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: 5db4e28dc5926
Sample: 5db4e28dc5926

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Summary
ID: 5db4e28dc5926
Date: Sun Oct 27 01:27:30 2019
Strain: lineage3.1.2.1;lineage2;lineage1.2.1;lineage4.1.1.3
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRkatG p.Ser315Thr (1.00)
Rifampicin
EthambutolRembB p.Met306Ile (0.69), embB p.Ala356Val (0.36), embB p.Asn399Asp (0.20)
Pyrazinamide
Streptomycin
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage3East-African-IndianCASRD750
lineage2East-AsianBeijingRD105
lineage3.1East-African-IndianNon-CAS1-DelhiRD750
lineage1.2.1Indo-OceanicEAI2RD239
lineage3.1.2East-African-IndianCAS;CAS2RD750
lineage4.1.1.3Euro-American (Haarlem)X1;X3RD193
lineage3.1.2.1East-African-IndianCAS2RD750

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6106c.867C>A0.152
gyrB6115c.876A>G0.364
gyrB6122p.Ala295Lys0.154
gyrB6127c.888G>C0.255
gyrB6172c.933C>T0.643
gyrB6184c.945C>G0.186
gyrB6190c.951A>G0.618
gyrB6214c.975G>C0.483
gyrB6238c.999G>A0.348
gyrB6242p.Arg335Lys0.337
gyrB6253c.1014G>C0.333
gyrB6265c.1026C>T0.241
gyrA7349c.48A>G0.250
gyrA7361c.60C>T0.278
gyrA7362p.Glu21Gln1.000
gyrA7391c.90C>T0.397
gyrA7394c.93T>C0.413
gyrA7412c.111C>G0.466
gyrA7422c.121C>T0.455
gyrA7433c.132G>C0.400
gyrA7451c.150C>G0.250
gyrA7457c.156T>C0.233
gyrA7480p.Phe60Tyr0.208
gyrA7484c.183T>C0.278
gyrA7490c.189C>G0.339
gyrA7502c.201C>T0.397
gyrA7526c.225G>T0.413
gyrA7532c.231T>C0.423
gyrA7541c.240C>G0.427
gyrA7547c.246C>T0.457
gyrA7585p.Ser95Thr1.000
gyrA7601c.300C>G0.312
gyrA7626c.325C>T0.289
gyrA7631c.330G>C0.260
gyrA7643c.342C>T0.231
gyrA7646c.345C>T0.250
gyrA7676c.375G>C0.163
gyrA7679c.378G>C0.222
gyrA7697c.396C>G0.431
gyrA7706c.405C>G0.475
gyrA7725c.424C>T0.485
gyrA7728c.427A>C0.485
gyrA7763c.462T>C0.585
gyrA7769c.468C>T0.582
gyrA7787c.486G>A0.500
gyrA7793c.492G>C0.506
gyrA7797c.496C>T0.458
gyrA7820c.519G>C0.458
gyrA7832c.531G>T0.405
gyrA7835c.534A>G0.410
gyrA7859c.558A>C0.288
gyrA7865c.564T>C0.254
gyrA7868c.567C>T0.214
gyrA8121c.820T>C0.182
gyrA8126c.825G>C0.219
gyrA8156c.855T>C0.250
gyrA8168c.867A>G0.255
gyrA8177c.876A>C0.260
gyrA8189c.888G>C0.225
gyrA8192c.891C>G0.216
gyrA8198c.897T>C0.196
gyrA8201c.900C>G0.184
gyrA8207c.906T>C0.130
gyrA8253p.Ile318Leu0.149
gyrA8267c.966G>C0.214
gyrA8270c.969G>C0.224
gyrA8283p.Ile328Leu0.291
gyrA8288c.987T>C0.287
gyrA8294c.993T>C0.418
gyrA8324c.1023T>C0.412
gyrA8339c.1038A>G0.385
gyrA8340p.Ala347Ser0.379
gyrA8360c.1059G>A0.354
gyrA8372c.1071G>T0.290
gyrA8375c.1074G>C0.268
gyrA8382p.Leu361Met0.231
gyrA8531c.1230G>T0.137
gyrA8535p.Glu412Gln0.160
gyrA8543c.1242C>T0.200
gyrA8546c.1245T>C0.214
gyrA8555c.1254G>C0.293
gyrA8561c.1260A>G0.311
gyrA8585c.1284C>T0.421
gyrA8588c.1287G>A0.422
gyrA8619c.1318T>C0.468
gyrA8624c.1323G>T0.434
gyrA8627c.1326C>A0.427
gyrA8636c.1335A>C0.438
gyrA8642c.1341A>G0.425
gyrA8655p.Ile452Val0.365
gyrA8672c.1371A>G0.262
gyrA8678c.1377G>A0.167
gyrA9197c.1896G>C0.263
gyrA9230c.1929T>C0.315
gyrA9236c.1935G>C0.326
gyrA9242c.1941A>C0.305
gyrA9248c.1947G>C0.305
gyrA9252p.Val651Ile0.309
gyrA9266c.1965C>T0.316
gyrA9284c.1983T>C0.150
gyrA9287c.1986G>C0.117
gyrA9291c.1990C>T0.113
gyrA9304p.Gly668Asp1.000
gyrA9326c.2025G>A0.143
gyrA9338c.2037G>A0.183
gyrA9341c.2040C>G0.183
gyrA9345c.2044A>C0.185
gyrA9368c.2067G>A0.181
gyrA9383c.2082T>C0.165
gyrA9386c.2085T>C0.156
gyrA9395c.2094G>C0.179
gyrA9398c.2097T>C0.183
rpoB759615c.-192A>AC0.511
rpoB759629c.-178T>C0.381
rpoB759647c.-160T>C0.234
rpoB759746c.-61C>T1.000
rpoB760070c.264T>G0.136
rpoB760091c.285G>C0.238
