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: 5d761423658e6
Sample: 5d761423658e6

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Summary
ID: 5d761423658e6
Date: Mon Sep 9 10:00:47 2019
Strain: lineage4.2.2
Drug-resistance: MDR

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRkatG p.Ser315Thr (1.00)
RifampicinRrpoB p.His445Cys (0.69)
EthambutolRembA c.-16C>T (1.00), embB p.Met306Ile (1.00)
Pyrazinamide
StreptomycinRrrs r.799c>t (0.16), rrs r.888g>a (0.18)
EthionamideRethA p.Met1Arg (1.00)
Fluoroquinolones
AmikacinRrrs r.1402c>a (0.19), rrs r.1484g>t (0.25)
CapreomycinRrrs r.1402c>a (0.19), rrs r.1484g>t (0.25)
KanamycinRrrs r.1402c>a (0.19), rrs r.1484g>t (0.25)

Lineage2FamilyMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.2Euro-AmericanH;T;LAMNone
lineage4.2.2Euro-American (Ural)T;LAM7-TURNone

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA7859c.558A>G0.173
gyrA8688p.Ala463Ser1.000
gyrA9304p.Gly668Asp1.000
rpoB760910c.1104C>T0.181
rpoB760982c.1176G>C0.153
rpoB760988c.1182C>T0.147
rpoB760991c.1185G>C0.147
rpoB760997c.1191G>C0.149
rpoB761018p.Glu404Asp0.138
rpoB761127p.Ser441Ala0.278
rpoB761132c.1326G>T0.233
rpoB761133c.1327T>C0.208
rpoB761147c.1341C>T0.176
rpoB761150c.1344A>T0.268
rpoB761156c.1350G>C0.152
rpoB761159c.1353G>A0.145
rpoB761165c.1359G>C0.150
rpoB761489c.1683G>A1.000
rpoB762197c.2391C>T0.162
rpoB762200c.2394C>T0.189
rpoB762221c.2415G>A0.181
rpoB762233c.2427G>C0.188
rpoB762234p.Pro810Ser0.170
rpoB762239c.2433G>A0.206
rpoB762245c.2439G>C0.245
rpoB762281c.2475G>A0.176
rpoB762287c.2481C>T0.161
rpoB762293c.2487T>C0.158
rpoB762879p.Met1025Leu0.173
rpoB762920c.3114C>T0.143
rpoB762962c.3156C>T0.173
rpoB762971c.3165G>C0.183
rpoB762983c.3177C>T0.159
rpoB762989c.3183G>C0.200
rpoB762995c.3189G>T0.175
rpoC763642c.273G>T0.151
rpoC763648c.279C>T0.134
rpoC763660c.291T>G0.165
rpoC763666c.297G>T0.160
rpoC763699c.330G>T0.163
rpoC763702c.333C>T0.151
rpoC763708c.339G>C0.171
rpoC763717c.348T>C0.188
rpoC763726c.357C>T0.130
rpoC763732c.363C>T0.167
rpoC763751p.Ile128Val0.182
rpoC763756c.387C>T0.112
rpoC763772p.Val135Met0.156
rpoC764485c.1116G>T0.184
rpoC764498p.Ser377Ala0.151
rpoC764524c.1155C>T0.154
rpoC764530c.1161C>T0.192
rpoC764545c.1176C>G0.120
rpoC764548c.1179G>C0.120
rpoC764593c.1224C>T0.147
rpoC764602c.1233C>T0.169
rpoC764605c.1236G>T0.185
rpoC764611c.1242G>T0.181
rpoC764692c.1323C>T0.191
rpoC764706p.Leu446Gln0.191
rpoC764731c.1362G>C0.140
rpoC764737c.1368G>T0.155
rpoC764746c.1377G>T0.139
rpoC767125c.3756G>C0.124
rpoC767129p.Ile1254Leu0.124
rpoC767134c.3765C>T0.123
rpsL781395c.-165T>C1.000
rpsL781667c.108C>T0.163
rpsL781766c.207C>T0.165
rpsL781796p.Met79Ile0.225
rpsL781802c.243G>C0.146
rpsL781811c.252C>T0.152
rpsL781814c.255C>T0.153
rpsL781817c.258G>T0.156
embR1416234p.Cys372Gly0.165
rrs1471866r.21c>t0.204
rrs1472023r.178g>c0.270
rrs1472102r.257g>a0.176
rrs1472106r.261g>a0.380
rrs1472108r.263c>t0.310
rrs1472112r.267c>t0.201
rrs1472113r.268t>c0.234
rrs1472122r.277g>t0.214
rrs1472123r.278a>t0.223
rrs1472124r.279c>t0.274
rrs1472127r.282c>t0.225
rrs1472129r.284g>c0.175
