- finalAssignmentsDF[which(finalAssignmentsDF$taxonID!="Iter"),] presentSpecies<-merge(taxonNames, finalAssignmentsDF, by.y="taxonID", by.x="taxonID" ,all.y=T) presentSpecies[presentSpecies[,"taxonID"]=="unknown",][,"scientName"]<-"unknown" presentSpecies<-presentSpecies[as.numeric(order(presentSpecies[,"finalAssignments"]), decreasing=TRUE),] presentSpecies.allInfo<-merge(presentSpecies, poster.probM, by.y="taxonID", by.x="taxonID", all.y=T) presentSpecies.allInfo<-presentSpecies.allInfo[order(as.numeric(presentSpecies.allInfo[,"finalAssignments"]), decreasing=TRUE),] summary.name <- paste(outDir, "/presentSpecies_assignedReads.tsv", sep="") ###Classification Probability noSpecies<-nrow(presentSpecies) mean1000<-output100$abundances[GibbsCycles,2:(noSpecies+1)] zij<-output100$pijs %*% diag(mean1000) sumProd<-rowSums(zij) zijFinal <- as.matrix(zij / sumProd) colnames(zijFinal)<-colnames(output100$pijs) zijFinal<-zijFinal[,presentSpecies[,"taxonID"]] assignedReads<-list() classProb<-list() for (i in presentSpecies[,"taxonID"]){ assignedReads[[i]]<-rownames(output100$assignedReads[output100$assignedReads[,i]>0,]) classProb[[i]]<-zijFinal[assignedReads[[i]], i] } scientNames<-vector() for (i in names(classProb)) { scN<-presentSpecies[presentSpecies[,"taxonID"]==i, "scientName"] scientNames<-append(scientNames, scN) } names(classProb)<-scientNames step4<-list("result"=result, "pij.sparse.mat"=pijSparseUnknown, "presentSpecies.allInfo"=presentSpecies.allInfo, "output100"=output100, "assignedReads"=assignedReads, "classProb"=classProb) if (!is.null(outDir)) { histograms.name<-paste(outDir, "/histograms_cdf.pdf", sep="") pdf(histograms.name) for (i in names(classProb)) { temp<-data.frame(read=names(classProb[[i]]), prob=classProb[[i]], stringsAsFactors=F) temp2<-merge(temp, read.weights, by= "read", all.x=T ) temp3<-temp2[rep(seq_len(nrow(temp2)), temp2$weight),c("read", "prob")] # ploti<-ggplot(temp3, aes(x=get('prob'))) + stat_bin(aes(y=..count../sum(..count..), fill = ..count../sum(..count..))) + stat_ecdf() + labs(list(title = paste(nrow(temp3),"reads assigned to ", i), x = "Classification probability", y = "Percentage of reads")) + guides(fill=guide_legend(title="Percentage of reads")) + scale_x_continuous(breaks=c(0,0.1, 0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1) ) + theme(plot.title = element_text(size = 12)) ploti<-ggplot(temp3, aes(x=get('prob'))) + stat_bin(aes(y=..count../sum(..count..), fill = ..count../sum(..count..)), breaks=c(0,0.1, 0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1)) + stat_ecdf() + labs(list(title = paste(nrow(temp3),"reads assigned to ", i), x = "Classification probability", y = "Percentage of reads")) + guides(fill=guide_legend(title="Percentage of reads")) + scale_x_continuous(breaks=c(0,0.1, 0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1) ) + theme(plot.title = element_text(size = 12)) #print(ploti) #suppressMessages(print(ploti)) suppressMessages(suppressWarnings(print(ploti))) } dev.off() traceplot1<-paste(outDir, "/logLikelihood_traceplot_all.pdf", sep="") pdf(traceplot1) plot(result$slave1$record[1:nIter,"logL"], type="l", xlab="All iterations", ylab="Log-likelihood", main="Parallel Tempering - Coldest Chain", lwd=1.5) dev.off() traceplot2<-paste(outDir, "/logLikelihood_traceplot_80.pdf", sep="") pdf(traceplot2) plot(result$slave1$record[(nIter*burnin):nIter,"logL"], type="l", col="dodgerblue", xlab="Last 80% of iterations", ylab="Log-likelihood", main="Parallel Tempering - Coldest Chain", lwd=1.5) dev.off() #message("Results in ", summary.name) write.table(presentSpecies.allInfo, summary.name, sep="\t") step4.name <- paste(outDir, "/step4.RData", sep="") save(step4, file=step4.name) rm(list= ls()[!ls() %in% c("step4")]) gc() } else { rm(list= ls()[!ls() %in% c("step4")]) gc() } return(step4) } metaMix/R/metaMix-package.r0000644000176200001440000000060313403500106015226 0ustar liggesusers#' Example output of generative.prob() for use in the vignette/examples #' #' @name step1 #' @format A list with 5 elements NULL #' Example output of reduce.space() for use in the vignette/examples #' #' @name step2 #' @format A list with 6 elements NULL #' Example output of parallel.temper() for use in the vignette/examples #' #' @name step3 #' @format A list with 2 elements NULL metaMix/R/EM.R0000644000176200001440000000352313403500106012476 0ustar liggesusersEM = function(pij, iter, species, abund, readWeights) { time1 <- Sys.time() ####### Matrices to record the mixing weights and species assignments through iterations abundances<-matrix(0, ncol=(length(species)+1), nrow=iter) abundances[,1]=1:iter logLs<-matrix(0, ncol=2, nrow=iter) logLs[,1]=1:iter rowWeights <- as.numeric(readWeights[ rownames(pij) ,"weight"]) ####### Create progress bar # pb <- txtProgressBar(min = 0, max = iter, style = 3) #### select the species you want and at the same time rearrange columns of pij.temp to be same with species vector, so multiplication work pij.temp<-pij[,species] timeA <- Sys.time() ####### Begin iterations for (i in 1:iter) { # print(i) w<-as.numeric(abund) #####Do at the same time STEP1 and STEP2 ######## STEP1.Calculate zij {zij=pijwj/\sum_j(pijwj)} - Expectation Step zij<-(t(t(pij.temp)*w)) sumProd<-rowSums(zij) zijFinal <- zij / sumProd rm(zij) gc() # rowWeights <- as.numeric(readWeights[ dimnames(zijFinal)[[1]] ,"weight"]) zijWeighted<-zijFinal*rowWeights rm(zijFinal) gc() ######## STEP2. Compute wj - Maximization step abund<- colSums(zijWeighted)/sum(colSums(zijWeighted)) names(abund)<-colnames(zijWeighted) ### record log-likelihood logL<-colSums(log(pij.temp%*%abund)*readWeights[rownames(pij.temp),"weight"]) ###### record output abundances[i,2:(length(species)+1)]<-w logLs[i,2]<-logL #### update progress bar # setTxtProgressBar(pb, i) } ###end of iterat ###close progress bar # close(pb) ### Processing time time2<-Sys.time() timeDiff<-time2-time1 iterTimeDiff<-time2-timeA abundances=data.frame(abundances) names(abundances)<-c("Iter", colnames(pij.temp)) result<-list("abundances"=abundances, "logL"=logLs, "RunningTime"=timeDiff) return(result) } metaMix/R/logmean.R0000644000176200001440000000021313403500106013610 0ustar liggesuserslogmean <- function(logL) { my.max <- max(logL) my.mod.logL <- logL - my.max return( log(mean(exp(my.mod.logL))) + my.max) } metaMix/R/computePenalty.R0000644000176200001440000000146113403500106015205 0ustar liggesuserscomputePenalty<-function(readSupport, readWeights, pUnknown){ totalReads<-sum(readWeights[,"weight"]) pij<-matrix(data=0, ncol=2, nrow=totalReads) LLunknown<-totalReads*log(pUnknown) pij[,1]<-pUnknown pij[1:readSupport,2]<-1 abund<-c((totalReads - readSupport)/totalReads, readSupport/totalReads) lpenalty<-LLunknown-colSums(log(pij%*%abund)) return(lpenalty) } computePenalty.nucl<-function(readSupport, readWeights, pUnknown, median.genome.length){ totalReads<-sum(readWeights[,"weight"]) pij<-matrix(data=0, ncol=2, nrow=totalReads) LLunknown<-totalReads*log(pUnknown) pij[,1]<-pUnknown pij[1:readSupport,2]<-1/median.genome.length abund<-c((totalReads - readSupport)/totalReads, readSupport/totalReads) lpenalty<-LLunknown-colSums(log(pij%*%abund)) return(lpenalty) } metaMix/R/step3_parallelTemper.R0000644000176200001440000013766413427027322016314 0ustar liggesusers################################################ Perform Parallel Tempering MCMC ############################################### #' @name parallel.temper #' @title Parallel Tempering MCMC NULL #' @rdname parallel.temper #' @title parallel.temper #' @description Performs Parallel Tempering MCMC to explore the species state space. Two types of moves are implemented: a mutation step (within chain) and an exchange step (between neighboring chains). If working with BLASTn data, use parallel.temper.nucl(). #' @param readSupport The number of reads the user requires in order to believe in the presence of the species. It is used to compute the penalty factor. The default value is 10. We compute the logarithmic penalty value as the log-likelihood difference between two models: one where all N reads belong to the "unknown" category and one where r reads have a perfect match to some unspecified species and the remaining reads belong to the "unknown" category. #' @param noChains The number of parallel chains to run. The default value is 12. #' @param iter The number of MCMC iterations. The default behavior of metaMix is to take into account the number of potential species after step 2 in order in order to compute the number of MCMC iterations. By default metaMix will choose the greater value between a) the user-specified value for iter and b) the product of (5 * the number of potential species). This behavior can by bypassed by setting the bypass parameter to TRUE. Then the MCMC will run for exactly the user-specified number iter. #' @param bypass A logical flag. If set to TRUE the MCMC will run for exactly "iter" iterations. If FALSE, metaMix defaults to choosing the greater value between "iter" and "5*(nrow(ordered.sepcies))". #' @param seed Optional argument that sets the random seed (default is 1) to make results reproducible. #' @param step2 list. The output from reduce.space(). Alternatively, it can be a character string containing the path name of the ".RData" file where step2 list was saved. #' @return step3: A list with two elements. The first one (result) is a list that records MCMC information from each parallel chain. The second one (duration) records how much time the MCMC exploration took. #' @seealso \code{\link{parallel.temper.nucl}} This function should be used when working with BLASTn data. #' @keywords parallel.temper #' @export parallel.temper #' @import Rmpi Matrix #' @importFrom gtools rdirichlet #' @importFrom stats runif #' @examples #' ## See vignette for more details #' #' \dontrun{ #' # Either load the object created by previous step (i.e from function reduce.space() ) #' data(step2) ## example output of reduce.space #' step3<-parallel.temper(step2=step2) #' #' # or alternatively point to the location of the step2.RData object #' step3 <- parallel.temper(step2="/pathtoFile/step2.RData") #' } ###################################################################################################################### parallel.temper = function(step2, readSupport=10, noChains=12, seed=1, iter=500, bypass=FALSE){ if (is.character(step2)) { load(step2) } should.be.in.the.list <- c("pij.sparse.mat", "ordered.species", "read.weights", "outDir", "gen.prob.unknown") if (sum (!( should.be.in.the.list %in% names(step2)) ) > 0) { message('Missing the following arguments') print(names(step2)[!