TB Profiler
This tool processes raw sequence data to infer strain type and identify known drug resistance markers.
A stand alone version of this tool is now available and can now be run on linux or mac. Installation instructions can be found on GitHub and on the bioconda page.



This tool is for Research Use Only. Data and information provided through use of this tool are not intended for medical purpose or objective and should not be used for clinical diagnosis, patient management, or human clinical trials.
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Single nucleotide polymorphisms (SNPs) in coding regions are annotated using the reference amino acid, codon number and alternative amino acid (e.g. Ser315Thr in katG). SNPs in non-coding regions (i.e. RNA genes and intergenic regions) are annotated using the reference nucleotide, gene coordinate and alternative nucleotide (e.g. A1401G in rrs or C-37A in eis promoter). Indels are annotated using the reference VCF allele, gene coordinate and alternative VCF allele (e.g. T902TA insertion in katG).
Name: 5d1230a3bfaa3
Sample: 5d1230a3bfaa3

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Summary
ID: 5d1230a3bfaa3
Date: Tue Jun 25 15:36:17 2019
Strain: lineage4.3.3
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
RifampicinRrpoB p.Ser450Asn (0.28), rpoB p.Leu464Met (0.28)
Ethambutol
Pyrazinamide
Streptomycin
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.3Euro-American (LAM)mainly-LAMNone
lineage4.3.3Euro-American (LAM)LAM;TRD115

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB5723p.Ala162Ser1.000
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA8040p.Gly247Ser1.000
gyrA9304p.Gly668Asp0.982
rpoB760997c.1191G>C0.310
rpoB761015c.1209G>C0.327
rpoB761021c.1215G>C0.316
rpoB761027c.1221A>G0.231
rpoB761031p.Gln409Asn0.245
rpoB761036c.1230G>C0.208
rpoB761037c.1231T>C0.250
rpoB761054c.1248G>C0.418
rpoB761058p.Val418Thr0.500
rpoB761088c.1282A>T0.568
rpoB761096c.1290G>C0.507
rpoB761102c.1296A>G0.482
rpoB761127p.Ser441Ala0.432
rpoB761132c.1326G>C0.429
rpoB761133c.1327T>C0.417
rpoB761150c.1344A>C0.304
rpoB761159c.1353G>C0.323
rpoB761165c.1359G>C0.348
rpoB761180c.1374A>C0.323
rpoB761189c.1383T>C0.286
rpoB761193p.Gly463Ser0.214
rpoB761213c.1407G>C0.255
rpoB761217p.Pro471Thr0.173
rpoB761231c.1425C>G0.125
rpoB761234c.1428G>C0.180
rpoB761534c.1728G>C0.237
rpoB761535p.Pro577Ala0.136
rpoB761567p.Met587Ile0.137
rpoB761579c.1773G>C0.151
rpoB761600c.1794T>C0.184
rpoB761612c.1806G>C0.207
rpoB761615c.1809A>C0.167
rpoB761633c.1827G>C0.154
rpoB762024p.Val740Met0.272
rpoB762053c.2247T>C0.337
rpoB762057p.Ile751Val0.337
rpoB762062c.2256T>C0.344
rpoB762065c.2259T>C0.348
rpoB762083c.2277T>C0.255
rpoB762086c.2280G>C0.252
rpoB762092c.2286G>A0.147
rpoB762110c.2304G>C0.233
rpoB762114p.Ile770Val0.242
rpoB762122p.Asp772Glu0.175
rpoB762125c.2319G>A0.167