rpoB760101c.295T>C0.273
rpoB760112c.306T>C0.319
rpoB760118c.312T>C0.333
rpoB760121c.315T>C0.376
rpoB760130p.Asp108Glu0.393
rpoB760139c.333A>G0.435
rpoB760142c.336C>G0.443
rpoB760145c.339C>G0.461
rpoB760181c.375T>A0.500
rpoB760184c.378A>G0.496
rpoB760196c.390C>G0.504
rpoB760235c.429T>C0.531
rpoB760244c.438G>C0.524
rpoB760274c.468G>A0.480
rpoB760295c.489C>T0.415
rpoB760307c.501T>C0.330
rpoB760310c.504G>C0.303
rpoB760328c.522G>C0.281
rpoB760331c.525G>C0.274
rpoB760337c.531C>G0.218
rpoB760340c.534G>T0.174
rpoB760358c.552C>G0.134
rpoB760361c.555T>C0.134
rpoB760370c.564C>G0.203
rpoB760376p.Asp190Glu0.190
rpoB760380p.Thr192Leu0.194
rpoB760412c.606C>T0.391
rpoB760418c.612G>C0.403
rpoB760424c.618C>G0.411
rpoB760430c.624T>C0.436
rpoB760457c.651C>T0.420
rpoB760472c.666C>T0.179
rpoB760475c.669A>G0.182
rpoB760478c.672C>T0.164
rpoB760481c.675G>T0.167
rpoB760484c.678A>G0.161
rpoB760493c.687C>G0.145
rpoB760547c.741G>C0.224
rpoB760563p.Arg253Met0.246
rpoB760591p.Val262Ala0.329
rpoB760601c.795C>T0.329
rpoB760611c.805T>C0.310
rpoB760622c.816C>T0.341
rpoB760646c.840C>G0.208
rpoB760649c.843G>C0.215
rpoB760655c.849A>G0.256
rpoB760661c.855A>C0.250
rpoB760667c.861G>A0.197
rpoB760670c.864G>C0.208
rpoB760674c.868T>C0.217
rpoB760679c.873A>G0.250
rpoB760683c.877T>C0.271
rpoB760724c.918T>C0.479
rpoB760730c.924T>C0.474
rpoB760748c.942C>G0.521
rpoB760757c.951T>C0.479
rpoB760759p.Val318Ala0.473
rpoB760769c.963C>G0.442
rpoB760793c.987A>G0.368
rpoB760805c.999G>C0.353
rpoB760817c.1011A>G0.301
rpoB760820c.1014T>C0.295
rpoB760826c.1020C>G0.316
rpoB760830c.1024T>C0.346
rpoB760841c.1035T>C0.376
rpoB760845p.Thr347Pro0.386
rpoB760856c.1050C>G0.475
rpoB760886c.1080A>G0.473
rpoB760916c.1110C>G0.372
rpoB760919c.1113C>G0.364
rpoB760925c.1119T>C0.351
rpoB760928c.1122G>C0.297
rpoB760931c.1125C>G0.299
rpoB760937c.1131G>A0.345
rpoB760946c.1140A>G0.404
rpoB760973c.1167G>C0.299
rpoB760982c.1176G>T0.247
rpoB760985c.1179G>T0.247
rpoB760991c.1185G>T0.234
rpoB761006c.1200C>T0.217
rpoB761015c.1209G>C0.220
rpoB761021c.1215G>C0.222
rpoB761027c.1221A>G0.198
rpoB761132c.1326G>T0.253
rpoB761133c.1327T>C0.263
rpoB761150c.1344A>C0.414
rpoB761168c.1362C>G0.456
rpoB761180c.1374A>C0.430
rpoB761189c.1383T>G0.438
rpoB761192c.1386C>G0.438
rpoB761195c.1389G>C0.398
rpoB761198c.1392G>C0.396
rpoB761240c.1434C>T0.457
rpoB761249c.1443A>G0.433
rpoB761255c.1449T>C0.443
rpoB761261c.1455G>T0.427
rpoB761264c.1458C>G0.451
rpoB761282c.1476C>G0.444
rpoB761327c.1521A>G0.366
rpoB761345c.1539G>T0.356
rpoB761354c.1548C>T0.344
rpoB761360c.1554T>C0.321
rpoB761362p.Ser519Thr0.341
rpoB761374p.Val523Glu0.378
rpoB761414c.1608A>G0.327
rpoB761423c.1617T>C0.283
rpoB761465c.1659G>A0.221
rpoB761471c.1665C>T0.257
rpoB761477c.1671C>T0.278
rpoB761492c.1686G>C0.267
rpoB761504c.1698C>G0.321
rpoB761510c.1704T>C0.310
rpoB761531c.1725C>G0.365
rpoB761537c.1731C>G0.385
rpoB761558c.1752C>G0.402
rpoB761570c.1764T>C0.364
rpoB761573c.1767C>G0.348
rpoB761579c.1773G>C0.389
rpoB761606c.1800C>G0.396
rpoB761612c.1806G>T0.420
rpoB761615c.1809A>C0.427
rpoB761636c.1830G>T0.481
rpoB761645c.1839C>A0.407
rpoB761648c.1842T>C0.396
rpoB761666c.1860G>C0.384
rpoB761690c.1884G>C0.337
rpoB761725p.Glu640Ala0.152
rpoB761732c.1926C>G0.157
rpoB761735c.1929C>G0.176
rpoB761750c.1944G>C0.295
rpoB761765c.1959T>C0.243
rpoB761772p.His656Ala0.185
rpoB761778p.Asn658Asp0.183
rpoB761791p.Arg662His0.177
rpoB761813c.2007T>C0.217
rpoB761885c.2079T>C0.176
rpoB761909c.2103T>C0.165
rpoB761912c.2106T>C0.162
rpoB761913p.Asp703Gln0.164
rpoB761916p.Asp704Asn0.162
rpoB761921c.2115C>T0.197
rpoB761930c.2124G>C0.380