(should.be.in.the.list %in% names(step2))] ) stop() } else { # parallel.temper.wrapped<-function(readSupport.internal=readSupport, noChains.internal=noChains, pij.sparse.mat=step2$pij.sparse.mat, read.weights=step2$read.weights, ordered.species=step2$ordered.species, gen.prob.unknown=step2$gen.prob.unknown, outDir=step2$outDir, seed.internal=seed){ parallel.temper.wrapped<-function(readSupport.internal=readSupport, noChains.internal=noChains, pij.sparse.mat=step2$pij.sparse.mat, read.weights=step2$read.weights, ordered.species=step2$ordered.species, gen.prob.unknown=step2$gen.prob.unknown, outDir=step2$outDir, seed.internal=seed, iter.internal=iter){ set.seed(seed.internal); #print(warnings()) StartTime<-Sys.time() sieve <- function(n) { n <- as.integer(n) if(n > 1e6) stop("n too large") primes <- rep(TRUE, n) primes[1] <- FALSE last.prime <- 2L for(i in last.prime:floor(sqrt(n))) { primes[seq.int(2L*last.prime, n, last.prime)] <- FALSE last.prime <- last.prime + min(which(primes[(last.prime+1):n])) } which(primes) } list.integers <- sieve(1000) node.ids <- list.integers[ 1:noChains.internal ] mpi.spawn.Rslaves(nslaves = noChains.internal) #number of slaves to spawn, should be equal to individual chains # In case R exits unexpectedly, have it automatically clean up # resources taken up by Rmpi (slaves, memory, etc...) .Last <- function(){ if (is.loaded("mpi_initialize")){ if (mpi.comm.size(1) > 0){ print("Please use mpi.close.Rslaves() to close slaves.") mpi.close.Rslaves() } print("Please use mpi.quit() to quit R") .Call("mpi_finalize", PACKAGE='metaMix') } } pij.sparse.mat<-cbind(pij.sparse.mat, "unknown"=gen.prob.unknown) #rm(step2) gc() allSpecies<-ordered.species[,c("taxonID", "samplingWeight")] lenSp<-nrow(allSpecies) lpenalty<-computePenalty(readSupport=readSupport.internal, readWeights=read.weights, pUnknown=gen.prob.unknown) ### penalty for accepting a new species ~ Use pij for the r readSupport perfect reads (=1/median(protein length)). Likelihood jump for 10 reads moving from unknown bin (pij=gen.prob.unknown, default 1e-10) to species (1/1500). ### EMiter EMiter<-10 ### PT parameters exchangeInterval<-1 ###leave chains run in parallel for that many iterations if (bypass==FALSE){ if (iter.internal > 5*(nrow(ordered.species))) { ### choose the number of iterations that is greater between 1) the user-defined number 2) the product of the number of potential species times 5 ExternIter<-iter.internal } else { ExternIter<-5*(nrow(ordered.species)) ### make chains communicate 1 times } } else { ExternIter<-iter.internal } TotalIter<-exchangeInterval * ExternIter ##Tempering Vector --Power Decay temper<-vector() K<-0.001 a<-3/2 for (n in 2:noChains.internal){ temper[1]<-1 temper[n]<-(temper[n-1]-K)^a } for (i in 1:noChains.internal) {names(temper)[i]<- paste("slave",i, sep="")} ###names ### flag for adding /removing species stepAdd<-vector(mode = "logical") #### broadcast necessary objects/functions to slaves mpi.bcast.Robj2slave(exchangeInterval) mpi.bcast.Robj2slave(ExternIter) mpi.bcast.Robj2slave(TotalIter) mpi.bcast.Robj2slave(list.integers) mpi.bcast.Robj2slave(node.ids) mpi.bcast.Robj2slave(ordered.species) mpi.bcast.Robj2slave(read.weights) mpi.bcast.Robj2slave(pij.sparse.mat) mpi.bcast.Robj2slave(lpenalty) mpi.bcast.Robj2slave(EM) mpi.bcast.Robj2slave(allSpecies) mpi.bcast.Robj2slave(lenSp) mpi.bcast.Robj2slave(EMiter) mpi.bcast.Robj2slave(noChains.internal) mpi.bcast.Robj2slave(temper) mpi.bcast.Robj2slave(gen.prob.unknown) ##########################---------------------------------------SINGLE CHAIN FUNCTION -----------------------------------------------------------------------------------------------####################### singleChain <- function(TotalIter, exchangeInterval){ if (file.exists('~/.Rprofile')) source('~/.Rprofile') print(.libPaths()) ind <- mpi.comm.rank() # Each slave gets its own copy of ind and chain based on mpi process rank print(ind) estimNew<-matrix(0, nrow=TotalIter, ncol=1) ### Create matrix that will hold the estimator of the log-likelihood estimNew[1,]<- sum(read.weights[,"weight"])*log(gen.prob.unknown)*temper[ind] print(estimNew[1,]) presentSpecies<-"unknown" ## create object that receives the species deemed as present, from previous (swapInterv*j) iteration. abundUsedSp<-c("unknown"=1) ### Create 2 lists. One that holds species names and one with their abundances. Each list has 2 elements. Element1: present species and Element2: tentative species being explored in current iteration. speciestoUse<-list("presentSp"=presentSpecies, "tentativeSp"=NULL) abundUsedSpecies<-list("presentSp"= abundUsedSp, "tentativeSp"=NULL) message("\nThis is the temperature for this slave") print(temper[ind]) ### create matrix to hold info on which species was added or removed, which species were present and logL , through iterations record<-matrix(0, ncol=(5+lenSp), nrow=(TotalIter)) record<-as.data.frame(record) colnames(record)<-c("Iter", "Move", "Candidate Species", allSpecies[,1], "unknown", "logL") record[,1]=1:(TotalIter) record[1, presentSpecies]<-1 record[1,(5+lenSp)]<-estimNew[1,] ###last colum is logL swaps.attempted<-0 swaps.accepted<-0 oddFlag<-0 ################ ----------------------------------- Begin MCMC (within single chain) ------------------------------------------------------------------------------------------############ for (i in 2:TotalIter) { cat('\n',i,'\n') ### temporary - debugging purposes #### Create 3 functions to use repeatedly in adding/removing species steps. ######################### 1a. For add step: species I sample my candidate species from. potentialSpecies<-function() { toChooseFrom <- allSpecies[,1][!(allSpecies[,1] %in% speciestoUse[[1]])] ### Species remaining after omitting "present species" toChooseFrom<-as.character(toChooseFrom) potentialSp<- allSpecies[allSpecies$taxonID %in% toChooseFrom,] resultPS<-list("potentialSp"=potentialSp, "toChooseFrom"=toChooseFrom) return(resultPS) } ######################## 1b. For add step, sample candidate organism to add and create object for tentative species moveAdd<-function() { randSp <- sample(as.character(potentialSp[,1]),1, prob=potentialSp[,2]) ### choose random species, weights need not sum to one. Here weights are based on intial read counts. cat('Add species', randSp, '\n') ### temporary - debugging purposes speciestoUse[[2]]<-c(randSp, speciestoUse[[1]]) ### tentative present species, to use in Gibbs below. record[i, 2]<- "Add" ### record info on species we are adding record[i,3]<- randSp result<-list("record"=record, "speciestoUse"=speciestoUse) return(result) } ######################## 2. For remove step, sample candidate organism to remove and create object for tentative species moveRemove<-function() { toremoveFrom <- speciestoUse[[1]][!(speciestoUse[[1]]%in%"unknown")] ### species set from which to remove (i.e present ones bar unknown) toremoveFrom<-as.character(toremoveFrom) removeProb<-(1/abundUsedSpecies[[1]][toremoveFrom])/sum(1/abundUsedSpecies[[1]][toremoveFrom]) ###### sampling weight inversely proportional to assigned read counts. ###Flatten removal probabilities percentiles<-quantile(removeProb, probs=c(0.2, 0.8)) removeProb[which(removeProb >= percentiles["80%"])] <- percentiles["80%"] removeProb[which(removeProb <= percentiles["20%"])] <- percentiles["20%"] ### sample candidate species to remove randSp<-sample(toremoveFrom, 1, prob=removeProb ) ### weights need not sum to one cat('Remove species', randSp, '\n') ### temporary - debugging purposes speciestoUse[[2]] <- speciestoUse[[1]][!(speciestoUse[[1]] %in% randSp)] ### tentative present species, to use in Gibbs below. record[i, 2]<- "Remove" ### record info on species we are adding record[i,3]<- randSp result<-list("record"=record, "speciestoUse"=speciestoUse) return(result) } addStep <-0.5 ####proability of doing add step ######################################################## Add species ######################################## if (runif(1)<= addStep) { resultPS<-potentialSpecies() potentialSp<-as.data.frame(resultPS$potentialSp) toChooseFrom<-as.character(resultPS$toChooseFrom) if (length(toChooseFrom) != 0L){ result<-moveAdd() speciestoUse<-result$speciestoUse record<-result$record } else { ################## ### If pool of species to add empty, go to remove step message("No more species to choose from, all are kept as present.") result<-moveRemove() speciestoUse<-result$speciestoUse record<-result$record addStep<-0 ### so do remove step with prob=1 } } ###close if runif(1)<=addStep else { ################################################### Remove species ################################################# toremoveFrom <- speciestoUse[[1]][!(speciestoUse[[1]]%in%"unknown")] ### species set from which to remove (i.e present ones bar unknown) toremoveFrom<-as.character(toremoveFrom) #### First check that more than 1 species are present, so don't risk of remaining only with X bin and wasting iteration. if (length(toremoveFrom) > 1) { result<-moveRemove() speciestoUse<-result$speciestoUse record<-result$record } else if (length(speciestoUse[[1]])==1) { #### speciestoUse[[1]]==1 when only unknown bin is there / We can only add message("We cannot remove, we only have unknown bin") potentialSp<-allSpecies result<-moveAdd() speciestoUse<-result$speciestoUse record<-result$record addStep <- 1 ### so do add step with prob=1 } else { ### we are adding species instead. Removing would leave us just with X-bin again. message("\nCannot remove a species, so instead we add\n") ### temporary resultPS<-potentialSpecies() potentialSp<-as.data.frame(resultPS$potentialSp) toChooseFrom<-as.character(resultPS$toChooseFrom) result<-moveAdd() speciestoUse<-result$speciestoUse record<-result$record addStep <- 1 } } ###close else (remove species) noSpecies<-length(speciestoUse[[2]]) print(noSpecies) hyperP<-rep(1, noSpecies) startW<-rdirichlet(1, hyperP) output100Tent<-EM(pij=pij.sparse.mat, iter=EMiter, species=speciestoUse[[2]], abund=startW, readWeights = read.weights) ### EM function estimator <- output100Tent$logL[EMiter,2] + (noSpecies * lpenalty) #### penalise likelihood message("EM took: ", output100Tent$RunningTime) mean1<-as.numeric(output100Tent$abundances[EMiter,2:(noSpecies+1)]) names(mean1)<-names(output100Tent$abundances[EMiter,2:(noSpecies+1)]) abundUsedSpecies[[2]]<-mean1 estimNew[i,]<-estimator*temper[ind] ###tempered likelihood message('\n', estimNew[i,] , ' ', estimNew[i-1,]) ### temporary print - which values am I comparing? ####### flag of adding/removing if (record[i,2]=="Add") { stepAdd<-TRUE } else {stepAdd<-FALSE} removeStep <- 1 - addStep ##remove step if (stepAdd) { candidateAdd<-allSpecies[allSpecies[,1]==(as.character(record[i,3])),2] removeProba<-(1/abundUsedSpecies[[2]])/sum(1/abundUsedSpecies[[2]]) ###### sampling weight inversely proportional to size. Tentative Species ###Flattening the sampling probabilities percentiles<-quantile(removeProba, probs=c(0.2, 0.8)) removeProba[which(removeProba >= percentiles["80%"])] <- percentiles["80%"] removeProba[which(removeProba <= percentiles["20%"])] <- percentiles["20%"] candidateRemove<-removeProba[as.character(record[i,3])] print(candidateRemove) print(candidateAdd) if (runif(1) < min( 1, exp(estimNew[i] - estimNew[i-1] + log(removeStep) - log(addStep) + log(candidateRemove) - log(candidateAdd) ))) { ### accept "add species" with prob