rpoB762126p.Val774Ser0.167
rpoB762134c.2328C>T0.222
rpoB762143c.2337T>C0.264
rpoB762149c.2343G>C0.278
rpoB762156p.Val784Ile0.274
rpoB762173c.2367G>A0.158
rpoB762176c.2370T>C0.320
rpoB762177p.Arg791Thr0.200
rpoB762181p.Asp792Ala0.227
rpoB762185c.2379G>C0.365
rpoB762194c.2388G>C0.413
rpoB762212c.2406G>C0.231
rpoB762233c.2427G>C0.272
rpoB762234p.Pro810Ser0.264
rpoB762239c.2433G>A0.245
rpoB762245c.2439G>C0.375
rpoB762254c.2448T>C0.392
rpoB762266c.2460T>C0.255
rpoB762287c.2481C>T0.149
rpoB762441p.Leu879Met0.129
rpoB762452c.2646G>C0.164
rpoB762470c.2664G>C0.200
rpoB762474p.Gly890Ser0.197
rpoB762488c.2682G>C0.250
rpoB762491c.2685T>C0.137
rpoB762503c.2697G>C0.226
rpoB762509c.2703T>C0.137
rpoB762839c.3033G>A0.162
rpoB762855p.Val1017Ile0.397
rpoB762858p.Thr1018Ser0.397
rpoB762863c.3057T>G0.397
rpoB762871p.Met1022Thr0.282
rpoB762878p.Ile1024Met0.267
rpoB762879p.Met1025Leu0.381
rpoB762887c.3081G>C0.511
rpoB762899c.3093G>C0.464
rpoB762926c.3120C>G0.539
rpoB762929c.3123G>T0.448
rpoB762947c.3141C>G0.470
rpoB762971c.3165G>C0.555
rpoB762980c.3174T>C0.459
rpoB762989c.3183G>C0.571
rpoB762995c.3189G>C0.486
rpoB763005p.Cys1067Val0.375
rpoB763014p.Met1070Leu0.396
rpoB763017p.Gln1071Glu0.407
rpoB763028c.3222T>C0.218
rpoB763031c.3225T>C0.444
rpoB763038p.Thr1078Ala0.497
rpoB763043c.3237G>C0.438
rpoB763053c.3247T>C0.482
rpoB763070c.3264T>C0.443
rpoB763077p.Val1091Thr0.473
rpoB763103c.3297G>C0.453
rpoB763115c.3309T>C0.455
rpoB763119p.Asn1105Asp0.439
rpoB763127c.3321G>C0.440
rpoB763133c.3327G>C0.434
rpoC763666c.297G>C0.130
rpoC763699c.330G>T0.151
rpoC763714c.345G>C0.141
rpoC763717c.348T>C0.142
rpoC763718p.Leu117Val0.129
rpoC763726c.357C>T0.124
rpoC763732c.363C>T0.133
rpoC763747c.378G>A0.136
rpoC763751p.Ile128Val0.155
rpoC763772p.Val135Met0.150
rpoC764485c.1116G>C0.359
rpoC764491c.1122G>T0.349
rpoC764497c.1128A>G0.215
rpoC764503c.1134G>T0.239
rpoC764509c.1140G>C0.311
rpoC764512c.1143G>C0.257
rpoC764521c.1152T>C0.270
rpoC764524c.1155C>T0.225
rpoC764530c.1161C>T0.225
rpoC764536c.1167G>C0.383
rpoC764543p.Thr392Ala0.349
rpoC764548c.1179G>T0.318
rpoC764566c.1197C>G0.392
rpoC764573p.Leu402Ile0.461
rpoC764578c.1209C>G0.437
rpoC764581c.1212T>C0.486
rpoC764582p.Leu405Met0.505
rpoC764602c.1233C>T0.455
rpoC764605c.1236G>T0.500
rpoC764611c.1242G>T0.455
rpoC764632c.1263T>C0.210
rpoC764647c.1278C>T0.377
rpoC764650c.1281G>T0.456
rpoC764653c.1284G>C0.433
rpoC764656c.1287C>T0.338
rpoC764662c.1293G>C0.535
rpoC764677c.1308C>G0.421
rpoC764678p.Lys437Gln0.411
rpoC764683c.1314G>C0.205
rpoC764706p.Leu446Gln0.440
rpoC764713c.1344G>C0.381
rpoC764731c.1362G>C0.411
rpoC764737c.1368G>C0.399
rpoC764746c.1377G>C0.281
rpoC764995c.1626C>G0.969
rpsL781395c.-165T>C1.000
rpsL781682c.123T>G0.217
rpsL781751c.192G>C0.383
rpsL781760c.201T>C0.383
rpsL781766c.207C>T0.486
rpsL781796p.Met79Ile0.564
rpsL781802c.243G>C0.561
rpsL781811c.252C>T0.541
