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: 5d9fc95de04aa
Sample: 5d9fc95de04aa

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Summary
ID: 5d9fc95de04aa
Date: Fri Oct 11 01:15:38 2019
Strain: lineage4.8
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
StreptomycinRrrs r.514a>c (0.68), rrs r.799c>t (0.27)
Ethionamide
Fluoroquinolones
AmikacinRrrs r.1402c>a (0.40), rrs r.1484g>t (0.41)
CapreomycinRrrs r.1402c>a (0.40), rrs r.1484g>t (0.41)
KanamycinRrrs r.1402c>a (0.40), rrs r.1484g>t (0.41)

Lineage2FamilyMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.8Euro-American (mainly T)T1;T2;T3;T5RD219

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
gyrA7859c.558A>C0.162
gyrA8567p.Ile422Met0.412
rpoB760916c.1110C>T0.162
rpoB760920p.Leu372Ile0.162
rpoB760925c.1119T>C0.171
rpoB760926p.Thr374Ala0.171
rpoB760946c.1140A>G0.167
rpoB761015c.1209G>C0.188
rpoB761027c.1221A>G0.196
rpoB761036c.1230G>C0.204
rpoB761037c.1231T>C0.204
rpoB761051c.1245G>C0.233
rpoB761054c.1248G>C0.244
rpoB761057c.1251G>C0.250
rpoB761060c.1254C>G0.250
rpoB761064p.Ala420Ser0.250
rpoB761084c.1278C>G0.275
rpoB761087c.1281C>G0.275
rpoB761097c.1291A>T0.297
rpoB761102c.1296A>G0.306
rpoB761105c.1299C>T0.684
rpoB761132c.1326G>C0.138
rpoB761133c.1327T>C0.172
rpoB761138c.1332C>G0.143
rpoB761207c.1401C>T0.227
rpoB761213c.1407G>C0.238
rpoB761217p.Pro471Thr0.227
rpoB761234c.1428G>C0.222
rpoB761249c.1443A>G0.240
rpoB761255c.1449T>C0.240
rpoB761261c.1455G>T0.208
rpoB761264c.1458C>G0.217
rpoB761273c.1467T>C0.208
rpoB761276c.1470G>C0.190
rpoB761288c.1482G>C0.150
rpoB761289p.Ser495Ala0.150
rpoB761299p.Ala498Gly0.208
rpoB761304p.Val500Ile0.200
rpoB761318c.1512G>C0.208
rpoB761322p.Ile506Val0.208
rpoB761327c.1521A>G0.208
rpoB761961p.Pro719Ser0.263
rpoB761981c.2175C>T0.256
rpoB762002c.2196C>G0.135
rpoB762003p.Asn733Gln0.132
rpoB762011c.2205G>C0.135
rpoB762014c.2208C>G0.143
rpoB762015p.Glu737Gln0.143
rpoB762020p.Glu738Asp0.147
rpoB762030p.Thr742Ser0.250
rpoB762053c.2247T>C0.186
rpoB762057p.Ile751Val0.182
rpoB762062c.2256T>C0.182
rpoB762065c.2259T>G0.182
rpoB762080c.2274G>C0.200
rpoB762083c.2277T>A0.196
rpoB762084p.Ala760Pro0.196
rpoB762098c.2292C>G0.244
rpoB762101c.2295C>G0.256
rpoB762114p.Ile770Val0.256
rpoB762122p.Asp772Glu0.261
rpoB762128c.2322G>C0.244
rpoB762131c.2325C>G0.238
rpoB762134c.2328C>G0.233
rpoB762140c.2334G>C0.227
rpoB762143c.2337T>C0.250
rpoB762149c.2343G>C0.250
rpoB762156p.Val784Ile0.227
rpoB762167c.2361T>C0.209
rpoB762181p.Asp792Gly0.146
rpoB762194c.2388G>C0.171
rpoB762218c.2412T>C0.140
rpoB762233c.2427G>C0.128
rpoB762236c.2430G>C0.128
rpoB762251c.2445G>C0.135
rpoB762293c.2487T>G0.125
rpoB762299c.2493G>C0.118
rpoB762426p.Ser874Thr0.483
rpoB762434c.2628T>C0.500