rpoB761954c.2148C>G0.466
rpoB762008c.2202C>G0.469
rpoB762014c.2208C>T0.424
rpoB762047c.2241G>A0.327
rpoB762053c.2247T>C0.304
rpoB762062c.2256T>C0.271
rpoB762065c.2259T>C0.255
rpoB762083c.2277T>C0.208
rpoB762086c.2280G>C0.234
rpoB762101c.2295C>G0.288
rpoB762114p.Ile770Val0.272
rpoB762131c.2325C>G0.288
rpoB762134c.2328C>G0.288
rpoB762143c.2337T>C0.317
rpoB762167c.2361T>C0.396
rpoB762185c.2379G>C0.439
rpoB762233c.2427G>T0.461
rpoB762254c.2448T>G0.437
rpoB762257c.2451C>G0.419
rpoB762266c.2460T>C0.437
rpoB762278c.2472C>T0.416
rpoB762281c.2475G>A0.419
rpoB762284c.2478G>C0.411
rpoB762293c.2487T>C0.443
rpoB762317c.2511A>G0.412
rpoB762338c.2532T>C0.381
rpoB762341c.2535G>C0.384
rpoB762347c.2541T>C0.425
rpoB762362p.Glu852Asp0.383
rpoB762369c.2563T>C0.383
rpoB762395c.2589G>C0.237
rpoB762398c.2592T>C0.240
rpoB762401c.2595G>C0.227
rpoB762404c.2598T>C0.239
rpoB762410c.2604T>C0.386
rpoB762416c.2610A>G0.377
rpoB762431c.2625C>T0.471
rpoB762434c.2628T>G0.493
rpoB762449c.2643C>A0.469
rpoB762470c.2664G>C0.571
rpoB762491c.2685T>C0.489
rpoB762509c.2703T>G0.447
rpoB762510p.Ala902Pro0.433
rpoB762533c.2727T>C0.311
rpoB762536c.2730T>C0.308
rpoB762537c.2731T>C0.308
rpoB762551c.2745C>T0.281
rpoB762563c.2757G>A0.202
rpoB762581c.2775T>C0.149
rpoB762818c.3012C>G0.140
rpoB762827c.3021G>C0.197
rpoB762833c.3027C>T0.235
rpoB762857c.3051C>G0.383
rpoB762860c.3054G>T0.402
rpoB762902c.3096C>T0.521
rpoB762917c.3111C>T0.472
rpoB762929c.3123G>T0.415
rpoB762962c.3156C>T0.376
rpoB762983c.3177C>G0.336
rpoB762995c.3189G>T0.340
rpoB763031c.3225T>C1.000
rpoB763034c.3228C>G0.406
rpoB763040c.3234C>G0.384
rpoB763070c.3264T>C0.427
rpoB763082c.3276C>T0.470
rpoB763085c.3279C>G0.475
rpoB763115c.3309T>C0.508
rpoB763127c.3321G>C0.500
rpoB763166c.3360A>G0.433
rpoB763169c.3363A>G0.427
rpoB763202c.3396A>C0.162
rpoC763351c.-19T>C0.333
rpoC763352c.-18T>A0.333
rpoC763402c.33C>T0.475
rpoC763409c.40C>T0.444
rpoC763414c.45T>G0.438
rpoC763441c.72C>T0.464
rpoC763444c.75T>C0.464
rpoC763456c.87A>G0.527
rpoC763486c.117T>G0.492
rpoC763528c.159G>A0.532
rpoC763546c.177A>G0.550
rpoC763570c.201G>C0.567
rpoC763594c.225C>T0.574
rpoC763603c.234C>T0.544
rpoC763618c.249C>T0.548
rpoC763636c.267T>C0.500
rpoC763660c.291T>G0.429
rpoC763669c.300C>G0.405
rpoC763675c.306C>G0.382
rpoC763726c.357C>T0.211
rpoC763732c.363C>G0.227
rpoC763741c.372C>T0.178
rpoC763744c.375G>C0.219
rpoC763765c.396T>G0.321
rpoC763771c.402C>T0.333
rpoC763780c.411C>G0.375
rpoC763792p.Glu141Asp0.400
rpoC763801c.432C>G0.382
rpoC763807c.438T>C0.368
rpoC763836p.Ala156Val0.287
rpoC763858c.489A>G0.145
rpoC763872p.Gly168Ala0.297
rpoC763876p.Glu169Asp0.246
rpoC763879c.510A>G0.227
rpoC763888c.519G>C0.283
rpoC763891c.522G>C0.293
rpoC763894c.525A>G0.312
rpoC763936c.567C>G0.425
rpoC763939c.570G>A0.425
rpoC763951c.582G>A0.382
rpoC763963c.594C>G0.328
rpoC763967p.Gly200Ser0.288
rpoC763972c.603C>T0.273
rpoC763987c.618C>T0.317
rpoC763996c.627T>C0.233
rpoC764005c.636G>C0.276
rpoC764011c.642T>C0.244
rpoC764024c.655T>C0.261
rpoC764040p.Ser224Thr0.308
rpoC764044c.675T>G0.327
rpoC764059c.690G>T0.462
rpoC764083c.714A>G0.500
rpoC764101c.732C>G0.526
rpoC764140c.771C>T0.556
rpoC764159c.790C>T0.488
rpoC764167c.798G>A0.453
rpoC764188c.819A>G0.434
rpoC764195p.Ser276Ile0.412
rpoC764215c.846A>C0.356
rpoC764218c.849C>T0.340
rpoC764242c.873C>T0.328
rpoC764245c.876C>A0.299
rpoC764246c.877C>T0.312
rpoC764263c.894G>C0.379
rpoC764266c.897T>C0.377
rpoC764278c.909A>G0.387
rpoC764293c.924G>C0.434
rpoC764317c.948C>G0.442
rpoC764320c.951C>G0.460
rpoC764365c.996C>T0.380
rpoC764377c.1008C>G0.172
rpoC764380c.1011G>C0.130