rpsL781814c.255C>T0.535
rpsL781817c.258G>T0.516
rpsL781832c.273T>C0.356
rpsL781835c.276T>C0.289
rpsL781841c.282C>T0.264
rpsL781845p.Lys96Arg0.259
rpsL781851p.Ile98Val0.250
rpsL781868c.309T>C0.177
rpsL781871c.312G>C0.177
rrs1471981r.136c>t0.392
rrs1471996r.151c>t0.204
rrs1472023r.178g>c0.485
rrs1472068r.223t>g0.582
rrs1472075r.230a>g0.850
rrs1472078r.233c>t0.270
rrs1472087r.242a>g0.573
rrs1472089r.244c>t0.586
rrs1472106r.261g>a0.568
rrs1472108r.263c>t0.332
rrs1472122r.277g>t0.558
rrs1472123r.278a>t0.516
rrs1472124r.279c>t0.682
rrs1472148r.303t>c0.251
rrs1472150r.305t>a0.926
rrs1472155r.310c>t0.576
rrs1472160r.315c>t0.781
rrs1472172r.327t>c0.319
rrs1472225r.380c>a0.523
rrs1472251r.406g>c0.201
rrs1472258r.413a>g0.689
rrs1472259r.414c>a0.826
rrs1472286r.441c>g0.326
rrs1472289r.444t>g0.357
rrs1472290r.445c>g0.325
rrs1472314r.469a>g0.141
rrs1472325r.480g>c0.703
rrs1472328r.483g>c0.147
rrs1472330r.485g>t0.384
rrs1472338r.493a>g0.416
rrs1472344r.499c>t0.841
rrs1472379r.534t>g0.374
rrs1472382r.537g>a0.405
rrs1472389r.544g>a0.362
rrs1472396r.551a>t0.339
rrs1472398r.553t>c0.290
rrs1472400r.555c>t0.855
rrs1472412r.567a>c0.389
rrs1472422r.577t>c0.652
rrs1472427r.582t>g0.446
rrs1472435r.590t>c0.273
rrs1472436r.591g>t0.250
rrs1472437r.592t>g0.250
rrs1472438r.593t>c0.156
rrs1472451r.606c>t0.200
rrs1472462r.617t>g0.387
rrs1472464r.619a>g0.419
rrs1472473r.628g>t0.342
rrs1472474r.629c>g0.342
rrs1472476r.631a>g0.359
rrs1472484r.639a>t0.181
rrs1472489r.644a>t0.241
rrs1472494r.649a>g0.718
rrs1472496r.651t>a0.460
rrs1472498r.653c>t0.737
rrs1472507r.662c>g0.355
rrs1472513r.668t>c0.492
rrs1472517r.672t>a0.346
rrs1472518r.673g>t0.347
rrs1472530r.685g>a0.358
rrs1472537r.692c>t0.359
rrs1472544r.699c>a0.352
rrs1472545r.700a>t0.343
rrs1472549r.704g>a0.531
rrs1472566r.721g>a0.340
rrs1472571r.726g>c0.398
rrs1472579r.734g>c0.335
rrs1472580r.735c>t0.308
rrs1472581r.736a>t0.444
rrs1472584r.739a>t0.474
rrs1472598r.753a>c0.346
rrs1472599r.754g>t0.321
rrs1472616r.771g>a0.386
rrs1472647r.802c>t0.357
rrs1472655r.810g>a0.735
rrs1472658r.813g>a0.218
rrs1472660r.815t>c0.667
rrs1472661r.816a>g0.226
rrs1472673r.828t>g0.211
rrs1472674r.829t>g0.290
rrs1472675r.830t>g0.322
rrs1472678r.833t>a0.339
rrs1472679r.834t>c0.352
rrs1472680r.835c>t0.194
rrs1472682r.837t>c0.362
rrs1472683r.838t>g0.237
rrs1472686r.841g>t0.285
rrs1472687r.842a>t0.640
rrs1472690r.845c>a0.209
rrs1472692r.847t>c0.268
rrs1472697r.852t>c0.441
rrs1472714r.869a>g0.644
rrs1472715r.870c>t0.375
rrs1472744r.899a>g0.235
rrs1472779r.934g>a0.346
rrs1472781r.936c>t0.309
rrs1472790r.945t>c0.225
rrs1472793r.948a>t0.574
rrs1472803r.958t>a0.549
rrs1472824r.979t>a0.631
rrs1472825r.980g>a0.324
rrs1472828r.983t>c0.663
rrs1472840r.995a>c0.259
rrs1472841r.996g>a0.212
rrs1472846r.1001c>g0.171
rrs1472847r.1002g>t0.171
rrs1472849r.1004c>g0.171
rrs1472873r.1028c>t0.132
rrs1472874r.1029c>t0.146