rpoB762443c.2637G>C0.517
rpoB762470c.2664G>C0.370
rpoB762474p.Gly890Ser0.346
rpoB762485c.2679G>C0.357
rpoB762491c.2685T>C0.357
rpoB762849p.Tyr1015Asp0.179
rpoB762857c.3051C>G0.179
rpoB762858p.Thr1018Ala0.179
rpoB762863c.3057T>C0.172
rpoB762879p.Met1025Leu0.250
rpoB762887c.3081G>C0.303
rpoB762899c.3093G>C0.306
rpoB762917c.3111C>G0.324
rpoB762923c.3117C>G0.316
rpoB762929c.3123G>C0.316
rpoB762947c.3141C>G0.366
rpoB762962c.3156C>T0.341
rpoB762995c.3189G>C0.310
rpoB763005p.Cys1067Val0.278
rpoB763014p.Met1070Leu0.273
rpoB763017p.Gln1071Glu0.265
rpoB763022c.3216C>G0.250
rpoB763028c.3222T>C0.293
rpoB763040c.3234C>G0.304
rpoB763052c.3246G>C0.267
rpoB763053c.3247T>C0.267
rpoB763070c.3264T>C0.227
rpoB763115c.3309T>C0.278
rpoB763127c.3321G>C0.211
rpoB763130p.Glu1108Asp0.214
rpoB763131p.Pro1109Ser0.214
rpoB763142c.3336C>G0.235
rpoB763157c.3351G>T0.208
rpoB763166c.3360A>G0.184
rpoB763169c.3363A>G0.178
rpoB763170p.Leu1122Met0.182
rpoB763181c.3375G>C0.170
rpoB763187c.3381C>G0.146
rpoC763462c.93G>C0.236
rpoC763468c.99G>C0.250
rpoC763480c.111C>G0.237
rpoC763483c.114G>C0.233
rpoC763486c.117T>G0.230
rpoC763504c.135C>G0.267
rpoC763507c.138G>C0.262
rpoC763528c.159G>T0.237
rpoC763531c.162G>C0.246
rpoC763534c.165T>G0.246
rpoC763537c.168C>G0.276
rpoC763546c.177A>G0.306
rpoC763570c.201G>C0.280
rpoC763615c.246G>C0.289
rpoC763618c.249C>G0.297
rpoC763622p.Ala85Ser0.297
rpoC763630c.261G>C0.289
rpoC763633c.264T>C0.282
rpoC763642c.273G>C0.282
rpoC763660c.291T>C0.289
rpoC763675c.306C>G0.289
rpoC763686p.Tyr106Phe0.289
rpoC763702c.333C>G0.268
rpoC763708c.339G>C0.194
rpoC763711c.342G>C0.171
rpoC763714c.345G>C0.171
rpoC763717c.348T>C0.167
rpoC763723c.354G>C0.162
rpoC763894c.525A>G0.140
rpoC763900c.531G>C0.163
rpoC763921c.552G>C0.149
rpoC763933c.564C>T0.146
rpoC763945c.576T>C0.156
rpoC763951c.582G>C0.156
rpoC763960c.591T>G0.136
rpoC764452c.1083T>C0.184
rpoC764461c.1092A>G0.194
rpoC764491c.1122G>C0.200
rpoC764497c.1128A>G0.147
rpoC764498p.Ser377Ala0.152
rpoC764507p.Ala380Ser0.229
rpoC764521c.1152T>C0.206
rpoC764533c.1164C>T0.194
rpoC764536c.1167G>C0.179
rpoC764539c.1170C>G0.184
rpoC764542c.1173C>G0.179
rpoC764545c.1176C>G0.179
rpoC764548c.1179G>C0.179
rpoC764551c.1182G>C0.179
rpoC764573p.Leu402Ile0.171
rpoC764581c.1212T>C0.179
rpoC764582p.Leu405Met0.175
rpoC764611c.1242G>C0.200
rpoC764632c.1263T>C0.182
rpoC764650c.1281G>T0.191
rpoC764662c.1293G>C0.213
rpoC764706p.Leu446Gln0.264
rpoC764716c.1347G>C0.259
rpoC764722c.1353G>C0.246
rpoC764746c.1377G>C0.259
rpoC764749c.1380G>C0.259
rpoC764764c.1395T>C0.255
rpoC764780c.1411A>T0.208
rpoC764785c.1416C>G0.220
rpoC764797c.1428G>C0.216
rpoC764804p.Gln479Ala0.196
rpoC764812c.1443C>G0.188
rpoC764813p.Gln482Val0.184
rpoC764824c.1455T>C0.184
rpoC764833c.1464A>G0.209