rpoC764381c.1012T>A0.161
rpoC764387c.1018T>C0.153
rpoC764428c.1059G>C0.141
rpoC764431c.1062G>C0.156
rpoC764434c.1065A>G0.156
rpoC764446c.1077T>C0.222
rpoC764449c.1080G>C0.222
rpoC764452c.1083T>C0.219
rpoC764458c.1089G>C0.239
rpoC764461c.1092A>G0.239
rpoC764497c.1128A>G0.347
rpoC764503c.1134G>C0.500
rpoC764521c.1152T>C0.477
rpoC764527c.1158C>T0.478
rpoC764536c.1167G>T0.425
rpoC764539c.1170C>G0.432
rpoC764554c.1185C>T0.452
rpoC764575c.1206T>G0.440
rpoC764578c.1209C>G0.455
rpoC764593c.1224C>T0.432
rpoC764605c.1236G>A0.431
rpoC764626c.1257C>T0.468
rpoC764650c.1281G>T0.519
rpoC764668c.1299C>T0.538
rpoC764686c.1317C>T0.474
rpoC764746c.1377G>C0.411
rpoC764749c.1380G>C0.404
rpoC764752c.1383G>C0.411
rpoC764764c.1395T>C0.425
rpoC764782c.1413C>T0.464
rpoC764797c.1428G>C0.466
rpoC764803c.1434C>G0.466
rpoC764809c.1440C>T0.446
rpoC764815c.1446A>G0.417
rpoC764858c.1489T>C0.375
rpoC764887c.1518G>C0.231
rpoC764888c.1519T>C0.214
rpoC764896c.1527C>T0.256
rpoC764902c.1533C>T0.298
rpoC764911c.1542A>G0.277
rpoC764923c.1554A>G0.333
rpoC764932c.1563C>G0.342
rpoC764948c.1579T>C0.366
rpoC764968c.1599T>C0.375
rpoC765007c.1638T>G0.306
rpoC765008c.1639T>C0.301
rpoC765013c.1644C>T0.277
rpoC765019c.1650A>G0.269
rpoC765278c.1909C>T0.134
rpoC765283c.1914C>G0.127
rpoC765292c.1923G>T0.138
rpoC765300p.Val644Ala0.143
rpoC765328p.His653Gln0.120
rpoC765330p.Ser654Asn0.130
rpoC765334c.1965C>T0.125
rpoC765343c.1974G>A0.169
rpoC765352c.1983G>C0.226
rpoC765367c.1998C>G0.256
rpoC765370c.2001G>C0.326
rpoC765383p.Met672Leu0.361
rpoC765391c.2022C>T0.380
rpoC765406c.2037G>T0.370
rpoC765409c.2040T>C0.373
rpoC765412c.2043T>C0.393
rpoC765421c.2052C>G0.471
rpoC765452p.Ala695Ser0.388
rpoC765466c.2097C>T0.351
rpoC765478c.2109T>C0.309
rpoC765493c.2124G>C0.241
rpoC765499c.2130C>G0.241
rpoC765508c.2139C>G0.254
rpoC765517c.2148C>G0.197
rpoC765529c.2160C>T0.304
rpoC765541c.2172C>G0.349
rpoC765553c.2184C>T0.448
rpoC765556c.2187G>C0.435
rpoC765562c.2193G>C0.480
rpoC765578c.2209C>T0.518
rpoC765622p.Glu751Asp0.548
rpoC765625c.2256C>T0.508
rpoC765628c.2259G>C0.504
rpoC765658c.2289C>T0.532
rpoC765670c.2301C>T0.516
rpoC765728p.Gln787Lys0.442
rpoC765734c.2365T>C0.416
rpoC765739c.2370G>C0.390
rpoC765752p.Asp795Ser0.262
rpoC765772c.2403C>G0.338
rpoC765784c.2415C>G0.377
rpoC765790c.2421C>T0.333
rpoC765793c.2424C>G0.329
rpoC765796c.2427C>T0.346
rpoC765814c.2445A>G0.362
rpoC765826c.2457T>C0.389
rpoC765835c.2466C>T0.431
rpoC765883c.2514C>G0.475
rpoC765886c.2517C>G0.479
rpoC765892c.2523T>C0.490
rpoC765904c.2535C>T0.536
rpoC765934c.2565C>T0.445
rpoC765952c.2583G>T0.427
rpoC765967c.2598C>T0.405
rpoC765982c.2613C>G0.410
rpoC765994c.2625A>T0.393
rpoC766012c.2643C>G0.398
rpoC766021c.2652G>C0.430
rpoC766061p.Val898Ile0.363
rpoC766082p.Ala905Gln0.134
rpoC766093c.2724C>A0.128
rpoC766095p.Thr909Ser0.128
rpoC766105c.2736C>T0.119
rpoC766270c.2901G>C0.169
rpoC766273c.2904T>C0.188
rpoC766274p.Ala969Thr0.188
rpoC766280p.Ser971Gly0.222
rpoC766288c.2919C>G0.326
rpoC766309c.2940G>A0.402
rpoC766315c.2946C>G0.414
rpoC766321c.2952C>G0.431
rpoC766348c.2979A>G0.500
rpoC766369c.3000C>G0.436
rpoC766381c.3012C>T0.421
rpoC766384c.3015A>G0.435
rpoC766393c.3024C>G0.433
rpoC766402c.3033C>G0.441
rpoC766408c.3039C>T0.466
rpoC766426c.3057C>T0.471
rpoC766456c.3087C>G0.486
rpoC766486c.3117A>G0.374
rpoC766492c.3123T>C0.371
rpoC766522c.3153C>G0.341
rpoC766528c.3159T>C0.353
rpoC766530p.Arg1054Gln0.357
rpoC766549c.3180G>C0.397
rpoC766573c.3204T>C0.421
rpoC766585c.3216T>C0.449
rpoC766594c.3225G>C0.446
rpoC766607p.Ile1080Leu0.468
rpoC766630c.3261G>T0.455
rpoC766660c.3291G>A0.465