min{1, P(D|i)*P(removeSpecies)*P(remove Specific Species)/P(D|i-1)*P(addSpecies)*P(add specific species) ######## Accept move ####### estimNew[i,]<-estimNew[i,] ### if move is accepted, record new logL speciestoUse[[1]]<-speciestoUse[[2]] ### if move is accepted, tentative species becomes present species. abundUsedSpecies[[1]]<-abundUsedSpecies[[2]] ### -->>-->>-- , abundances of new set of species are kept cat('Present species become:', speciestoUse[[1]], '\n') } else { ######### Reject Move ######## estimNew[i,]<-estimNew[i-1,] ### if move is rejected, record previous logL speciestoUse[[1]]<-speciestoUse[[1]] ### if move is rejected, keep present species as it is. abundUsedSpecies[[1]]<-abundUsedSpecies[[1]] cat('Present species remain:', speciestoUse[[1]], '\n') ### temporary } } ### close if(stepAdd==TRUE) else { ######################################## type of move was to remove species ############## removeProba<-(1/abundUsedSpecies[[1]])/sum(1/abundUsedSpecies[[1]]) ###### sampling weight inversely proportional to size. Do this for present Species candidateRemove<-removeProba[as.character(record[i,3])] candidateAdd<-allSpecies[allSpecies[,1]==(as.character(record[i,3])),2] if (runif(1) < min( 1, exp(estimNew[i] - estimNew[i-1] + log(addStep) - log(removeStep) + log(candidateAdd) - log(candidateRemove) ))) {############# Accept "remove species" estimNew[i,]<-estimNew[i,] speciestoUse[[1]]<-speciestoUse[[2]] ### tentative species becomes present species. abundUsedSpecies[[1]]<-abundUsedSpecies[[2]] cat('Present species become:', speciestoUse[[1]], '\n') } else { ######## Reject Move ########### estimNew[i,]<-estimNew[i-1,] speciestoUse[[1]]<-speciestoUse[[1]] abundUsedSpecies[[1]]<-abundUsedSpecies[[1]] cat('Present species remain:', speciestoUse[[1]], '\n') } } ###close else (i.e (stepAdd==FALSE)) #################################edw tha kanw attempt to direct swap between slaves, without going through master if( i%%exchangeInterval == 0 ){ ### every nth (2nd for now) iteration message("\n\nTime to attempt an exchange") oddFlag<-oddFlag+1 swap<-0 estim.current<-estimNew[i,]/temper[ind] ######### need untempered logL ########################################### CREATE prime tags for object to send around allowedLength<-175 Nsubobjects<-round(length(abundUsedSpecies[[1]])/allowedLength)+1 object.ids <- list.integers[ (noChains.internal+1):(noChains.internal + 4 + Nsubobjects) ] ### 4 objcts for logL, swap message, untempered , species PLUS as many as necessary for abundances if (ind%%2 == oddFlag%%2) { ###when oddFlag zero , the following code concerns even-numbered slaves. For oddFlag 1, it concerns odd-numbered slaves. ind.partner<-ind+1 if (0 1e6) stop("n too large") primes <- rep(TRUE, n) primes[1] <- FALSE last.prime <- 2L for(i in last.prime:floor(sqrt(n))) { primes[seq.int(2L*last.prime, n, last.prime)] <- FALSE last.prime <- last.prime + min(which(primes[(last.prime+1):n])) } which(primes) } list.integers <- sieve(1000) node.ids <- list.integers[ 1:noChains ] mpi.spawn.Rslaves(nslaves = noChains) #number of slaves to spawn, should be equal to individual chains # In case R exits unexpectedly, have it automatically clean up # resources taken up by Rmpi (slaves, memory, etc...) .Last <- function(){ if (is.loaded("mpi_initialize")){ if (mpi.comm.size(1) > 0){ print("Please use mpi.close.Rslaves() to close slaves.") mpi.close.Rslaves() } print("Please use mpi.quit() to quit R") .Call("mpi_finalize", PACKAGE='metaMix') } } pij.sparse.mat<-cbind(pij.sparse.mat, "unknown"=gen.prob.unknown) #rm(step2) gc() allSpecies<-ordered.species[,c("taxonID", "samplingWeight")] lenSp<-nrow(allSpecies) lpenalty<-computePenalty(readSupport=readSupport, readWeights=read.weights, pUnknown=gen.prob.unknown) ### penalty for accepting a new species ### EMiter EMiter<-10 ### PT parameters exchangeInterval<-1 ###leave chains run in parallel for that many iterations before attempting exchange #ExternIter<-5*(nrow(ordered.species)) ### make chains communicate 1 times if (bypass==FALSE){ if (iter > 5*(nrow(ordered.species))) { ### choose the number of iterations that is greater between 1) the user-defined number 2) the product of the number of potential species times 5 ExternIter<-iter } else { ExternIter<-5*(nrow(ordered.species)) ### make chains communicate 1 times } } else { ExternIter<-iter } TotalIter<-exchangeInterval * ExternIter ##Tempering Vector --Power Decay temper<-vector() K<-0.001 a<-3/2 for (n in 2:noChains){ temper[1]<-1 temper[n]<-(temper[n-1]-K)^a } for (i in 1:noChains) {names(temper)[i]<- paste("slave",i, sep="")} ###names ### flag for adding /removing species stepAdd<-vector(mode = "logical") #### broadcast necessary objects/functions to slaves mpi.bcast.Robj2slave(exchangeInterval) mpi.bcast.Robj2slave(ExternIter) mpi.bcast.Robj2slave(TotalIter) mpi.bcast.Robj2slave(list.integers) mpi.bcast.Robj2slave(node.ids) mpi.bcast.Robj2slave(ordered.species) mpi.bcast.Robj2slave(read.weights) mpi.bcast.Robj2slave(pij.sparse.mat) mpi.bcast.Robj2slave(lpenalty) mpi.bcast.Robj2slave(EM) mpi.bcast.Robj2slave(allSpecies) mpi.bcast.Robj2slave(lenSp) mpi.bcast.Robj2slave(EMiter) mpi.bcast.Robj2slave(noChains) mpi.bcast.Robj2slave(temper) mpi.bcast.Robj2slave(gen.prob.unknown) ##########################---------------------------------------SINGLE CHAIN FUNCTION -----------------------------------------------------------------------------------------------####################### singleChain <- function(TotalIter, exchangeInterval){ if (file.exists('~/.Rprofile')) source('~/.Rprofile') print(.libPaths()) ind <- mpi.comm.rank() # Each slave gets its own copy of ind and chain based on mpi process rank print(ind) estimNew<-matrix(0, nrow=TotalIter, ncol=1) ### Create matrix that will hold the estimator of the log-likelihood estimNew[1,]<- sum(read.weights[,"weight"])*log(gen.prob.unknown)*temper[ind] print(estimNew[1,]) presentSpecies<-"unknown" ## create object that receives the species deemed as present, from previous (swapInterv*j) iteration. abundUsedSp<-c("unknown"=1) ### Create 2 lists. One that holds species names and one with their abundances. Each list has 2 elements. Element1: present species and Element2: tentative species being explored in current iteration. speciestoUse<-list("presentSp"=presentSpecies, "tentativeSp"=NULL) abundUsedSpecies<-list("presentSp"= abundUsedSp, "tentativeSp"=NULL) message("\nThis is the temperature for this slave") print(temper[ind]) ### create matrix to hold info on which species was added or removed, which species were present and logL , through iterations record<-matrix(0, ncol=(5+lenSp), nrow=(TotalIter)) record<-as.data.frame(record) colnames(record)<-c("Iter", "Move", "Candidate Species", allSpecies[,1], "unknown", "logL") record[,1]=1:(TotalIter) record[1, presentSpecies]<-1 record[1,(5+lenSp)]<-estimNew[1,] ###last colum is logL swaps.attempted<-0 swaps.accepted<-0 oddFlag<-0 ################ ----------------------------------- Begin MCMC (within single chain) ------------------------------------------------------------------------------------------############ for (i in 2:TotalIter) { cat('\n',i,'\n') ### temporary - debugging purposes #### Create 3 functions to use repeatedly in adding/removing species steps. ######################### 1a. For add step: species I sample my candidate species from. potentialSpecies<-function() { toChooseFrom <- allSpecies[,1][!(allSpecies[,1] %in% speciestoUse[[1]])] ### Species remaining after omitting "present species" toChooseFrom<-as.character(toChooseFrom) potentialSp<- allSpecies[allSpecies$taxonID %in% toChooseFrom,] resultPS<-list("potentialSp"=potentialSp, "toChooseFrom"=toChooseFrom) return(resultPS) } ######################## 1b. For add step, sample candidate organism to add and create object for tentative species moveAdd<-function() { randSp <- sample(as.character(potentialSp[,1]),1, prob=potentialSp[,2]) ### choose random species, weights need not sum to one. Here weights are based on intial read counts. cat('Add species', randSp, '\n') ### temporary - debugging purposes speciestoUse[[2]]<-c(randSp, speciestoUse[[1]]) ### tentative present species, to use in Gibbs below. record[i, 2]<- "Add" ### record info on species we are adding record[i,3]<- randSp result<-list("record"=record, "speciestoUse"=speciestoUse) return(result) } ######################## 2. For remove step, sample candidate organism to remove and create object for tentative species moveRemove<-function() { toremoveFrom <- speciestoUse[[1]][!(speciestoUse[[1]]%in%"unknown")] ### species set from which to remove (i.e present ones bar unknown) toremoveFrom<-as.character(toremoveFrom) removeProb<-(1/abundUsedSpecies[[1]][toremoveFrom])/sum(1/abundUsedSpecies[[1]][toremoveFrom]) ###### sampling weight inversely proportional to assigned read counts. ###Flatten removal probabilities percentiles<-quantile(removeProb, probs=c(0.2, 0.8)) removeProb[which(removeProb >= percentiles["80%"])] <- percentiles["80%"] removeProb[which(removeProb <= percentiles["20%"])] <- percentiles["20%"] ### sample candidate species to remove randSp<-sample(toremoveFrom, 1, prob=removeProb ) ### weights need not sum to one cat('Remove species', randSp, '\n') ### temporary - debugging purposes speciestoUse[[2]] <- speciestoUse[[1]][!(speciestoUse[[1]] %in% randSp)] ### tentative present species, to use in Gibbs below. record[i, 2]<- "Remove" ### record info on species we are adding record[i,3]<- randSp result<-list("record"=record, "speciestoUse"=speciestoUse) return(result) } addStep <-0.5 ####proability of doing add step ######################################################## Add species ######################################## if (runif(1)<= addStep) { resultPS<-potentialSpecies() potentialSp<-as.data.frame(resultPS$potentialSp) toChooseFrom<-as.character(resultPS$toChooseFrom) if (length(toChooseFrom) != 0L){ result<-moveAdd() speciestoUse<-result$speciestoUse record<-result$record } else { ################## ### If pool of species to add empty, go to remove step message("No more species to choose from, all are kept as present.") result<-moveRemove() speciestoUse<-result$speciestoUse record<-result$record addStep<-0 ### so do remove step with prob=1 } } ###close if runif(1)<=addStep else { ################################################### Remove species ################################################# toremoveFrom <- speciestoUse[[1]][!