rrs1472875r.1030t>c0.352
rrs1472895r.1050c>t0.870
rrs1472954r.1109t>c0.795
rrs1472956r.1111t>c0.856
rrs1472957r.1112c>t0.813
rrs1472973r.1128a>g0.861
rrs1472990r.1145a>g0.860
rrs1472992r.1147a>g0.683
rrs1473005r.1160c>t0.700
rrs1473035r.1190g>a0.836
rrs1473055r.1210c>t0.657
rrs1473056r.1211a>t0.921
rrs1473062r.1217t>a0.248
rrs1473066r.1221a>g0.685
rrs1473068r.1223a>g0.245
rrs1473080r.1235c>t0.297
rrs1473081r.1236c>t0.446
rrs1473088r.1243a>g0.733
rrs1473093r.1248c>t0.420
rrs1473100r.1255g>a0.885
rrs1473102r.1257c>t0.323
rrs1473104r.1259c>t0.733
rrs1473110r.1265t>g0.748
rrs1473111r.1266a>g0.938
rrs1473121r.1276t>c0.942
rrs1473123r.1278a>t0.850
rrs1473130r.1285g>a0.309
rrs1473145r.1300c>t0.583
rrs1473148r.1303g>t0.436
rrs1473163r.1318c>a0.424
rrs1473166r.1321g>a0.582
rrs1473172r.1327t>g0.332
rrs1473173r.1328c>t0.648
rrs1473192r.1347a>g0.239
rrs1473205r.1360t>c0.236
rrs1473221r.1376c>t0.644
rrs1473252r.1407t>c0.730
rrs1473259r.1414c>t0.794
rrs1473262r.1417t>c0.159
rrs1473276r.1431a>c0.957
rrs1473277r.1432g>a0.705
rrs1473288r.1443c>g0.496
rrs1473289r.1444t>a0.250
rrs1473294r.1449a>g0.667
rrs1473300r.1455c>t0.637
rrs1473301r.1456t>g0.899
rrs1473316r.1471c>t0.923
rrl1473384c.-274A>G0.583
rrl1473389c.-269CA>C0.700
rrl1473679r.22t>c0.428
rrl1473698r.41g>a0.260
rrl1473704r.47c>t0.151
rrl1473717r.60g>t0.138
rrl1473719r.62g>c0.152
rrl1473720r.63a>g0.173
rrl1473722r.65g>c0.193
rrl1473862r.205c>t0.149
rrl1473896r.239c>t0.160
rrl1473899r.242a>t0.159
rrl1473922r.265a>t0.133
rrl1473923r.266c>g0.222
rrl1474130r.473c>t0.172
rrl1474140r.483c>t0.216
rrl1474151r.494c>t0.658
rrl1474155r.498g>a0.634
rrl1474156r.499g>a0.198
rrl1474163r.506c>t0.318
rrl1474164r.507c>t0.719
rrl1474181r.524c>a0.841
rrl1474184r.527c>t0.832
rrl1474197r.540c>t0.858
rrl1474199r.542g>c0.762
rrl1474249r.592g>t0.914
rrl1474271r.614a>g0.677
rrl1474272r.615c>t0.680
rrl1474275r.618t>g0.882
rrl1474306r.649a>t0.644
rrl1474308r.651g>t0.585
rrl1474310r.653t>g0.703
rrl1474348r.691c>t0.754
rrl1474351r.694g>t0.915
rrl1474353r.696a>g0.250
rrl1474354r.697c>t0.661
rrl1474355r.698a>g0.206
rrl1474356r.699t>c0.612
rrl1474359r.702c>g0.614
rrl1474362r.705a>g0.921
rrl1474363r.706a>t0.602
rrl1474365r.708g>c0.596
rrl1474383r.726g>t0.712
rrl1474384r.727c>g0.595
rrl1474387r.730c>t0.915
rrl1474393r.736a>g0.188
rrl1474402r.745t>c0.188
rrl1474435r.778g>t0.314
rrl1474439r.782a>g0.184
rrl1474448r.791t>c0.693
rrl1474467r.810a>g0.915
rrl1474488r.831g>t0.859
rrl1474495r.838g>a0.875
rrl1474496r.839c>g0.214
rrl1474497r.840g>a0.207
rrl1474498r.841g>t0.664
rrl1474505r.848c>g0.674
rrl1474506r.849c>t0.211
rrl1474508r.851c>t0.879
rrl1474516r.859c>a0.890
rrl1474527r.870t>c0.809
rrl1474537r.880g>a0.931
rrl1474542r.885a>g0.806
rrl1474551r.894g>a0.228
rrl1474626r.969t>c0.312
rrl1474632r.975g>t0.211
rrl1474634r.977t>c0.740
rrl1474636r.979a>c0.904
rrl1474637r.980c>t0.644