rpoC766666c.3297C>G0.433
rpoC766672c.3303T>C0.409
rpoC766700c.3331C>T0.466
rpoC766726c.3357T>C0.441
rpoC766733c.3364C>T0.409
rpoC766738c.3369G>C0.395
rpoC766741c.3372G>C0.403
rpoC766750c.3381C>G0.396
rpoC766765c.3396A>C0.416
rpoC766774c.3405T>C0.447
rpoC766798c.3429C>G0.438
rpoC766801c.3432C>G0.431
rpoC766804c.3435A>G0.444
rpoC766843c.3474T>G0.477
rpoC766864c.3495G>C0.434
rpoC766876c.3507C>T0.394
rpoC766883p.Ser1172Ala0.370
rpoC766894c.3525T>C0.243
rpoC766895c.3526T>C0.253
rpoC766900c.3531T>C0.265
rpoC766903c.3534C>T0.292
rpoC766918c.3549C>T0.375
rpoC766933c.3564A>G0.440
rpoC766945c.3576A>G0.443
rpoC766963c.3594T>C0.505
rpoC766996c.3627C>G0.450
rpoC767002c.3633G>C0.419
rpoC767009c.3640T>A0.304
rpoC767014c.3645G>C0.309
rpoC767033c.3664T>A0.484
rpoC767059c.3690T>G0.512
rpoC767062c.3693C>A0.533
rpoC767098c.3729T>C0.591
rpoC767119c.3750A>G0.575
rpoC767134c.3765C>A0.538
rpoC767158c.3789T>A0.406
rpoC767167c.3798C>G0.411
rpoC767180p.Ala1271Gln0.389
rpoC767191c.3822C>G0.372
rpoC767206c.3837C>G0.308
rpoC767209c.3840T>C0.293
rpoC767221c.3852C>G0.310
rpoC767230c.3861G>C0.319
rpoC767233c.3864T>C0.290
rpoC767263c.3894T>G0.274
rpoC767264p.Ala1299Gln0.263
rpoC767278c.3909T>C0.213
rpoC767281c.3912C>G0.208
rpoC767284c.3915C>T0.211
rpsL781395c.-165T>C1.000
rpsL781571c.12C>T0.221
rpsL781595c.36T>C0.296
rpsL781598c.39G>C0.293
rpsL781605p.Ile16Val0.286
rpsL781608p.Ser17Ala0.293
rpsL781628c.69T>C0.422
rpsL781655c.96T>C0.449
rpsL781658c.99A>G0.435
rpsL781682c.123T>C0.364
rpsL781715c.156T>C0.372
rpsL781718c.159C>G0.372
rpsL781721c.162C>T0.378
rpsL781728c.169T>C0.385
rpsL781736c.177T>C0.390
rpsL781751c.192G>C0.333
rpsL781754c.195G>C0.331
rpsL781760c.201T>C0.359
rpsL781766c.207C>T0.372
rpsL781772c.213C>G0.351
rpsL781793c.234G>C0.336
rpsL781808c.249C>T0.363
rpsL781832c.273T>G0.297
rpsL781835c.276T>C0.282
rpsL781859c.300T>G0.264
rpsL781865c.306G>C0.224
rpsL781868c.309T>C0.224
rpsL781871c.312G>C0.218
rpsL781883c.324G>A0.167
rpsL781886c.327C>T0.172
rpsL781892c.333A>G0.175
rpsL781898c.339A>T0.179
rpsL781916c.357T>C0.235
rpsL781929p.Gly124Ser0.309
rpsL781933374G>A0.345
rrs1471923r.78t>c0.333
rrs1471925r.80t>c0.321
rrs1471932r.87a>g0.330
rrs1471934r.89a>g0.355
rrs1471970r.125g>a0.505
rrs1472030r.185g>t0.395
rrs1472031r.186g>t0.390
rrs1472033r.188a>g0.405
rrs1472034r.189t>c0.417
rrs1472040r.195t>c0.442
rrs1472053r.208agc>a0.500
rrs1472061r.216a>t0.452
rrs1472075r.230a>g0.468
rrs1472460r.615t>c0.171
rrs1472461r.616g>c0.171
rrs1472463r.618g>c0.173
rrs1472464r.619a>g0.183
rrs1472489r.644a>g0.319
rrs1472686r.841g>a0.460
rrs1472847r.1002g>c0.277
rrs1472848r.1003t>g0.273
rrs1472849r.1004c>g0.273
rrs1472850r.1005t>c0.273
rrs1472857r.1012a>g0.305
rrs1472858r.1013g>t0.305
rrs1472859r.1014g>c0.305
rrs1472860r.1015c>g0.305
rrs1472969r.1124a>g0.425
rrs1472970r.1125c>g0.409
rrs1472977r.1132g>c0.405
rrs1472978r.1133t>c0.420
rrs1473105r.1260g>a0.459
rrs1473120r.1275c>ct0.348
rrs1473123r.1278a>t0.364
rrs1473288r.1443c>t0.430
rrs1473290r.1445c>t0.443
rrs1473291r.1446g>t0.438
rrl1473401c.-257G>A0.214
rrl1473403c.-255C>T0.217
rrl1473408c.-250C>T0.208
rrl1473417c.-241C>T0.205
rrl1473420c.-238A>G0.205
rrl1473421c.-237G>A0.208
rrl1473437c.-221T>C0.175
rrl1473659r.2t>c0.310
rrl1473668r.11c>t0.341
rrl1473676r.19g>a0.400
rrl1473758r.101g>t0.450
rrl1473797r.140g>t0.411
rrl1473806r.149c>t0.405
rrl1473813r.156c>t0.438
rrl1473831r.174g>a0.431
rrl1473876r.219g>a0.397
rrl1473887r.230t>a0.406
rrl1473888r.231t>a0.413
rrl1473899r.242a>t0.387
rrl1473918r.261c>t0.325
rrl1473943r.286g>c0.185
rrl1473945r.288t>a0.185