(speciestoUse[[1]]%in%"unknown")] ### species set from which to remove (i.e present ones bar unknown) toremoveFrom<-as.character(toremoveFrom) #### First check that more than 1 species are present, so don't risk of remaining only with X bin and wasting iteration. if (length(toremoveFrom) > 1) { result<-moveRemove() speciestoUse<-result$speciestoUse record<-result$record } else if (length(speciestoUse[[1]])==1) { #### speciestoUse[[1]]==1 when only unknown bin is there / We can only add message("We cannot remove, we only have unknown bin") potentialSp<-allSpecies result<-moveAdd() speciestoUse<-result$speciestoUse record<-result$record addStep <- 1 ### so do add step with prob=1 } else { ### we are adding species instead. Removing would leave us just with X-bin again. message("\nCannot remove a species, so instead we add\n") ### temporary resultPS<-potentialSpecies() potentialSp<-as.data.frame(resultPS$potentialSp) toChooseFrom<-as.character(resultPS$toChooseFrom) result<-moveAdd() speciestoUse<-result$speciestoUse record<-result$record addStep <- 1 } } ###close else (remove species) noSpecies<-length(speciestoUse[[2]]) print(noSpecies) hyperP<-rep(1, noSpecies) startW<-rdirichlet(1, hyperP) output100Tent<-EM(pij=pij.sparse.mat, iter=EMiter, species=speciestoUse[[2]], abund=startW, readWeights = read.weights) ### EM function estimator <- output100Tent$logL[EMiter,2] + (noSpecies * lpenalty) #### penalise likelihood message("EM took: ", output100Tent$RunningTime) mean1<-as.numeric(output100Tent$abundances[EMiter,2:(noSpecies+1)]) names(mean1)<-names(output100Tent$abundances[EMiter,2:(noSpecies+1)]) abundUsedSpecies[[2]]<-mean1 estimNew[i,]<-estimator*temper[ind] ###tempered likelihood message('\n', estimNew[i,] , ' ', estimNew[i-1,]) ### temporary print - which values am I comparing? ####### flag of adding/removing if (record[i,2]=="Add") { stepAdd<-TRUE } else {stepAdd<-FALSE} removeStep <- 1 - addStep ##remove step if (stepAdd) { candidateAdd<-allSpecies[allSpecies[,1]==(as.character(record[i,3])),2] removeProba<-(1/abundUsedSpecies[[2]])/sum(1/abundUsedSpecies[[2]]) ###### sampling weight inversely proportional to size. Tentative Species ###Flattening the sampling probabilities percentiles<-quantile(removeProba, probs=c(0.2, 0.8)) removeProba[which(removeProba >= percentiles["80%"])] <- percentiles["80%"] removeProba[which(removeProba <= percentiles["20%"])] <- percentiles["20%"] candidateRemove<-removeProba[as.character(record[i,3])] print(candidateRemove) print(candidateAdd) if (runif(1) < min( 1, exp(estimNew[i] - estimNew[i-1] + log(removeStep) - log(addStep) + log(candidateRemove) - log(candidateAdd) ))) { ### accept "add species" with prob min{1, P(D|i)*P(removeSpecies)*P(remove Specific Species)/P(D|i-1)*P(addSpecies)*P(add specific species) ######## Accept move ####### estimNew[i,]<-estimNew[i,] ### if move is accepted, record new logL speciestoUse[[1]]<-speciestoUse[[2]] ### if move is accepted, tentative species becomes present species. abundUsedSpecies[[1]]<-abundUsedSpecies[[2]] ### -->>-->>-- , abundances of new set of species are kept cat('Present species become:', speciestoUse[[1]], '\n') } else { ######### Reject Move ######## estimNew[i,]<-estimNew[i-1,] ### if move is rejected, record previous logL speciestoUse[[1]]<-speciestoUse[[1]] ### if move is rejected, keep present species as it is. abundUsedSpecies[[1]]<-abundUsedSpecies[[1]] cat('Present species remain:', speciestoUse[[1]], '\n') ### temporary } } ### close if(stepAdd==TRUE) else { ######################################## type of move was to remove species ############## removeProba<-(1/abundUsedSpecies[[1]])/sum(1/abundUsedSpecies[[1]]) ###### sampling weight inversely proportional to size. Do this for present Species candidateRemove<-removeProba[as.character(record[i,3])] candidateAdd<-allSpecies[allSpecies[,1]==(as.character(record[i,3])),2] if (runif(1) < min( 1, exp(estimNew[i] - estimNew[i-1] + log(addStep) - log(removeStep) + log(candidateAdd) - log(candidateRemove) ))) {############# Accept "remove species" estimNew[i,]<-estimNew[i,] speciestoUse[[1]]<-speciestoUse[[2]] ### tentative species becomes present species. abundUsedSpecies[[1]]<-abundUsedSpecies[[2]] cat('Present species become:', speciestoUse[[1]], '\n') } else { ######## Reject Move ########### estimNew[i,]<-estimNew[i-1,] speciestoUse[[1]]<-speciestoUse[[1]] abundUsedSpecies[[1]]<-abundUsedSpecies[[1]] cat('Present species remain:', speciestoUse[[1]], '\n') } } ###close else (i.e (stepAdd==FALSE)) #################################edw tha kanw attempt to direct swap between slaves, without going through master if( i%%exchangeInterval == 0 ){ ### every nth (2nd for now) iteration message("\n\nTime to attempt an exchange") oddFlag<-oddFlag+1 swap<-0 estim.current<-estimNew[i,]/temper[ind] ######### need untempered logL ########################################### CREATE prime tags for object to send around allowedLength<-175 Nsubobjects<-round(length(abundUsedSpecies[[1]])/allowedLength)+1 object.ids <- list.integers[ (noChains+1):(noChains + 4 + Nsubobjects) ] ### 4 objcts for logL, swap message, untempered , species PLUS as many as necessary for abundances if (ind%%2 == oddFlag%%2) { ###when oddFlag zero , the following code concerns even-numbered slaves. For oddFlag 1, it concerns odd-numbered slaves. ind.partner<-ind+1 if (0>= options(tidy=TRUE, width=80) @ \section{What is new} \textbf{Version 0.2:} Added Bayes Factor computation. \textbf{Version 0.3:} Allow user to specify number of MCMC iterations (Step 3) and Burn-in percentage (Step 4). Due to NCBI phasing out GI numbers, added support for protein accession identifier file for mapping to taxon (STEP1). Fixed bug in step4 for Bayes Factor calculation when only one species is present, that is only human and unknown. Also fixed bug with semi-colon separated taxonids in custom BLAST format, as well as NAs (STEP 1). Replaced deprecated cBind function with cbind. \section{Installation} You will need to have openMPI (Message Passage Interface) installed to be able to install the R package \verb!Rmpi!, which provides the interface to openMPI. \verb!Rmpi! is one of the package dependencies, along with \verb!data.table!, \verb!Matrix!, \verb!gtools! and \verb!ggplot2!. You can check whether you have openMPI installed using the command \verb!mpirun! and you can find more information here:\\ \url{http://www.open-mpi.org/software/ompi} \section{Introduction} metaMix is a tool designed to identify the set of species most likely to be present in a metagenomic community. metaMix also estimates their relative abundances and resolves ambiguous assignments by considering all reads simultaneously. metaMix considers the competing models that could accommodate our observed data, i.e the BLASTx results and compares them. The different mixture models represent different sets of species being present in the sample. The method is structured in the following manner: in the first instance we assume that a set of species is present in the sample and we estimate the parameters given the data. At the next step, we randomly add or remove a species and fit this new model. The process is iterated in order to explore the model state space and we record the MCMC choices over time. Additionally we parallelise the process, running $n$ (usually 12) parallel chains, allowing exchange of information between them. Using this Bayesian Mixture Model framework, we finally perform model averaging in order to account for model uncertainty. The initial motivation for developing metaMix was the analysis of deep transcriptome sequencing datasets, with a particular focus on viral pathogen detection. However the ideas are applicable more generally to all types of metagenomics mixtures. Some bionformatics processing is required prior to using metaMix. This is usually filtering out the low quality, duplicate and host reads. The user may wish to attempt some assembly step as well prior to resolving the mixture; however this step is not necessary. More importantly, the similarities between the short reads (and/or contigs) and a reference database must be provided. At the end of the analysis, the user will obtain a probabilistic summary of present species and some supporting plots. The implementation of the ideas described here is computationally intensive and requires a supercomputer. However for the purposes of this tutorial, we demonstrate the usage on a toy example and all the steps can be performed on a single machine. %\newpage \section{Tutorial} \subsection*{Step1} The work described here is similarity-based, therefore the starting point is to obtain the sequence similarity between a query and a target sequence. The obvious choice for this is BLAST. Both nucleotide and amino acid similarities are supported. We demonstrate the use of metaMix working with the latter, i.e we have used BLASTx. \begin{description} \item[Default BLAST output] The default output tabular file is supported, obtained using \verb!-outfmt 6! in the BLAST command. <>= blastx -db referenceDB -query input.fa -outfmt 6 -max_target_seqs 10 @ The default output file has the following fields:\\ \verb!Query ID!, \verb!Subject ID!, \verb!% Identity!, \verb!Alignment Length!, \verb!Mismatches!, \verb!Gap Openings!, \verb!Query Start!, \verb!Query End!, \verb!Subject Start!, \verb!Subject End!, \verb!E-value!, \verb!Bit Score!. <>= library(metaMix) ###Location of input files. datapath <- system.file("extdata", package="metaMix") blastOut.default<-file.path(datapath, "blastOut_default.tab") read.table(blastOut.default, nrows=2, sep="\t") @ metaMix needs information on the read lengths as well as a file mapping the gi identifiers to the taxon identifiers. These are not included in the default output of BLAST, therefore should be provided as additional arguments. <>= read.lengths<-file.path(datapath, "read_lengths.tab") read.weights<-file.path(datapath, "read_weights.tab") taxon.file<-file.path(datapath, "gi_taxid_prot_example.dmp") read.table(read.lengths, nrows=2, sep="\t") read.table(read.weights, nrows=2, sep="\t") read.table(taxon.file, nrows=2, sep="\t") @ \item[Custom BLAST output] Alternatively, metaMix accepts a custom BLAST output file that has already incorporated the read lengths and the taxon identifiers. At the moment, only the output that is produced by the following command is supported: <>= blastx -db referenceDB -query input.fa -max_target_seqs 10 -outfmt "6 qacc qlen sacc slen mismatch bitscore length pident evalue staxids" @ Therefore the fields are \\ \verb!Query ID!, \verb!Query Length!, \verb!Subject ID!, \verb!Subject Length!, \verb!Mismatches!, \verb!Bit Score!, \verb!Alignment Length!, \verb!