rrl1474638r.981c>g0.764
rrl1474640r.983c>t0.604
rrl1474658r.1001a>g0.212
rrl1474663r.1006c>t0.380
rrl1474675r.1018c>g0.686
rrl1474676r.1019t>a0.220
rrl1474677r.1020a>g0.920
rrl1474709r.1052g>a0.624
rrl1474716r.1059a>c0.417
rrl1474717r.1060a>t0.714
rrl1474734r.1077g>t0.880
rrl1474749r.1092c>t0.653
rrl1474754r.1097c>g0.691
rrl1474760r.1103a>g0.885
rrl1474779r.1122g>a0.649
rrl1474780r.1123c>t0.633
rrl1474782r.1125g>a0.663
rrl1474794r.1137c>t0.971
rrl1474802r.1145t>c0.645
rrl1474823r.1166c>g0.690
rrl1474824r.1167a>g0.296
rrl1474830r.1173a>g0.907
rrl1474831r.1174a>c0.283
rrl1474832r.1175a>t0.637
rrl1474864r.1207c>t0.848
rrl1474901r.1244a>g0.430
rrl1474903r.1246t>c0.359
rrl1474904r.1247g>c0.587
rrl1474913r.1256t>c0.847
rrl1474933r.1276a>g0.487
rrl1474934r.1277c>t0.489
rrl1475016r.1359c>t0.275
rrl1475018r.1361g>c0.310
rrl1475026r.1369g>c0.737
rrl1475031r.1374g>c0.740
rrl1475062r.1405a>t0.661
rrl1475079r.1422t>a0.647
rrl1475090r.1433a>t0.722
rrl1475104r.1447t>a0.744
rrl1475114r.1457c>t0.787
rrl1475124r.1467a>t0.743
rrl1475171r.1514c>t0.564
rrl1475172r.1515a>g0.493
rrl1475452r.1795c>a0.348
rrl1475460r.1803a>g0.282
rrl1475499r.1842c>t0.601
rrl1475508r.1851a>t0.412
rrl1475526r.1869c>t0.608
rrl1475532r.1875a>g0.512
rrl1475538r.1881t>a0.258
rrl1475539r.1882a>t0.662
rrl1475542r.1885a>g0.207
rrl1475544r.1887a>t0.465
rrl1475545r.1888t>g0.769
rrl1475548r.1891c>t0.549
rrl1475549r.1892t>c0.551
rrl1475550r.1893a>g0.313
rrl1475573r.1916g>t0.567
rrl1475574r.1917c>g0.248
rrl1475576r.1919c>t0.337
rrl1475591r.1934g>t0.331
rrl1475596r.1939g>a0.315
rrl1475649r.1992a>g0.741
rrl1475655r.1998t>g0.713
rrl1475657r.2000a>g0.137
rrl1475659r.2002g>a0.799
rrl1475672r.2015c>t0.617
rrl1475673r.2016t>c0.654
rrl1475686r.2029c>g0.732
rrl1475696r.2039t>c0.813
rrl1475699r.2042c>t0.871
rrl1475703r.2046a>g0.813
rrl1475715r.2058g>c0.646
rrl1475751r.2094c>a0.883
rrl1475760r.2103c>a0.193
rrl1475762r.2105g>t0.263
rrl1475763r.2106c>t0.397
rrl1475764r.2107a>g0.333
rrl1475765r.2108a>g0.272
rrl1475767r.2110g>t0.289
rrl1475767r.2110g>gggt0.410
rrl1475774r.2117c>t0.324
rrl1475777r.2120a>t0.888
rrl1475881r.2224t>c0.466
rrl1475883r.2226a>c0.896
rrl1475884r.2227a>g0.670
rrl1475896r.2239a>g0.202
rrl1475897r.2240t>c0.207
rrl1475898r.2241a>g0.794
rrl1475899r.2242g>a0.810
rrl1475900r.2243a>g0.261
rrl1475906r.2249c>t0.528
rrl1475916r.2259c>g0.887
rrl1475937r.2280a>t0.847
rrl1475943r.2286g>a0.905
rrl1475945r.2288c>a0.779
rrl1475952r.2295a>g0.863
rrl1475970r.2313c>t0.901
rrl1475975r.2318c>t0.705
rrl1475977r.2320a>g0.876
rrl1475988r.2331a>g0.842
rrl1475993r.2336c>t0.159
rrl1475995r.2338g>c0.629
rrl1475997r.2340a>t0.747
rrl1475998r.2341c>t0.200
rrl1476000r.2343g>a0.542
rrl1476001r.2344t>c0.831
rrl1476030r.2373a>g0.539
rrl1476033r.2376t>g0.516
rrl1476034r.2377c>t0.508
rrl1476035r.2378g>t0.217
rrl1476040r.2383c>t0.134
rrl1476044r.2387t>g0.452
rrl1476046r.2389g>c0.433