rpoC764843p.Ala492Thr0.220
rpoC764857c.1488G>C0.179
rpoC764858c.1489T>C0.184
rpoC764869c.1500C>T0.172
rpoC764872c.1503A>G0.172
rpoC766837c.3468G>C0.385
rpoC766843c.3474T>C0.385
rpoC766846c.3477C>G0.370
rpsL781395c.-165T>C1.000
rrs1471866r.21c>t0.464
rrs1471967r.122g>a0.320
rrs1471969r.124t>c0.320
rrs1471970r.125g>a0.308
rrs1471972r.127t>c0.320
rrs1471980r.135g>t0.296
rrs1471998r.153g>t0.296
rrs1472005r.160t>g0.296
rrs1472061r.216a>t0.143
rrs1472062r.217g>t0.143
rrs1472068r.223t>g0.441
rrs1472075r.230a>g0.469
rrs1472078r.233c>t0.471
rrs1472108r.263c>t0.500
rrs1472148r.303t>c0.371
rrs1472150r.305t>a0.371
rrs1472172r.327t>c0.410
rrs1472225r.380c>a0.289
rrs1472251r.406g>a0.302
rrs1472259r.414c>a0.286
rrs1472285r.440a>g0.143
rrs1472286r.441c>g0.143
rrs1472289r.444t>g0.143
rrs1472290r.445c>g0.143
rrs1472293r.448c>a0.139
rrs1472313r.468g>a0.135
rrs1472315r.470t>g0.139
rrs1472324r.479g>c0.147
rrs1472325r.480g>c0.147
rrs1472328r.483g>c0.143
rrs1472338r.493a>g0.212
rrs1472344r.499c>t0.250
rrs1472379r.534t>c0.318
rrs1472382r.537g>a0.341
rrs1472400r.555c>t0.390
rrs1472422r.577t>c0.366
rrs1472437r.592t>c0.161
rrs1472456r.611t>c0.172
rrs1472460r.615t>c0.179
rrs1472461r.616g>t0.172
rrs1472462r.617t>g0.172
rrs1472464r.619a>g0.172
rrs1472467r.622g>t0.172
rrs1472471r.626g>a0.172
rrs1472473r.628g>t0.172
rrs1472474r.629c>g0.179
rrs1472476r.631a>g0.179
rrs1472494r.649a>g0.294
rrs1472496r.651t>g0.312
rrs1472498r.653c>t0.312
rrs1472504r.659a>t0.355
rrs1472558r.713g>a0.370
rrs1472569r.724g>a0.370
rrs1472574r.729t>a0.367
rrs1472581r.736a>c0.344
rrs1472583r.738t>c0.344
rrs1472607r.762g>a0.321
rrs1472655r.810g>t0.238
rrs1472660r.815t>c0.222
rrs1472674r.829t>c0.195
rrs1472675r.830t>c0.200
rrs1472677r.832c>a0.200
rrs1472682r.837t>a0.175
rrs1472683r.838t>c0.195
rrs1472687r.842a>t0.190
rrs1472697r.852t>c0.250
rrs1472701r.856t>a0.250
rrs1472714r.869a>g0.295
rrs1472755r.910g>a0.250
rrs1472790r.945t>c0.283
rrs1472880r.1035g>a0.129
rrs1472895r.1050c>t0.265
rrs1472952r.1107t>c0.265
rrs1472956r.1111t>c0.212
rrs1472969r.1124a>g0.222
rrs1472970r.1125c>g0.222
rrs1472973r.1128a>t0.222
rrs1472977r.1132g>c0.216
rrs1472978r.1133t>c0.222
rrs1472987r.1142g>a0.250
rrs1472990r.1145a>g0.250
rrs1473035r.1190g>a0.154
rrs1473055r.1210c>t0.167
rrs1473056r.1211a>t0.167
rrs1473066r.1221a>g0.250
rrs1473100r.1255g>a0.256
rrs1473105r.1260g>a0.256
rrs1473110r.1265t>g0.244
rrs1473111r.1266a>g0.244
rrs1473121r.1276t>c0.239
rrs1473122r.1277t>a0.239
rrs1473145r.1300c>t0.279
rrs1473166r.1321g>a0.326
rrs1473252r.1407t>c0.400
rrs1473276r.1431a>g0.419
rrs1473290r.1445c>t0.333
rrs1473294r.1449a>g0.343
rrs1473301r.1456t>c0.389
rrs1473315r.1470t>c0.405
rrs1473316r.1471c>t0.405
rrl1473807r.150t>g0.167
rrl1473812r.155g>t0.188
rrl1473815r.158t>c0.188