%Identity!, \verb!E-value!, \verb!Taxon ID!. <>= blastOut.custom<-file.path(datapath, "blastOut_custom.tab") read.table(blastOut.custom, nrows=2, sep="\t") @ \end{description} \vspace{5mm} The first step in the analysis is to compute the read-species generative probabilities based on the BLASTx data. We achieve this by using the \verb!generative.prob()! function. In this instance we will work with the custom BLAST output file. <>= step1 <-generative.prob(blast.output.file = blastOut.custom, contig.weight.file=read.weights, blast.default=FALSE, outDir=NULL) @ where \verb!blast.default! denotes whether we are working with the BLAST default output (TRUE) or with the specified above custom output (FALSE). \verb!blast.output.file! is the tabular BLASTx output file. If we are working with unassembled reads, we can omit the argument \verb!contig.weight.file! as the weight is set by default to be 1, same for all reads. However if an assembly step has been performed, as in this example, we need to provide information on the number of reads that make up each contig. This will be a two column tab-separated file, where the first column is the contig identifier and the second the number of reads. Finally \verb!outDir! is the directory where the results are written and where an object from each step is saved. When it is set to NULL no objects will be saved. \vspace{3mm} \emph{NOTE}: If we were using the default BLAST output the command would look like so: <>= step1 <-generative.prob(blast.output.file = blastOut.default, read.length.file=read.lengths, contig.weight.file=read.weights, gi.taxon.file = taxon.file, blast.default=TRUE, outDir=NULL) @ The information missing from the BLAST file is now provided with two extra arguments: \verb!read.length.file! can be either the file mapping each read to its sequence length or a numerical value, representing the average read length (default value=100). \verb!'gi_taxid_prot.dmp'! is a taxonomy file, mapping each protein gi identifier to the corresponding taxon identifier. It can be downloaded from \\ \url{ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_prot.dmp.gz} \\ The function \verb!generative.prob! creates a list of five elements. One of these is a sparse matrix \verb!pij.sparse.mat! where each row corresponds to one read and each column to a species. The value of the cell is the generative probability $p_{ij}$. Additionally a \verb!data.frame! with all the species that correspond to the proteins in the BLASTx output file. Finally the \verb!read.weights!, \verb!gen.prob.unknown! and \verb!outDir! are the other three elements of the list \verb!step1!, carried forward to be used in the second step. <>= ###The resulting list consists of five elements names(step1) ### The sparse matrix of generative probs. step1$pij.sparse.mat[1:5,c("374840", "258", "unknown")] ### There are that many potential species in the sample: nrow(step1$ordered.species) @ \subsection*{Step2} Having the generative probabilities from the previous step (generative.prob), we could proceed directly with the PT MCMC to explore the state space. However, typically the number of all potential species $S$ is large. We are therefore interested in reducing the size of the species pool, from the thousands to the low hundreds. In this simple example we have only 224 organisms but still we attempt to reduce it for demonstrating the usage of the function. We achieve this by fitting a mixture model with 224 categories, considering all 224 potential species simultaneously. Post fitting, we retain only the species categories that are not empty, that is the categories that have at least one read assigned to them. The required argument is simply the list created in the first step, i.e using the \verb!generative.prob! function. <>= step2 <- reduce.space(step1=step1) @ Alternatively, if the list created in the first step was saved in a ``step1.RData'' file, a character string containing the path to the file could be provided, i.e <>= step2 <- reduce.space(step1="/pathtoFile/step1.RData") @ To speed up computations, we have already performed step2 and saved the output which we will now load: <>= data(step2) @ <>= ##These are the elements of the step2 list. names(step2) ## After this approximating step, there are now that many potential species in ##the sample: nrow(step2$ordered.species) ## And these are: step2$ordered.species @ We see that even though we started with 224 potential organisms, we reduced the species space to 7. Bear in mind that this a simple example and the usual scenario is to move from thousands of species to hundreds. \subsection*{Step3} In this step, the different models are considered and compared. The space exploration by the parallel tempering MCMC is implemented by the function \verb!parallel.temper!: <>= step3<-parallel.temper(step2=step2) @ The required argument is simply the list created in the second step (or the character string containing the path to the respective .RData file where the step2 list was saved to), i.e using the \verb!reduce.space! function. An important optional argument of this function is \verb!readSupport!. For the type of data we analyse (i.e from mostly sterile human tissues) we expect that parsimonious models with a limited number of species are more likely. Therefore our default model prior uses a penalty limiting the number of species in the model. We approximate this penalty factor based on \verb!readSupport!, which represents the species read support required from the user in order to believe in the presence of a species in the sample. The default value is 10 and it is suitable for when we want to detect rare signal. We have found this value to work well in most human RNA-seq datasets. Same as before, we have already performed step3 and saved the output which we now load: <>= data(step3) @ <>= ##These are the elements of the step3 list. names(step3) @ <>= ## Steps MCMC took during some iterations. step3$result$slave1$record[10:15,] @ For each parallel chain, the MCMC trajectory has been recorded. There is information on what steps were proposed, which were accepted or rejected throughout the iterations. For example at iteration 10, removing species 645687 was proposed but not accepted, as denoted by the 1 in the column 645687. We can also see that between iterations 13 and 14 an exchange of the sets of species between Chain 1 and Chain 2 occurred. At iter. 13 species 2 was present, while at the next one, it no longer is there. That means that the attempt at swapping the values of the two neighboring chains was successful. This information is also recorded, i.e how many swaps were attempted and how many accepted. Each chain will produce a log file that will be printed in your working directory. \subsection*{Step4} Having explored the different possible models, the final step is to perform model averaging. We study the MCMC choices for Chain 1 and produce a probabilistic summary for the presence of the species. <>= ## Location of the taxonomy names file. taxon.file<-file.path(datapath, "names_example.dmp") step4<-bayes.model.aver(step2=step2, step3=step3, taxon.name.map=taxon.file) @ The required arguments are the lists created in the second and third steps, i.e using the \verb!reduce.space! and the \verb!parallel.temper! functions. Additionally the taxonomy names file 'names.dmp', which can be downloaded and extracted from \url{ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz} <>= ##These are the elements of the step4 list. names(step4) ##This is the species summary print(step4$presentSpecies.allInfo) @ We find four species with a posterior probability greater than 0.9 (default value), plus the unknown category. Finally we also produce log-likelihood traceplots for Chain 1. We discard the first 20\% of the iterations as burn-in and we look at the mixing of the chain. Due to having very few iterations for this toy example, the produced traceplot would not be representative or insightful. Instead we present below the log-likelihood traceplot from a real dataset. <>= PTastro<-file.path(datapath, "PT_plots.RData") load(PTastro) nIter<- length(PTresult$result$slave1$record[,'logL']) plot(PTresult$result$slave1$record[(nIter/5):nIter,'logL'], type='l', col='dodgerblue', xlab='Last 80% of iterations', ylab='Log-likelihood', main='Parallel Tempering - Coldest Chain', lwd=1.5) @ \section{Submit jobs on cluster compute servers} In order to run steps 1, 2 and 4 of metaMix (i.e \verb!generative.prob!, \verb!reduce.space!, \verb!bayes.model.aver!) efficiently, these should be submitted as jobs to a compute cluster. In our experience, 4G of memory, 1 hour of wall clock time and 1 processor should be plenty. In order to run the parallel tempering efficiently (step3), we need at least 12 parallel chains. I usually request 6 or 12 threads, each with 2G of RAM. The wall clock time depends on how many iterations will be performed. A larger number of reads mean that the computations will become slower. We typically submit all 4 steps in one go using one submission script. I usually assess the size of the dataset, but 12 hours for all 4 steps should be safe. This is a sample submission script, it requests 6 processors on 1 node for 12 hours (more processors, less time necessary). \begin{verbatim} #!/bin/bash #$ -S /bin/bash #$ -o cluster/out #$ -e cluster/error #$ -cwd #$ -pe smp 6 #$ -l tmem=2G,h_vmem=2G #$ -l h_rt=12:00:00 #$ -V #$ -R y mpirun -np 1 R-3.0.1/bin/R --slave CMD BATCH --no-save --no-restore allsteps.R \end{verbatim} an example allsteps.R looks like this: \begin{verbatim} library(metaMix) step1<-generative.prob(blast.output.file="sample_diamond.tab", read.length.file="read_lengths.tab", contig.weight.file="contig_weights.tab", outDir="./", gi.taxon.file="gi_taxid_prot.dmp", blast.default=TRUE, gi.or.prot="gi") step2<-reduce.space(step1="step1.RData") step3<-parallel.temper(step2="step2.RData") step4<-bayes.model.aver(step2="step2.RData", step3="step3.RData", taxon.name.map="names.dmp") \end{verbatim} \section{Technical information about the R session} <>= sessionInfo() @ \end{document} metaMix/vignettes/guide.Rnw.bck0000644000176200001440000003651613403500106016214 0ustar liggesusers%\VignetteEngine{knitr::knitr} %\VignetteIndexEntry{metaMix User Guide} \documentclass[a4paper]{article} \usepackage[margin=1.5cm,includefoot,footskip=30pt]{geometry} \usepackage[colorlinks=true]{hyperref} \usepackage{fullpage} \title{metaMix user guide} \author{Sofia Morfopoulou} \date{\today} \begin{document} \maketitle %\tableofcontents %\newpage <>= options(tidy=TRUE, width=80) @ \section{Installation} You will need to have openMPI (Message Passage Interface) installed to be able to install the R package \verb!Rmpi!, which provides the interface to openMPI. \verb!Rmpi! is one of the package dependencies, along with \verb!data.table!, \verb!Matrix!, \verb!gtools! and \verb!ggplot2!. You can check whether you have openMPI installed using the command \verb!mpirun! and you can find more information here:\\ \url{http://www.open-mpi.org/software/ompi} \section{Introduction} metaMix is a tool designed to identify the set of species most likely to be present in a metagenomic community. metaMix also estimates their relative abundances and resolves ambiguous assignments by considering all reads simultaneously. metaMix considers the competing models that could accommodate our observed data, i.e the BLASTx results and compares them. The different mixture models represent different sets of species being present in the sample. The method is structured in the following manner: in the first instance we assume that a set of species is present in the sample and we estimate the parameters given the data. At the next step, we randomly add or remove a species and fit this new model. The process is iterated in order to explore the model state space and we