rrl1476049r.2392c>t0.480
rrl1476058r.2401t>c0.377
rrl1476059r.2402g>c0.367
rrl1476113r.2456t>g0.389
rrl1476131r.2474c>t0.766
rrl1476164r.2507a>g0.562
rrl1476179r.2522c>t0.702
rrl1476194r.2537a>g0.848
rrl1476200r.2543a>t0.862
rrl1476201r.2544c>t0.322
rrl1476204r.2547c>t0.328
rrl1476207r.2550t>c0.475
rrl1476214r.2557g>t0.557
rrl1476215r.2558c>t0.562
rrl1476221r.2564t>c0.460
rrl1476224r.2567a>g0.638
rrl1476227r.2570c>t0.271
rrl1476245r.2588c>t0.506
rrl1476251r.2594t>c0.487
rrl1476252r.2595t>g0.396
rrl1476256r.2599a>g0.389
rrl1476257r.2600g>c0.274
rrl1476260r.2603a>g0.804
rrl1476280r.2623a>c0.734
rrl1476293r.2636c>t0.580
rrl1476294r.2637a>g0.804
rrl1476295r.2638c>g0.796
rrl1476296r.2639c>t0.794
rrl1476297r.2640c>g0.508
rrl1476301r.2644a>t0.316
rrl1476311r.2654g>c0.829
rrl1476312r.2655t>c0.828
rrl1476313r.2656g>a0.684
rrl1476332r.2675g>c0.704
rrl1476338r.2681c>t0.573
rrl1476353r.2696g>a0.553
rrl1476358r.2701t>c0.777
rrl1476359r.2702c>t0.436
rrl1476369r.2712c>t0.396
rrl1476372r.2715t>c0.400
rrl1476382r.2725a>g0.785
rrl1476383r.2726t>a0.783
rrl1476408r.2751g>a0.371
rrl1476411r.2754g>a0.413
rrl1476425r.2768g>a0.333
rrl1476428r.2771c>t0.768
rrl1476429r.2772a>c0.306
rrl1476466r.2809c>t0.375
rrl1476481r.2824t>c0.899
rrl1476506r.2849t>c0.878
rrl1476513r.2856g>t0.337
rrl1476515r.2858c>t0.779
rrl1476517r.2860c>t0.333
rrl1476523r.2866t>c0.512
rrl1476524r.2867c>t0.333
rrl1476525r.2868a>g0.878
rrl1476528r.2871a>g0.232
rrl1476530r.2873c>t0.481
rrl1476536r.2879g>a0.602
rrl1476538r.2881a>g0.670
rrl1476539r.2882a>g0.772
rrl1476540r.2883c>g0.280
rrl1476547r.2890c>t0.283
rrl1476567r.2910c>t0.371
rrl1476584r.2927c>t0.939
rrl1476585r.2928a>g0.736
rrl1476594r.2937c>a0.221
rrl1476600r.2943a>c0.519
rrl1476603r.2946g>t0.236
rrl1476607r.2950c>t0.210
rrl1476608r.2951c>g0.845
rrl1476614r.2957a>t0.909
rrl1476616r.2959a>g0.628
rrl1476619r.2962c>t0.841
rrl1476628r.2971t>g0.701
rrl1476629r.2972c>a0.758
rrl1476630r.2973a>g0.397
rrl1476633r.2976a>g0.455
rrl1476661r.3004a>g0.343
rrl1476664r.3007t>a0.500
rrl1476665r.3008t>g0.326
rrl1476668r.3011c>t0.588
rrl1476675r.3018c>g0.807
rpsA1833661c.120A>G0.294
rpsA1833667c.126C>T0.280
rpsA1833668p.Ile43Val0.281
rpsA1833676c.135A>G0.286
rpsA1833679c.138G>C0.269
rpsA1833684p.Arg48His0.260
rpsA1833694c.153G>C0.333
rpsA1833721c.180A>G0.219
rpsA1833724c.183C>T0.215
rpsA1833727c.186G>C0.205
rpsA1833732p.Pro64Leu0.263
rpsA1833734p.Ala65Ser0.218
rpsA1833742c.201A>G0.293
rpsA1833764p.Asp75Asn0.228
rpsA1833770p.Asn77Asp0.260
rpsA1833775p.Glu78Asp0.171
rpsA1833928c.387G>C0.244
rpsA1833949c.408T>C0.324
rpsA1833970c.429G>C0.301
rpsA1833976c.435C>T0.212
rpsA1833979c.438T>C0.373
rpsA1833994c.453G>C0.268
rpsA1834009c.468C>T0.237
rpsA1834012c.471G>C0.213
rpsA1834024c.483G>C0.183
rpsA1834040p.Lys167Arg0.178
rpsA1834054c.513C>G0.223
rpsA1834093c.552G>C0.220
rpsA1834114c.573G>C0.210
rpsA1834189c.648G>C0.295