rrl1473832r.175c>a0.188
rrl1473845r.188g>c0.188
rrl1474181r.524c>a0.190
rrl1474183r.526t>c0.182
rrl1474184r.527c>t0.174
rrl1474186r.529a>g0.182
rrl1474201r.544t>c0.160
rrl1474202r.545t>a0.160
rrl1474218r.561t>a0.214
rrl1474249r.592g>t0.200
rrl1474281r.624a>g0.214
rrl1474290r.633t>c0.154
rrl1474305r.648g>c0.143
rrl1474306r.649a>t0.143
rrl1474316r.659t>c0.182
rrl1474348r.691c>t0.188
rrl1474351r.694g>t0.188
rrl1474353r.696a>g0.188
rrl1474354r.697c>t0.188
rrl1474356r.699t>c0.194
rrl1474359r.702c>g0.194
rrl1474362r.705a>g0.194
rrl1474381r.724t>g0.214
rrl1474387r.730c>t0.231
rrl1474402r.745t>c0.231
rrl1474558r.901g>t0.167
rrl1474626r.969t>c0.250
rrl1474627r.970g>a0.250
rrl1474630r.973t>c0.250
rrl1474632r.975g>t0.250
rrl1474636r.979a>t0.250
rrl1474637r.980c>t0.250
rrl1474638r.981c>g0.250
rrl1474639r.982g>c0.250
rrl1474660r.1003g>a0.348
rrl1474673r.1016t>c0.308
rrl1474676r.1019t>c0.296
rrl1474690r.1033c>t0.385
rrl1474734r.1077g>t0.320
rrl1474760r.1103a>g0.321
rrl1474777r.1120t>c0.321
rrl1474779r.1122g>a0.310
rrl1474782r.1125g>a0.310
rrl1474794r.1137c>t0.281
rrl1474823r.1166c>g0.333
rrl1474827r.1170c>t0.324
rrl1474831r.1174a>c0.324
rrl1474904r.1247g>c0.172
rrl1474905r.1248t>c0.172
rrl1474913r.1256t>c0.226
rrl1475508r.1851a>t0.278
rrl1475526r.1869c>a0.278
rrl1475538r.1881t>a0.238
rrl1475539r.1882a>t0.238
rrl1475544r.1887a>c0.227
rrl1475545r.1888t>g0.208
rrl1475548r.1891c>t0.208
rrl1475549r.1892t>c0.208
rrl1475550r.1893a>g0.200
rrl1475649r.1992a>g0.292
rrl1475655r.1998t>g0.292
rrl1475659r.2002g>a0.292
rrl1475753r.2096c>g0.286
rrl1475755r.2098t>g0.286
rrl1475757r.2100a>c0.286
rrl1475759r.2102c>g0.250
rrl1475769r.2112t>c0.250
rrl1475775r.2118g>t0.250
rrl1475776r.2119g>c0.235
rrl1475896r.2239a>g0.231
rrl1475897r.2240t>c0.231
rrl1475898r.2241a>g0.231
rrl1475899r.2242g>a0.231
rrl1475943r.2286g>a0.250
rrl1475952r.2295a>g0.250
rrl1475970r.2313c>t0.188
rrl1475975r.2318c>t0.176
rrl1475977r.2320a>g0.176
rrl1476131r.2474c>t0.333
rrl1476160r.2503t>c0.381
rrl1476194r.2537a>g0.429
rrl1476200r.2543a>t0.421
rrl1476201r.2544c>t0.421
rrl1476221r.2564t>c0.389
rrl1476224r.2567a>g0.429
rrl1476245r.2588c>t0.421
rrl1476251r.2594t>c0.421
rrl1476252r.2595t>g0.421
rrl1476256r.2599a>g0.421
rrl1476260r.2603a>g0.421
rrl1476281r.2624t>c0.364
rrl1476294r.2637a>g0.222
rrl1476295r.2638c>g0.211
rrl1476296r.2639c>t0.211
rrl1476297r.2640c>g0.211
rrl1476298r.2641c>g0.211
rrl1476300r.2643g>t0.200
rrl1476301r.2644a>t0.200
rrl1476309r.2652g>c0.190
rrl1476311r.2654g>c0.190
rrl1476312r.2655t>c0.190
rrl1476359r.2702c>g0.182
rrl1476381r.2724g>c0.174
rrl1476428r.2771c>t0.300
rrl1476466r.2809c>t0.500
rrl1476506r.2849t>c0.600
rrl1476515r.2858c>t0.556
rrl1476523r.2866t>c0.500
rrl1476524r.2867c>a0.474