record the MCMC choices over time. Additionally we parallelise the process, running $n$ (usually 12) parallel chains, allowing exchange of information between them. Using this Bayesian Mixture Model framework, we finally perform model averaging in order to account for model uncertainty. The initial motivation for developing metaMix was the analysis of deep transcriptome sequencing datasets, with a particular focus on viral pathogen detection. However the ideas are applicable more generally to all types of metagenomics mixtures. Some bionformatics processing is required prior to using metaMix. This is usually filtering out the low quality, duplicate and host reads. The user may wish to attempt some assembly step as well prior to resolving the mixture; however this step is not necessary. More importantly, the similarities between the short reads (and/or contigs) and a reference database must be provided. At the end of the analysis, the user will obtain a probabilistic summary of present species and some supporting plots. The implementation of the ideas described here is computationally intensive and requires a supercomputer. However for the purposes of this tutorial, we demonstrate the usage on a toy example and all the steps can be performed on a single machine. %\newpage \section{Tutorial} \subsection*{Step1} The work described here is similarity-based, therefore the starting point is to obtain the sequence similarity between a query and a target sequence. The obvious choice for this is BLAST. Both nucleotide and amino acid similarities are supported. We demonstrate the use of metaMix working with the latter, i.e we have used BLASTx. \begin{description} \item[Default BLAST output] The default output tabular file is supported, obtained using \verb!-outfmt 6! in the BLAST command. <>= blastx -db referenceDB -query input.fa -outfmt 6 -max_target_seqs 10 @ The default output file has the following fields:\\ \verb!Query ID!, \verb!Subject ID!, \verb!% Identity!, \verb!Alignment Length!, \verb!Mismatches!, \verb!Gap Openings!, \verb!Query Start!, \verb!Query End!, \verb!Subject Start!, \verb!Subject End!, \verb!E-value!, \verb!Bit Score!. <>= library(metaMix) ###Location of input files. datapath <- system.file("extdata", package="metaMix") blastOut.default<-file.path(datapath, "blastOut_default.tab") read.table(blastOut.default, nrows=2, sep="\t") @ metaMix needs information on the read lengths as well as a file mapping the gi identifiers to the taxon identifiers. These are not included in the default output of BLAST, therefore should be provided as additional arguments. <>= read.lengths<-file.path(datapath, "read_lengths.tab") read.weights<-file.path(datapath, "read_weights.tab") taxon.file<-file.path(datapath, "gi_taxid_prot_example.dmp") read.table(read.lengths, nrows=2, sep="\t") read.table(read.weights, nrows=2, sep="\t") read.table(taxon.file, nrows=2, sep="\t") @ \item[Custom BLAST output] Alternatively, metaMix accepts a custom BLAST output file that has already incorporated the read lengths and the taxon identifiers. At the moment, only the output that is produced by the following command is supported: <>= blastx -db referenceDB -query input.fa -max_target_seqs 10 -outfmt "6 qacc qlen sacc slen mismatch bitscore length pident evalue staxids" @ Therefore the fields are \\ \verb!Query ID!, \verb!Query Length!, \verb!Subject ID!, \verb!Subject Length!, \verb!Mismatches!, \verb!Bit Score!, \verb!Alignment Length!, \verb!%Identity!, \verb!E-value!, \verb!Taxon ID!. <>= blastOut.custom<-file.path(datapath, "blastOut_custom.tab") read.table(blastOut.custom, nrows=2, sep="\t") @ \end{description} \vspace{5mm} The first step in the analysis is to compute the read-species generative probabilities based on the BLASTx data. We achieve this by using the \verb!generative.prob()! function. In this instance we will work with the custom BLAST output file. <>= step1 <-generative.prob(blast.output.file = blastOut.custom, contig.weight.file=read.weights, blast.default=FALSE, outDir=NULL) @ where \verb!blast.default! denotes whether we are working with the BLAST default output (TRUE) or with the specified above custom output (FALSE). \verb!blast.output.file! is the tabular BLASTx output file. If we are working with unassembled reads, we can omit the argument \verb!contig.weight.file! as the weight is set by default to be 1, same for all reads. However if an assembly step has been performed, as in this example, we need to provide information on the number of reads that make up each contig. This will be a two column tab-separated file, where the first column is the contig identifier and the second the number of reads. Finally \verb!outDir! is the directory where the results are written and where an object from each step is saved. When it is set to NULL no objects will be saved. \vspace{3mm} \emph{NOTE}: If we were using the default BLAST output the command would look like so: <>= step1 <-generative.prob(blast.output.file = blastOut.default, read.length.file=read.lengths, contig.weight.file=read.weights, gi.taxon.file = taxon.file, blast.default=TRUE, outDir=NULL) @ The information missing from the BLAST file is now provided with two extra arguments: \verb!read.length.file! can be either the file mapping each read to its sequence length or a numerical value, representing the average read length (default value=100). \verb!'gi_taxid_prot.dmp'! is a taxonomy file, mapping each protein gi identifier to the corresponding taxon identifier. It can be downloaded from \\ \url{ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_prot.dmp.gz} \\ The function \verb!generative.prob! creates a list of five elements. One of these is a sparse matrix \verb!pij.sparse.mat! where each row corresponds to one read and each column to a species. The value of the cell is the generative probability $p_{ij}$. Additionally a \verb!data.frame! with all the species that correspond to the proteins in the BLASTx output file. Finally the \verb!read.weights!, \verb!gen.prob.unknown! and \verb!outDir! are the other three elements of the list \verb!step1!, carried forward to be used in the second step. <>= ###The resulting list consists of five elements names(step1) ### The sparse matrix of generative probs. step1$pij.sparse.mat[1:5,c("374840", "258", "unknown")] ### There are that many potential species in the sample: nrow(step1$ordered.species) @ \subsection*{Step2} Having the generative probabilities from the previous step (generative.prob), we could proceed directly with the PT MCMC to explore the state space. However, typically the number of all potential species $S$ is large. We are therefore interested in reducing the size of the species pool, from the thousands to the low hundreds. In this simple example we have only 224 organisms but still we attempt to reduce it for demonstrating the usage of the function. We achieve this by fitting a mixture model with 224 categories, considering all 224 potential species simultaneously. Post fitting, we retain only the species categories that are not empty, that is the categories that have at least one read assigned to them. The required argument is simply the list created in the first step, i.e using the \verb!generative.prob! function. <>= step2 <- reduce.space(step1=step1) @ Alternatively, if the list created in the first step was saved in a ``step1.RData'' file, a character string containing the path to the file could be provided, i.e <>= step2 <- reduce.space(step1="/pathtoFile/step1.RData") @ To speed up computations, we have already performed step2 and saved the output which we will now load: <>= data(step2) @ <>= ##These are the elements of the step2 list. names(step2) ## After this approximating step, there are now that many potential species in ##the sample: nrow(step2$ordered.species) ## And these are: step2$ordered.species @ We see that even though we started with 224 potential organisms, we reduced the species space to 7. Bear in mind that this a simple example and the usual scenario is to move from thousands of species to hundreds. \subsection*{Step3} In this step, the different models are considered and compared. The space exploration by the parallel tempering MCMC is implemented by the function \verb!parallel.temper!: <>= step3<-parallel.temper(step2=step2) @ The required argument is simply the list created in the second step (or the character string containing the path to the respective .RData file where the step2 list was saved to), i.e using the \verb!reduce.space! function. An important optional argument of this function is \verb!readSupport!. For the type of data we analyse (i.e from mostly sterile human tissues) we expect that parsimonious models with a limited number of species are more likely. Therefore our default model prior uses a penalty limiting the number of species in the model. We approximate this penalty factor based on \verb!readSupport!, which represents the species read support required from the user in order to believe in the presence of a species in the sample. The default value is 10 and it is suitable for when we want to detect rare signal. We have found this value to work well in most human RNA-seq datasets. Same as before, we have already performed step3 and saved the output which we now load: <>= data(step3) @ <>= ##These are the elements of the step3 list. names(step3) @ <>= ## Steps MCMC took during some iterations. step3$result$slave1$record[10:15,] @ For each parallel chain, the MCMC trajectory has been recorded. There is information on what steps were proposed, which were accepted or rejected throughout the iterations. For example at iteration 10, removing species 645687 was proposed but not accepted, as denoted by the 1 in the column 645687. We can also see that between iterations 13 and 14 an exchange of the sets of species between Chain 1 and Chain 2 occurred. At iter. 13 species 2 was present, while at the next one, it no longer is there. That means that the attempt at swapping the values of the two neighboring chains was successful. This information is also recorded, i.e how many swaps were attempted and how many accepted. \subsection*{Step4} Having explored the different possible models, the final step is to perform model averaging. We study the MCMC choices for Chain 1 and produce a probabilistic summary for the presence of the species. <>= ## Location of the taxonomy names file. taxon.file<-file.path(datapath, "names_example.dmp") step4<-bayes.model.aver(step2=step2, step3=step3, taxon.name.map=taxon.file) @ The required arguments are the lists created in the second and third steps, i.e using the \verb!reduce.space! and the \verb!parallel.temper! functions. Additionally the taxonomy names file 'names.dmp', which can be downloaded and extracted from \url{ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz} <>= ##These are the elements of the step4 list. names(step4) ##This is the species summary print(step4$presentSpecies.allInfo) @ We find four species with a posterior probability greater than 0.9 (default value), plus the unknown category. Finally we also produce log-likelihood traceplots for Chain 1. We discard the first 20\% of the iterations as burn-in and we look at the mixing of the chain. Due to having very few iterations for this toy example, the produced traceplot would not be representative or insightful. Instead we present below the log-likelihood traceplot from a real dataset. <>= PTastro<-file.path(datapath, "PT_plots.RData") load(PTastro) nIter<- length(PTresult$result$slave1$record[,'logL']) plot(PTresult$result$slave1$record[(nIter/5):nIter,'logL'], type='l', col='dodgerblue', xlab='Last 80% of iterations', ylab='Log-likelihood', main='Parallel Tempering - Coldest Chain', lwd=1.5) @ \section{Submit jobs on cluster compute servers} In order to run steps 1, 2 and 4 of metaMix (i.e \verb!generative.prob!, \verb!reduce.space!, \verb!bayes.model.aver!) efficiently, these should be submitted as jobs to a compute cluster. In our experience, 4G of memory, 1 hour of wall clock time and 1 processor should be plenty. In order to run the parallel tempering efficiently, we need at least 12 parallel chains, each with at least 1G-2G of RAM. The wall clock time depends on how many iterations will be performed. Also a larger number of reads mean that the computations will become slower. We typically ask for 12 hours to be on the safe side. This is a sample submission script for the third step. It requests 12 processors on 1 node for 12 hours. \begin{verbatim} #!