rrl1473946r.289a>t0.179
rrl1474001r.344c>t0.122
rrl1474009r.352a>g0.216
rrl1474011r.354g>a0.220
rrl1474018r.361g>a0.316
rrl1474030r.373g>a0.390
rrl1474061r.404t>c0.452
rrl1474089r.432c>t0.481
rrl1474093r.436g>a0.467
rrl1474100r.443c>t0.417
rrl1474103r.446a>t0.373
rrl1474110r.453a>c0.371
rrl1474111r.454t>c0.371
rrl1474130r.473c>t0.494
rrl1474140r.483c>t0.506
rrl1474181r.524c>t0.468
rrl1474249r.592g>t0.467
rrl1474291r.634tttcctctccggagga>t0.433
rrl1474308r.651g>t0.358
rrl1474310r.653t>g0.370
rrl1474433r.776g>t0.156
rrl1474447r.790g>a0.255
rrl1474627r.970g>a0.455
rrl1474632r.975g>t0.461
rrl1474639r.982g>a0.467
rrl1474717r.1060a>t0.500
rrl1474753r.1096a>g0.361
rrl1474760r.1103a>g0.370
rrl1474783r.1126g>a0.443
rrl1474794r.1137c>t0.457
rrl1474812r.1155g>a0.500
rrl1474831r.1174a>g0.512
rrl1474945r.1288c>t0.283
rrl1475013r.1356g>a0.226
rrl1475018r.1361g>a0.250
rrl1475027r.1370g>t0.256
rrl1475028r.1371g>t0.256
rrl1475061r.1404c>t0.390
rrl1475313r.1656g>a0.255
rrl1475315r.1658a>t0.275
rrl1475355r.1698c>t0.413
rrl1475369r.1712g>t0.455
rrl1475404r.1747a>g0.413
rrl1475405r.1748a>t0.412
rrl1475419r.1762c>t0.473
rrl1475429r.1772g>a0.413
rrl1475453r.1796t>a0.431
rrl1475480r.1823a>g0.373
rrl1475483r.1826c>t0.368
rrl1475487r.1830c>t0.386
rrl1475505r.1848g>a0.431
rrl1475526r.1869c>a0.430
rrl1475599r.1942a>g0.464
rrl1475604r.1947a>c0.400
rrl1475605r.1948a>t0.400
rrl1475608r.1951t>c0.394
rrl1475617r.1960c>g0.453
rrl1475625r.1968g>c0.479
rrl1475637r.1980t>a0.530
rrl1475642r.1985t>c0.517
rrl1475657r.2000a>g0.451
rrl1475659r.2002g>a0.460
rrl1475760r.2103c>t0.477
rrl1475763r.2106c>t0.459
rrl1475881r.2224t>c0.534
rrl1475988r.2331a>g0.538
rrl1475999r.2342g>t0.500
rrl1476030r.2373a>g0.320
rrl1476032r.2375c>t0.320
rrl1476033r.2376t>c0.327
rrl1476034r.2377c>g0.333
rrl1476045r.2388g>c0.333
rrl1476047r.2390g>a0.327
rrl1476049r.2392c>t0.327
rrl1476077r.2420t>c0.369
rrl1476086r.2429g>a0.288
rrl1476089r.2432t>c0.246
rrl1476095r.2438c>t0.241
rrl1476106r.2449a>t0.268
rrl1476115r.2458t>c0.368
rrl1476214r.2557g>t0.491
rrl1476215r.2558c>t0.491
rrl1476251r.2594t>c0.478
rrl1476580r.2923g>a0.512
rrl1476597r.2940g>a0.489
rrl1476619r.2962c>t0.420
rrl1476628r.2971t>a0.418
rrl1476689r.3032a>t0.312
rrl1476690r.3033c>t0.309
rrl1476693r.3036g>a0.309
rrl1476695r.3038t>a0.305
rrl1476716r.3059a>c0.310
rrl1476723r.3066t>a0.120
fabG11673475c.36A>C0.240
fabG11673499c.60T>C0.329
fabG11673505c.66A>T0.342
fabG11673517c.78G>C0.347
fabG11673524c.85C>T0.356
fabG11673535c.96A>G0.361
fabG11673547c.108T>C0.368
fabG11673565c.126G>C0.263
fabG11673758p.Lys107Glu0.133
fabG11673784c.345G>C0.145
fabG11673799c.360T>C0.172
fabG11673802c.363A>G0.161
fabG11673808c.369A>G0.161
inhA1674450c.249G>C0.298
inhA1674452p.Ala84Glu0.312
inhA1674463p.Leu88Ile0.394
inhA1674471c.270G>C0.377
inhA1674480c.279T>C0.419
inhA1674489c.288G>T0.461
inhA1674507c.306G>A0.461
inhA1674534c.333G>C0.180
inhA1674537c.336C>A0.180
inhA1674540c.339C>T0.184
inhA1674542p.Ala114Glu0.180
inhA1674549c.348G>C0.170
inhA1674555c.354G>A0.232
inhA1674561c.360C>T0.255
inhA1674585c.384T>C0.208
inhA1674588c.387G>A0.163
inhA1674589p.Met130Leu0.159
inhA1674601p.Leu134Val0.180
inhA1674618c.417C>T0.161
inhA1674619p.Pro140Ser0.173
inhA1674624c.423A>T0.164
inhA1674627c.426T>C0.167
inhA1674792c.591G>C0.208
inhA1674801c.600T>C0.276
inhA1674820c.619C>T0.433
inhA1674828c.627G>A0.459
inhA1674846p.Ile215Met0.462
inhA1674870c.669T>C0.581
inhA1674876c.675C>G0.570
inhA1674879c.678T>C0.571
inhA1674888c.687C>T0.593
inhA1674904p.Ala235Pro0.549
inhA1674909c.708G>C0.506
inhA1674915c.714C>G0.564
inhA1674939c.738G>A0.527