rrl1476525r.2868a>g0.474
rrl1476536r.2879g>a0.474
rrl1476538r.2881a>g0.474
rrl1476539r.2882a>g0.474
rrl1476540r.2883c>g0.474
rrl1476584r.2927c>t0.480
rrl1476585r.2928a>g0.480
rrl1476594r.2937c>t0.444
rrl1476603r.2946g>a0.444
rrl1476608r.2951c>g0.414
rrl1476614r.2957a>t0.400
rrl1476616r.2959a>g0.400
rrl1476619r.2962c>t0.400
rrl1476628r.2971t>a0.429
rrl1476629r.2972c>a0.429
rrl1476630r.2973a>g0.429
rrl1476661r.3004a>g0.452
rrl1476665r.3008t>g0.467
rrl1476668r.3011c>t0.467
rrl1476675r.3018c>g0.444
rpsA1833694c.153G>C0.125
rpsA1833697c.156C>G0.123
rpsA1833721c.180A>G0.151
rpsA1833727c.186G>C0.163
rpsA1833734p.Ala65Ser0.163
rpsA1833742c.201A>G0.188
rpsA1833763c.222C>G0.217
rpsA1833829c.288A>G0.129
rpsA1833835c.294C>T0.138
rpsA1833841c.300C>G0.133
rpsA1833847c.306C>G0.138
rpsA1833850c.309C>G0.138
rpsA1833856c.315A>G0.138
rpsA1833859c.318C>T0.143
rpsA1833874c.333T>C0.250
rpsA1833877c.336C>G0.241
rpsA1833886c.345C>G0.214
rpsA1833893p.Ala118Lys0.233
rpsA1833896p.Leu119Ile0.250
rpsA1833905p.Lys122Glu0.259
rpsA1833912p.Glu124Gly0.269
rpsA1833915p.Ala125Val0.269
rpsA1833921p.Lys127Thr0.308
rpsA1833928c.387G>C0.355
rpsA1833949c.408T>C0.375
rpsA1833955c.414G>C0.375
rpsA1833970c.429G>T0.379
rpsA1833979c.438T>C0.323
rpsA1833997c.456G>C0.317
rpsA1834000c.459G>C0.317
rpsA1834009c.468C>T0.333
rpsA1834012c.471G>T0.333
rpsA1834024c.483G>C0.286
rpsA1834030c.489C>G0.220
rpsA1834034p.Ile165Val0.200
rpsA1834069c.528G>C0.231
rpsA1834093c.552G>C0.225
rpsA1834099c.558C>G0.200
rpsA1834102c.561T>C0.188
rpsA1834105c.564C>T0.188
rpsA1834108c.567C>G0.188
rpsA1834114c.573G>C0.171
rpsA1834123c.582C>G0.162
rpsA1834129c.588C>G0.182
rpsA1834240c.699T>G0.167
rpsA1834243c.702G>C0.167
rpsA1834249c.708T>C0.162
rpsA1834261c.720A>C0.200
rpsA1834264c.723G>C0.200
rpsA1834294c.753G>C0.174
rpsA1834298p.Gln253Glu0.170
rpsA1834303c.762T>C0.163
rpsA1834306c.765T>C0.163
rpsA1834307p.Asp256Gln0.163
rpsA1834318c.777C>G0.176
rpsA1834327c.786G>T0.188
rpsA1834340p.Met267Phe0.167
rpsA1834348c.807T>C0.157
rpsA1834354c.813G>C0.157
rpsA1834357c.816T>C0.157
rpsA1834361c.820T>C0.160
rpsA1834366c.825A>G0.160
rpsA1834369c.828C>G0.160
rpsA1834378c.837T>G0.154
rpsA1834384c.843A>G0.154
rpsA1834395p.Arg285Gln0.120
rpsA1834397p.His286Ala0.122
rpsA1834408c.867C>G0.132
rpsA1834411c.870T>G0.135
rpsA1834417c.876G>C0.130
rpsA1834423c.882G>C0.125
rpsA1834427p.Ile296Val0.125
rpsA1834432c.891G>C0.130
rpsA1834435c.894G>C0.135
rpsA1834451c.910T>C0.146
tlyA1917972c.33A>G1.000
thyA3073953c.519A>G0.163
thyA3073956c.516C>G0.128
thyA3073959c.513A>G0.130
thyA3073977c.495T>C0.167
thyA3073989c.483A>G0.163
thyA3074004c.468A>G0.157
thyA3074007c.465G>C0.163
alr3840764c.657C>G1.000
embC4242643c.2781C>T1.000

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;