/bin/bash #$ -S /bin/bash #$ -o cluster/out #$ -e cluster/error #$ -cwd #$ -pe smp 12 #$ -l tmem=1.1G,h_vmem=1.1G #$ -l h_rt=12:00:00 #$ -V #$ -R y mpirun -np 1 R-3.0.1/bin/R --slave CMD BATCH --no-save --no-restore step3.R \end{verbatim} in step3.R, we simply load the object produced from \verb!reduce.space! and then call \verb!generative.prob!. 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The use of parallel Monte Carlo Markov chains for the exploration of the species space enables the identification of the set of species more likely to contribute to the mixture. License: GPL-3 LazyData: true SystemRequirements: Open MPI (>=1.4.3) RoxygenNote: 6.1.1 Encoding: UTF-8 NeedsCompilation: yes Packaged: 2019-02-07 15:41:40 UTC; sophia Repository: CRAN Date/Publication: 2019-02-11 16:20:03 UTC metaMix/man/0000755000176200001440000000000013403500106012421 5ustar liggesusersmetaMix/man/bayes.model.aver.Rd0000644000176200001440000000575513426035072016074 0ustar liggesusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/step4_bayesModelAver.R \name{bayes.model.aver} \alias{bayes.model.aver} \alias{bayes.model.aver.explicit} \title{Bayesian Model Averaging} \usage{ bayes.model.aver(step2, step3, taxon.name.map = NULL, poster.prob.thr = 0.9, burnin = 0.4) bayes.model.aver.explicit(result, pij.sparse.mat, read.weights, outDir, gen.prob.unknown, taxon.name.map = NULL, poster.prob.thr = 0.9, burnin = 0.4) } \arguments{ \item{step2}{list. The output from reduce.space(), i.e the second step of the pipeline. Alternatively, it can be a character string containing the path name of the ".RData" file where step2 list was saved.} \item{step3}{list. The output from parallel.temper(), i.e the third step of the pipeline. Alternatively, it can be a character string containing the path name of the ".RData" file where step3 list was saved.} \item{taxon.name.map}{The 'names.dmp' taxonomy names file, mapping each taxon identifier to the corresponding scientific name. It can be downloaded from \url{ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz}} \item{poster.prob.thr}{Posterior probability of presence of species threshold for reporting in the species summary.} \item{burnin}{Percentage of burn in iterations, default value is 0.4} \item{result}{The list produced by parallel.temper() (or paraller.temper.nucl()) . It holds a detailed record for each chain, what moves were proposed, which were accepted and which were rejected as well the log-likelihood through the iterations.} \item{pij.sparse.mat}{see ?reduce.space} \item{read.weights}{see ?reduce.space} \item{outDir}{see ?reduce.space} \item{gen.prob.unknown}{see ?reduce.space} } \description{ Perform Bayesian Model Averaging. We concentrate on the chain with temperature=1 , i.e the untempered posterior, to study the distribution over the model choices and perform model averaging. We consider as present the species that have a posterior probability greater than 0.9. We then fit the mixture model with these species in order to obtain relative abundances and read classification probabilities. A tab seperated file that has a species summary is produced, as well as log-likelihood traceplots and cumulative histogram plots. bayes.model.aver.explicit is the same function as bayes.model.aver with a more involved syntax. } \examples{ ## See vignette for more details \dontrun{ # Either load the object created by previous steps data(step2) ## example output of step2, i.e reduce.space() data(step3) ## example ouput of step3, i.e parallel.temper() step4<-bayes.model.aver(step2=step2, step3=step3, taxon.name.map="pathtoFile/taxon.file") # or alternatively point to the location of the step2.RData and step3.RData objects step4<-bayes.model.aver(step2="pathtoFile/step2.RData", step3="pathtoFile/step3.RData", taxon.name.map="pathtoFile/taxon.file") } } \keyword{bayes.model.aver} \keyword{bayes.model.aver.explicit} metaMix/man/step2.Rd0000644000176200001440000000046713426035072013766 0ustar liggesusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/metaMix-package.r \name{step2} \alias{step2} \title{Example output of reduce.space() for use in the vignette/examples} \format{A list with 6 elements} \description{ Example output of reduce.space() for use in the vignette/examples } metaMix/man/step3.Rd0000644000176200001440000000047513426035072013766 0ustar liggesusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/metaMix-package.r \name{step3} \alias{step3} \title{Example output of parallel.temper() for use in the vignette/examples} \format{A list with 2 elements} \description{ Example output of parallel.temper() for use in the vignette/examples } metaMix/man/generative.prob.Rd0000644000176200001440000001345313426035072016022 0ustar liggesusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/step1_preprocess.R \name{generative.prob} \alias{generative.prob} \alias{generative.prob.nucl} \title{Compute generative probabilities from BLAST output} \usage{ generative.prob(blast.output.file = NULL, read.length.file = 80, contig.weight.file = 1, gi.taxon.file = NULL, protaccession.taxon.file = NULL, gi.or.prot = "prot", gen.prob.unknown = 1e-06, outDir = NULL, blast.default = TRUE) generative.prob.nucl(blast.output.file = NULL, read.length.file = 80, contig.weight.file = 1, gi.taxon.file, gen.prob.unknown = 1e-20, outDir = NULL, genomeLength = NULL, blast.default = TRUE) } \arguments{ \item{blast.output.file}{This is the tabular BLASTx output format for generative.prob(), while it is the tabular BLASTn output format for generative.prob.nucl(). It can either be the default output format or a specific custom output format, incorporating read length and taxon identifier. Please see the vignette for column order and the exact BLAST command to use. You can also use DIAMOND instead of BLASTx which is much faster and produces default format according to BLAST default output specifications.} \item{read.length.file}{This argument can either be a file mapping each read to its length or a numerical value, representing the average read length.} \item{contig.weight.file}{This argument can either be a file where weights are assigned to reads and contigs. For unassembled reads the weight is equal to 1 while for contigs the weight should reflect the number of reads that assembled it.} \item{gi.taxon.file}{For generative.prob() this would be the 'gi_taxid_prot.dmp' taxonomy file, mapping each protein gi identifier to the corresponding taxon identifier. It can be downloaded from \url{ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_prot.dmp.gz} . For generative.prob.nucl() this would be the 'gi_taxid_nucl.dmp' taxonomy file, mapping each nucleotide gi identifier to the corresponding taxon identifier. It can be downloaded from \url{ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp.gz}.} \item{protaccession.taxon.file}{This parameter has been added as NCBI is phasing out the usage of GI identifiers. For generative.prob() this would be the prot.accession2taxid taxonomy file, mapping each protein accession identifier to the corresponding taxon identifier. It can be downloaded from \url{ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz}. I have found that it is useful to concatenate it with \url{ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/dead_prot.accession2taxid.gz} so you can search in both files for the protein identifier (sometimes obsolete sequences can still be present in latest RefSeq releases but not in taxonomy files and vice versa and these mismatches can cause loss of information). TODO add support for nucleotides as well.} \item{gi.or.prot}{This parameter specifies whether the user is using the GI identifiers or protein accession identifiers to map to taxon identifiers. Values are 'gi' or 'prot'. The default value is 'prot'.} \item{gen.prob.unknown}{User-defined generative probability for unknown category. Default value for generative.prob() is 1e-06, while for generative.prob.nucl() is 1e-20.} \item{outDir}{Output directory.} \item{blast.default}{logical. Is the input the default blast output tabular format? Default value is TRUE. That means that the BLAST output file needs to have the following fields:Query id, Subject id, percent identity, alignment length, mismatches, gap openings, query start, query end, subject start, subject end, e-value, bit score. Alternatively we can use the 'blast.default=FALSE' option, providing a custom blast output that has been produced using the option -outfmt '6 qacc qlen sacc slen stitle bitscore length pident evalue staxids'.} \item{genomeLength}{This is applicable only for generative.prob.nucl() . It is a file mapping each genome/nucleotide to its respective length. The file must be tab seperated and the first column the nucleotide gi identifier (integer) and the second the corresponding sequence length (integer). It will be used to correct the Poisson probabilities between each read and genome.