rpsA1834195c.654G>C0.510
rpsA1834213c.672G>C0.140
rpsA1834225c.684C>T0.124
rpsA1834228c.687C>T0.352
rpsA1834231c.690T>C0.156
rpsA1834234c.693G>C0.536
rpsA1834240c.699T>C0.537
rpsA1834246c.705G>T0.385
rpsA1834249c.708T>C0.618
rpsA1834258c.717G>A0.182
rpsA1834261c.720A>G0.611
rpsA1834264c.723G>C0.611
rpsA1834294c.753G>C0.593
rpsA1834298p.Gln253Glu0.578
rpsA1834306c.765T>C0.366
rpsA1834307p.Asp256Gln0.527
rpsA1834312c.771G>A0.493
rpsA1834327c.786G>T0.510
rpsA1834345c.804C>T0.425
rpsA1834348c.807T>C0.409
rpsA1834354c.813G>C0.366
rpsA1834357c.816T>C0.355
rpsA1834360c.819G>C0.325
rpsA1834361c.820T>C0.333
rpsA1834366c.825A>C0.175
rpsA1834375c.834G>C0.319
rpsA1834378c.837T>C0.350
rpsA1834387c.846C>T0.338
rpsA1834395p.Arg285Gln0.336
rpsA1834397p.His286Ala0.333
rpsA1834411c.870T>C0.400
rpsA1834417c.876G>C0.406
rpsA1834423c.882G>C0.364
rpsA1834427p.Ile296Val0.346
rpsA1834435c.894G>C0.390
rpsA1834451c.910T>C0.311
rpsA1834456c.915T>C0.200
rpsA1834459c.918G>C0.290
rpsA1834465c.924T>C0.286
rpsA1834468c.927A>G0.275
rpsA1834486p.Glu315Asp0.307
rpsA1834489c.948T>C0.318
rpsA1834501c.960G>C0.230
rpsA1834504c.963G>C0.257
rpsA1834522c.981C>T0.220
rpsA1834523p.Glu328Gln0.245
rpsA1834600c.1059G>C0.318
tlyA1917972c.33A>G1.000
kasA2518919p.Gly269Ser1.000
ribD2987188p.Leu117Gln0.196
thyA3073868p.Thr202Ala1.000
ald3086788c.-32T>C1.000
embC4242182p.Ala774Ser1.000
embC4242643c.2781C>T1.000
embA4243369p.Pro46Leu0.216
gid4408156p.Leu16Arg1.000

Analysis pipeline specifications

TBProfiler Version: 2.1.1

AnalysisProgram
Mappingbwa
Variant CallingBCFtools


Log

Drug Details
The estimated accuracy of drug resistance predictions is:

Drug1Sensitivity (%)Specificity (%)
Isoniazid 92.8 (89.9-95.7)100 (100-100)
Rifampicin 96.2 (93.9-98.5)98.1 (96.8-99.4)
Ethambutal 88.7 (83.6-93.8)81.7 (77.6-85.8)
Pyrazinamide70.9 (62.4-79.4)93.9 (90.6-97.2)
Streptomycin87.1 (82.7-91.5)89.7 (86.0-93.4)
Ethionamide 73.6 (66.7-80.5)93.3 (89.6-97.0)
Moxifloxacin60.0 (29.6-90.4)68.7 (52.6-84.8)
Ofloxacin 85.5 (79.1-91.9)94.9 (91.8-98.0)
Amikacin 82.9 (74.4-91.4)98.3 (96.0-100)
Capreomycin 60.7 (50.6-70.8)90.7 (87.2-94.2)
Kanamycin 87.3 (81.3-93.3)93.4 (89.9-96.9)
Para-aminosalisylic acidNot determinedNot determined
Linezolid Not determinedNot determined
Clofazimine Not determinedNot determined
Bedaquiline Not determinedNot determined
Multi drug resistance91.2 (87.8-94.6)98.4 (97.2-99.6)
Extremely drug resistance75.9 (64.5-87.3)98.4 (97.3-99.5)

Lineages
Lineage2LocationStrainRD type
lineage1Indo-OceanicEAIRD239
lineage1.1Indo-OceanicEAI3;EAI4;EAI5;EAI6RD239
lineage1.1.1Indo-OceanicEAI4;EAI5RD239
lineage1.1.1.1Indo-OceanicEAI4;ZERORD239
lineage1.1.2Indo-OceanicEAI3;EAI5RD239
lineage1.1.3Indo-OceanicEAI6RD239
lineage1.2Indo-OceanicEAI1;EAI2RD239
lineage1.2.1Indo-OceanicEAI2RD239
lineage1.2.2Indo-OceanicEAI1RD239
lineage2East-AsianBeijingRD105