inhA1674942c.741T>C0.533
inhA1674966c.765T>C0.435
inhA1674967p.Asp256Thr0.435
rpsA1833532c.-10A>C0.310
rpsA1833568c.27G>C0.404
rpsA1833589c.48A>T0.439
rpsA1833595c.54T>C0.448
rpsA1833613c.72C>A0.512
rpsA1833619c.78A>C0.485
rpsA1833661c.120A>G0.524
rpsA1833667c.126C>G0.544
rpsA1833703c.162C>T0.535
rpsA1833724c.183C>G0.481
rpsA1833727c.186G>C0.472
rpsA1833745c.204G>C0.508
rpsA1833760c.219C>T0.575
rpsA1833790c.249T>C0.449
rpsA1833793c.252C>T0.459
rpsA1833802c.261A>G0.460
rpsA1833808c.267G>C0.486
rpsA1833811c.270G>T0.462
rpsA1833832c.291G>A0.405
rpsA1833838c.297G>C0.379
rpsA1833841c.300C>G0.381
rpsA1833847c.306C>G0.421
rpsA1833856c.315A>G0.409
rpsA1833859c.318C>T0.369
rpsA1833874c.333T>C0.453
rpsA1833895c.354G>C0.481
rpsA1833928c.387G>C0.546
rpsA1833949c.408T>C0.500
rpsA1833970c.429G>A0.586
rpsA1833979c.438T>C0.540
rpsA1834015c.474G>C0.579
rpsA1834021c.480C>T0.567
rpsA1834102c.561T>C0.377
rpsA1834105c.564C>T0.370
rpsA1834165c.624A>G0.153
rpsA1834177c.636A>C0.323
rpsA1834186c.645C>G0.358
rpsA1834189c.648G>C0.376
rpsA1834195c.654G>C0.393
rpsA1834222c.681T>C0.431
rpsA1834225c.684C>G0.451
rpsA1834231c.690T>G0.477
rpsA1834249c.708T>C0.477
rpsA1834261c.720A>G0.431
rpsA1834264c.723G>C0.429
rpsA1834279c.738C>T0.446
rpsA1834297c.756C>T0.438
rpsA1834303c.762T>G0.437
rpsA1834336c.795C>G0.503
rpsA1834348c.807T>C0.552
rpsA1834366c.825A>G0.520
rpsA1834375c.834G>A0.496
rpsA1834396c.855G>T0.511
rpsA1834411c.870T>C0.461
rpsA1834423c.882G>T0.437
rpsA1834451c.910T>C0.436
rpsA1834456c.915T>G0.446
rpsA1834465c.924T>C0.450
rpsA1834468c.927A>G0.453
rpsA1834477c.936C>T0.450
rpsA1834489c.948T>C0.471
rpsA1834510c.969C>T0.511
rpsA1834519c.978G>C0.549
rpsA1834546c.1005T>C0.576
rpsA1834555c.1014T>G0.546
rpsA1834603c.1062G>A0.581
rpsA1834609c.1068T>C0.590
rpsA1834612c.1071G>A0.595
rpsA1834633c.1092A>G0.559
rpsA1834639c.1098T>C0.554
rpsA1834654c.1113G>A0.519
rpsA1834690c.1149T>C0.473
rpsA1834699p.Glu386Asp0.447
rpsA1834732c.1191T>C0.323
rpsA1834789c.1248T>C0.333
rpsA1834792c.1251G>C0.362
rpsA1834813c.1272G>A0.388
rpsA1834852c.1311C>G0.346
rpsA1834858c.1317G>A0.321
rpsA1834864c.1323T>C0.269
rpsA1834869p.Arg443His0.270
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
katG2155651p.Lys154Arg0.217
katG2155656c.456C>T0.213
katG2155661p.Val151Ile0.224
katG2155680c.432C>G0.320
katG2155691c.421A>G0.314
katG2155695c.417G>C0.320
katG2155716c.396A>G0.296
katG2155728c.384C>G0.348
pncA2289047c.195G>A1.000
kasA2518162c.48G>A0.306
kasA2518169p.Val19Leu0.320
kasA2518172p.Thr20Ala0.314
kasA2518190p.Ser26Ala0.305
kasA2518199p.Ile29Val0.316
kasA2518219c.105T>C0.295
kasA2518220c.106C>T0.290
kasA2518245p.His44Arg0.193
kasA2518723c.609G>A0.210
kasA2518735c.621C>T0.262
kasA2518747c.633C>G0.325
kasA2518768c.654C>G0.484
kasA2518783c.669T>C0.505
kasA2518789c.675G>C0.510
kasA2518795c.681C>A0.490
kasA2518798c.684G>C0.490
kasA2518825c.711T>C0.447
kasA2518840c.726C>G0.329
kasA2518843c.729T>G0.300
kasA2518846c.732G>C0.290
kasA2518855c.741C>G0.226
eis2714460c.873C>T1.000
ahpC2726105c.-88G>A1.000
ahpC2726591c.399C>G0.155
ahpC2726600c.408T>C0.158
ahpC2726627c.435G>A0.158
ahpC2726645c.453C>G0.161
ahpC2726654c.462G>T0.150
ahpC2726657c.465A>G0.150
ahpC2726660c.468C>T0.153
ahpC2726669c.477T>C0.136
ahpC2726675c.483A>G0.130
ahpC2726681c.489A>G0.150
thyX3067634c.312G>C0.138
thyX3067652c.294A>G0.154
thyX3067661c.285G>T0.151
thyX3067676c.270G>C0.140
thyX3067680p.Cys89Leu0.136
thyX3067685c.261T>C0.143
thyX3067693p.Ile85Val0.133
thyX3067694c.252C>G0.194
thyX3067718c.228G>C0.213
thyX3067765p.Leu61Ile0.136
thyX3067781c.165G>C0.234