} } \value{ step1: A list with five elements. The first one (pij.sparse.mat) is a sparse matrix with the generative probability between each read and each species. The second (ordered.species) is matrix containing all the potential species as recorded by BLAST, ordered by the number of reads. The third one (read.weights) is a data.frame mapping each contig to a weight which is essentially the number of reads that were used to assemble it. For unassembled reads the weight is equal to one. The fourth one is the generative probability for the unknown category (gen.prob.unknown), to be used in all subsequent steps. Finally we also record the output directory (outDir) where the results will be stored. } \description{ generative.prob() computes the probability for a read to be generated by a certain species, given that it originates from this species. The input for this function is the tabular BLAST output format, either default or custom. The function uses the recorded mismatches to produce a Poisson probability. generative.prob.nucl() for when we have nucleotide similarity, i.e we have performed BLASTn. } \examples{ # See vignette for more details \dontrun{ # When using custom BLAST output file step1 <-generative.prob(blast.output.file = "pathtoFile/blastOut.custom", blast.default=FALSE) # When using default BLAST output file step1 <-generative.prob(blast.output.file = "pathtoFile/blastOut.default", read.length.file="pathtoFile/read.lengths", contig.weight.file="pathtoFile/read.weights", gi.taxon.file = "pathtoFile/taxon.file") } } \keyword{generative.prob} \keyword{generative.prob.nucl} metaMix/man/parallel.temper.Rd0000644000176200001440000000645313426035072016021 0ustar liggesusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/step3_parallelTemper.R \name{parallel.temper} \alias{parallel.temper} \alias{parallel.temper.explicit} \title{Parallel Tempering MCMC} \usage{ parallel.temper(step2, readSupport = 10, noChains = 12, seed = 1, iter = 500, bypass = FALSE) parallel.temper.explicit(readSupport = 10, noChains = 12, pij.sparse.mat, read.weights, ordered.species, gen.prob.unknown, outDir, seed = 1, iter = 500, bypass = FALSE) } \arguments{ \item{step2}{list. The output from reduce.space(). Alternatively, it can be a character string containing the path name of the ".RData" file where step2 list was saved.} \item{readSupport}{The number of reads the user requires in order to believe in the presence of the species. It is used to compute the penalty factor. The default value is 10. We compute the logarithmic penalty value as the log-likelihood difference between two models: one where all N reads belong to the "unknown" category and one where r reads have a perfect match to some unspecified species and the remaining reads belong to the "unknown" category.} \item{noChains}{The number of parallel chains to run. The default value is 12.} \item{seed}{Optional argument that sets the random seed (default is 1) to make results reproducible.} \item{iter}{The number of MCMC iterations. The default behavior of metaMix is to take into account the number of potential species after step 2 in order in order to compute the number of MCMC iterations. By default metaMix will choose the greater value between a) the user-specified value for iter and b) the product of (5 * the number of potential species). This behavior can by bypassed by setting the bypass parameter to TRUE. Then the MCMC will run for exactly the user-specified number iter.} \item{bypass}{A logical flag. If set to TRUE the MCMC will run for exactly "iter" iterations. If FALSE, metaMix defaults to choosing the greater value between "iter" and "5*(nrow(ordered.sepcies))".} \item{pij.sparse.mat}{sparse matrix of generative probabilities, see value of ?reduce.space.} \item{read.weights}{see ?reduce.space.} \item{ordered.species}{see ?reduce.space.} \item{gen.prob.unknown}{see ?reduce.space.} \item{outDir}{see ?reduce.space.} } \value{ step3: A list with two elements. The first one (result) is a list that records MCMC information from each parallel chain. The second one (duration) records how much time the MCMC exploration took. } \description{ Performs Parallel Tempering MCMC to explore the species state space. Two types of moves are implemented: a mutation step (within chain) and an exchange step (between neighboring chains). If working with BLASTn data, use parallel.temper.nucl(). parallel.temper.explicit is the same function as parallel.temper but with a more involved syntax. } \examples{ ## See vignette for more details \dontrun{ # Either load the object created by previous step (i.e from function reduce.space() ) data(step2) ## example output of reduce.space step3<-parallel.temper(step2=step2) # or alternatively point to the location of the step2.RData object step3 <- parallel.temper(step2="/pathtoFile/step2.RData") } } \seealso{ \code{\link{parallel.temper.nucl}} This function should be used when working with BLASTn data. } \keyword{parallel.temper} \keyword{parallel.temper.explicit} metaMix/man/parallel.temper.nucl.Rd0000644000176200001440000000457113426035072016760 0ustar liggesusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/step3_parallelTemper_nucl.R \name{parallel.temper.nucl} \alias{parallel.temper.nucl} \alias{parallel.temper.nucl.explicit} \title{Parallel Tempering MCMC} \usage{ parallel.temper.nucl(step2, readSupport = 30, noChains = 12, seed = 1, median.genome.length = 284332) parallel.temper.nucl.explicit(readSupport = 30, noChains = 12, pij.sparse.mat, read.weights, ordered.species, gen.prob.unknown, outDir, seed = 1, median.genome.length = 284332) } \arguments{ \item{step2}{list. The output from reduce.space(). Alternatively, it can be a character string containing the path name of the ".RData" file where step2 list was saved.} \item{readSupport}{The number of reads the user requires in order to believe in the presence of the species. It is used to compute the penalty factor. The default value is 30. We compute the logarithmic penalty value as the log-likelihood difference between two models: one where all N reads belong to the "unknown" category and one where r reads have a perfect match to some unspecified species and the remaining reads belong to the "unknown" category.} \item{noChains}{The number of parallel chains to run. The default value is 12.} \item{seed}{Optional argument that sets the random seed (default is 1) to make results reproducible.} \item{median.genome.length}{To use in the penalty computation.} \item{pij.sparse.mat}{sparse matrix of generative probabilities, see value of ?reduce.space.} \item{read.weights}{see ?reduce.space.} \item{ordered.species}{see ?reduce.space.} \item{gen.prob.unknown}{see ?reduce.space.} \item{outDir}{see ?reduce.space.} } \value{ step3: A list with two elements. The first one (result) is a list that records MCMC information from each parallel chain. The second one (duration) records how much time the MCMC exploration took. } \description{ Performs Parallel Tempering MCMC to explore the species state space. Two types of moves are implemented: a mutation step (within chain) and an exchange step (between neighboring chains). If working with BLASTx data, use parallel.temper(). parallel.temper.nucl.explicit is the same function as parallel.temper.nucl with a more involved syntax. } \seealso{ \code{\link{parallel.temper}} This function should be used when working with BLASTx data. } \keyword{parallel.temper.nucl} \keyword{parallel.temper.nucl.explicit} metaMix/man/reduce.space.Rd0000644000176200001440000000707013426035072015267 0ustar liggesusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/step2_allInclusive_MM.R \name{reduce.space} \alias{reduce.space} \alias{reduce.space.explicit} \title{Reduce the space of potential species by fitting the mixture model with all potential species as categories} \usage{ reduce.space(step1, read.cutoff = 1, EMiter = 500, seed = 1) reduce.space.explicit(pij.sparse.mat, ordered.species, read.weights, outDir, gen.prob.unknown, read.cutoff = 1, EMiter = 500, seed = 1) } \arguments{ \item{step1}{list. The output from generative.prob() (or generative.prob.nucl(), that is the first step of the pipeline. Alternatively, it can be a character string containing the path name of the ".RData" file where step1 list was saved.} \item{read.cutoff}{numeric vector. This is the used to decide which species to retain for the subsequent MCMC exploration. Default value is 1, i.e keep all species that have at least one read assigned to them. If this number is still in the low thousands as opposed to the low hundreds the user may set this to a higher number, such as 10.} \item{EMiter}{Number of iterations for the EM algorithm. Default value is 500.} \item{seed}{Optional argument that sets the random seed (default is 1) to make results reproducible.} \item{pij.sparse.mat}{sparse Matrix of generative probabilities computed by generative.prob() / generative.prob.nucl().} \item{ordered.species}{data.frame with potential species ordered by numbers of reads matching them. Computed by generative.prob().} \item{read.weights}{data.frame mapping each read identifier to a weight. For contigs the weight is the number of reads that were used to assemble it. For unassembled reads the weight is equal to one.} \item{outDir}{character vector holding the path to the output directory where the results are written.} \item{gen.prob.unknown}{numeric vector. This is the generative probability for the unknown category. Default value for BLASTx-analysis is 1e-06 while for BLASTn-analysis is 1e-20.} } \value{ step2: A list with six elements. The first one (ordered.species) is a data.frame containing all the non-empty species categories, as decided by the all inclusive mixture model, ordered by the number of reads assigned to them. The second one (pij.sparse.mat) is a sparse matrix with the generative probability between each read and each species. read.weights, gen.prob.unknown, outDir are all carried forward from the "step1" object. Finally outputEM which records the species abundances throughout the EM iterations (not used in step3 and step4). } \description{ Having the generative probabilities from step1 (generative.prob() or generative.prob.nucl()), we could proceed directly with the PT MCMC to explore the state space. Typically the number of total potential species is large. Therefore we reduce the size of the state-space, by decreasing the number of species to the low hundreds. We achieve this by fitting a Mixture Model with as many categories as all the potential species. Post fitting, we retain only the species categories that are not empty, that is categories that have at least one read assigned to them. reduce.space.explicit is the same function as reduce.space but with more involved syntax. } \examples{ ## See vignette for more details. \dontrun{ # Either load the object created by previous step data(step1) ## example output of step1, i.e generative.prob() step2 <- reduce.space(step1=step1) # or alternatively point to the location of the step1.RData object step2 <- reduce.space(step1="/pathtoFile/step1.RData") } } \keyword{reduce.space} \keyword{reduce.space.explicit} metaMix/man/step1.Rd0000644000176200001440000000047513426035072013764 0ustar liggesusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/metaMix-package.r \name{step1} \alias{step1} \title{Example output of generative.prob() for use in the vignette/examples} \format{A list with 5 elements} \description{ Example output of generative.prob() for use in the vignette/examples }