lineage2.1East-Asian (non-Beijing)NoneNone
lineage2.2East-Asian (Beijing)Beijing-RD207RD105;RD207
lineage2.2.2East-Asian (Beijing)Beijing-RD105/RD207RD105;RD207
lineage2.2.1East-Asian (Beijing)Beijing-RD181RD105;RD207;RD181
lineage2.2.1.2East-Asian (Beijing)Beijing-RD142RD105;RD207;RD181;RD142
lineage2.2.1.1East-Asian (Beijing)Beijing-RD150RD105;RD207;RD181;RD150
lineage3East-African-IndianCASRD750
lineage3.1East-African-IndianNon-CAS1-DelhiRD750
lineage3.1.1East-African-IndianCAS1-KiliRD750
lineage3.1.2East-African-IndianCAS;CAS2RD750
lineage3.1.2.1East-African-IndianCAS2RD750
lineage3.1.2.2East-African-IndianCASRD750
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.1Euro-AmericanT;X;HNone
lineage4.1.2Euro-American (X-type)T;HNone
lineage4.1.2.1Euro-American (X-type)T1;H1RD182
lineage4.1.1Euro-American (X-type)X1;X2;X3None
lineage4.1.1.2Euro-American (X-type)X1None
lineage4.1.1.1Euro-American (X-type)X2RD183
lineage4.1.1.3Euro-American (Haarlem)X1;X3RD193
lineage4.2Euro-AmericanH;T;LAMNone
lineage4.2.2Euro-American (Ural)T;LAM7-TURNone
lineage4.2.2.1Euro-AmericanLAM7-TURNone
lineage4.2.1Euro-American (TUR)H3;H4None
lineage4.3Euro-American (LAM)mainly-LAMNone
lineage4.3.1Euro-American (LAM)LAM9None
lineage4.3.3Euro-American (LAM)LAM;TRD115
lineage4.3.4Euro-American (LAM)LAMRD174
lineage4.3.4.1Euro-American (LAM)LAM1;LAM2RD174
lineage4.3.4.2Euro-American (LAM)LAM1;LAM4;LAM11RD174
lineage4.3.4.2.1Euro-American (LAM)LAM11RD174
lineage4.3.2Euro-American (LAM)LAM3None
lineage4.3.2.1Euro-American (LAM)LAM3RD761
lineage4.4Euro-AmericanS;TNone
lineage4.4.2Euro-AmericanT1;T2None
lineage4.4.1Euro-American (S-type)S;TNone
lineage4.4.1.2Euro-AmericanT1None
lineage4.4.1.1Euro-AmericanS;OrphansNone
lineage4.5Euro-AmericanH;TRD122
lineage4.6Euro-AmericanT;LAMNone
lineage4.6.1Euro-American (Uganda)T2RD724
lineage4.6.1.1Euro-American T2-UgandaRD724
lineage4.6.1.2Euro-AmericanT2RD724
lineage4.6.2Euro-AmericanT;LAMRD726
lineage4.6.2.1Euro-AmericanT3RD726
lineage4.6.2.2Euro-American (Cameroon)LAM10-CAMRD726
lineage4.7Euro-American (mainly T)T1;T5None
lineage4.8Euro-American (mainly T)T1;T2;T3;T5RD219
lineage4.9Euro-American (H37Rv-like)T1None
lineage5West-Africa 1AFRI_2;AFRI_3RD711
lineage6West-Africa 2AFRI_1RD702
lineage7Lineage 7NoneNone
lineageBOVM. bovisBOV_1;BOV_2None

Citations
1. Coll F, et al. Rapid determination of anti-tuberculosis drug resistance from whole genome sequences. Genome Medicine (in press)
2. Coll F, et al. A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nature Communications 2014.

Disclaimer
This tool is for Research Use Only and is offered free for use. The London School of Hygiene and Tropical Medicine shall have no liability for any loss or damages of any kind, however sustained relating to the use of this tool.
© 2019 London School of Hygiene and Tropical Medicine;