thyX3067793c.153A>G0.247
thyX3067802c.144G>C0.171
thyX3067814c.132A>G0.171
thyX3067817c.129G>A0.176
thyX3067841c.105C>G0.203
thyA3073839c.633A>G0.158
thyA3073854c.618G>A0.289
thyA3073863c.609A>G0.247
thyA3073889p.Ser195Asp0.240
thyA3073892c.580A>G0.248
thyA3073905c.567G>C0.282
thyA3073925c.547A>G0.307
thyA3073929c.543A>G0.274
thyA3073944c.528G>A0.307
thyA3073953c.519A>G0.321
thyA3073956c.516C>G0.291
thyA3073959c.513A>G0.299
thyA3073968c.504G>C0.415
thyA3073977c.495T>C0.419
thyA3073989c.483A>G0.474
thyA3074001c.471G>C0.469
thyA3074004c.468A>G0.469
thyA3074037c.435G>C0.418
thyA3074053p.Arg140Gln0.325
thyA3074057p.Glu139Pro0.321
thyA3074070c.402G>A0.253
thyA3074076c.396G>C0.214
thyA3074334c.138A>G0.150
thyA3074337c.135G>C0.195
thyA3074360c.112A>G0.202
thyA3074361c.111A>G0.198
thyA3074364c.108A>G0.185
thyA3074372p.Met34Leu0.195
thyA3074373c.99C>T0.195
ald3086788c.-32T>C1.000
fbiA3640347c.-196A>G0.397
fbiA3640365c.-178C>G0.442
panD4044177c.105G>C0.175
panD4044180c.102G>A0.210
panD4044188c.94A>G0.265
panD4044195c.87A>G0.278
panD4044225c.57G>A0.295
panD4044233p.Cys17Gln0.292
panD4044237c.45C>G0.289
panD4044264c.18C>G0.282
embC4240495c.633T>C0.133
embC4240512p.Ser217Thr0.233
embC4240516c.654G>C0.219
embC4240519c.657T>C0.197
embC4240525c.663C>G0.173
embC4240561c.699C>G0.197
embC4240726c.864G>C0.288
embC4240729c.867C>G0.279
embC4240747c.885C>T0.264
embC4240759c.897C>G0.235
embC4240765c.903C>G0.237
embC4240783c.921G>C0.191
embC4240789c.927T>C0.182
embC4240795c.933C>G0.137
embC4241059c.1197G>A0.188
embC4241071c.1209C>G0.194
embC4241086c.1224G>C0.244
embC4241095c.1233C>T0.241
embC4241101c.1239G>C0.244
embC4241121p.Ser420Asn0.276
embC4241137c.1275G>C0.244
embC4241146c.1284C>G0.174
embC4241153p.Ile431Val0.115
embC4241377c.1515C>G0.148
embC4241378p.Val506Leu0.148
embC4241394p.Lys511Ser0.440
embC4241452c.1590G>C0.511
embC4241455c.1593C>T0.433
embC4241461c.1599C>G0.396
embC4241470c.1608C>G0.329
embC4242075p.Arg738Gln1.000
embC4242643c.2781C>T1.000
embA4245093p.Ile621Val0.154
embA4245101c.1869G>C0.214
embA4245125c.1893G>C0.287
embA4245137c.1905T>C0.255
embA4245149c.1917C>G0.309
embB4247425c.912G>C0.292
embB4247437c.924A>G0.361
embB4247452c.939C>G0.389
embB4247470c.957T>C0.432
embB4247497c.984T>C0.425
embB4247500c.987C>G0.418
embB4247506c.993C>G0.390
embB4247512c.999T>C0.362
embB4247527c.1014G>C0.333
embB4247539c.1026T>C0.330
embB4247550p.Ala346Asp0.356
embB4247554c.1041T>C0.388
embB4247566c.1053C>G0.333
embB4247572c.1059A>C0.315
embB4247590c.1077A>G0.350
embB4247629c.1116C>G0.242
embB4247632c.1119C>G0.213
embB4247638c.1125G>C0.203
embB4247677c.1164C>G0.232
embB4247684c.1171T>C0.232
embB4247722c.1209G>T0.205
embB4247725c.1212G>C0.211
embB4247729p.Gly406Pro0.216
embB4247753p.Val414Ile0.182
embB4247951p.Ser480Ala0.180
embB4247971c.1458C>A0.269
embB4247972p.Thr487Phe0.277
embB4247983c.1470G>C0.378
embB4248007c.1494C>A0.326
embB4248055c.1542G>C0.133
embB4248064c.1551G>C0.115
embB4248190c.1677G>C0.341
embB4248200p.Ile563Val0.411
embB4248206p.Ser565Gly0.440
embB4248211c.1698G>A0.457
embB4248220c.1707A>C0.480
embB4248241c.1728C>T0.551
embB4248277c.1764G>C0.528
embB4248298c.1785C>T0.450
embB4248304c.1791G>C0.441
embB4248316c.1803C>G0.349
embB4248319c.1806A>G0.345
embB4248322c.1809G>C0.333
ethA4327389p.Thr29Ser0.139
ethA4327396c.78A>C0.154
ethA4327399p.Asp25Glu0.141
ethA4327414c.60G>T0.154
ethA4327420c.54G>A0.182
ethA4327423c.51G>C0.147
ethA4327435c.39T>G0.156
ethA4327438c.36A>G0.159
ethA4327453c.21A>G0.147
gid4407657c.545 545del1.000

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;