rrs1472130r.285g>a0.173
rrs1472137r.292g>a0.192
rrs1472150r.305t>a0.566
rrs1472151r.306c>a0.289
rrs1472155r.310c>t0.211
rrs1472172r.327t>c0.419
rrs1472203r.358g>a0.182
rrs1472225r.380c>a0.208
rrs1472236r.391c>g0.143
rrs1472240r.395g>a0.149
rrs1472251r.406g>a0.652
rrs1472259r.414c>a0.395
rrs1472330r.485g>t0.148
rrs1472338r.493a>g0.545
rrs1472344r.499c>t0.679
rrs1472378r.533g>t0.187
rrs1472379r.534t>c0.760
rrs1472382r.537g>a0.440
rrs1472400r.555c>t0.775
rrs1472416r.571c>t0.339
rrs1472422r.577t>c0.496
rrs1472427r.582t>g0.123
rrs1472494r.649a>g0.370
rrs1472496r.651t>a0.355
rrs1472498r.653c>t0.376
rrs1472513r.668t>c0.313
rrs1472544r.699c>t0.145
rrs1472549r.704g>a0.332
rrs1472557r.712g>a0.157
rrs1472558r.713g>a0.432
rrs1472569r.724g>a0.429
rrs1472571r.726g>c0.145
rrs1472573r.728c>t0.332
rrs1472574r.729t>a0.212
rrs1472581r.736a>c0.350
rrs1472584r.739a>t0.343
rrs1472597r.752g>a0.199
rrs1472598r.753a>c0.140
rrs1472607r.762g>a0.209
rrs1472616r.771g>a0.162
rrs1472655r.810g>t0.522
rrs1472660r.815t>c0.523
rrs1472673r.828t>c0.193
rrs1472674r.829t>g0.171
rrs1472675r.830t>c0.193
rrs1472677r.832c>t0.181
rrs1472682r.837t>g0.222
rrs1472683r.838t>g0.157
rrs1472687r.842a>t0.240
rrs1472689r.844c>t0.155
rrs1472690r.845c>t0.222
rrs1472692r.847t>c0.319
rrs1472714r.869a>g0.454
rrs1472742r.897c>t0.178
rrs1472744r.899a>g0.199
rrs1472755r.910g>a0.154
rrs1472767r.922g>a0.223
rrs1472781r.936c>t0.240
rrs1472790r.945t>c0.440
rrs1472793r.948a>t0.230
rrs1472803r.958t>a0.216
rrs1472824r.979t>a0.163
rrs1472825r.980g>a0.133
rrs1472828r.983t>c0.151
rrs1472895r.1050c>t0.594
rrs1472952r.1107t>c0.178
rrs1472955r.1110c>t0.194
rrs1472956r.1111t>c0.603
rrs1472957r.1112c>t0.299
rrs1472958r.1113a>g0.299
rrs1472973r.1128a>t0.606
rrs1472974r.1129a>g0.287
rrs1472987r.1142g>a0.241
rrs1472988r.1143t>c0.319
rrs1472989r.1144g>a0.225
rrs1472990r.1145a>g0.641
rrs1473035r.1190g>a0.752
rrs1473053r.1208t>a0.149
rrs1473055r.1210c>t0.719
rrs1473056r.1211a>t0.783
rrs1473062r.1217t>a0.147
rrs1473066r.1221a>g0.621
rrs1473068r.1223a>g0.147
rrs1473088r.1243a>g0.617
rrs1473093r.1248c>t0.595
rrs1473100r.1255g>a0.459
rrs1473102r.1257c>t0.390
rrs1473104r.1259c>t0.434
rrs1473110r.1265t>g0.404
rrs1473111r.1266a>g0.409
rrs1473115r.1270g>t0.301
rrs1473121r.1276t>c0.500
rrs1473123r.1278a>t0.243
rrs1473129r.1284c>t0.207
rrs1473145r.1300c>t0.634
rrs1473148r.1303g>t0.246
rrs1473163r.1318c>a0.285
rrs1473166r.1321g>a0.630
rrs1473172r.1327t>g0.413
rrs1473173r.1328c>t0.423
rrs1473221r.1376c>t0.366
rrs1473226r.1381c>t0.232
rrs1473252r.1407t>c0.635
rrs1473259r.1414c>t0.655
rrs1473262r.1417t>c0.246
rrs1473270r.1425g>a0.405
rrs1473276r.1431a>g0.493
rrs1473277r.1432g>a0.141
rrs1473288r.1443c>t0.338
rrs1473290r.1445c>t0.333
rrs1473291r.1446g>t0.338
rrs1473301r.1456t>c0.457
rrs1473305r.1460g>t0.363
rrs1473316r.1471c>t0.568
rrl1473384c.-274A>G0.141
rrl1473676r.19g>a0.171
rrl1473679r.22t>c0.162
rrl1473697r.40c>t0.250
rrl1473698r.41g>a0.385
rrl1473718r.61g>t0.259
rrl1473721r.64g>a0.255
rrl1473722r.65g>t0.292
rrl1473731r.74t>a0.345
rrl1473744r.87t>c0.235
rrl1473746r.89t>a0.240
rrl1473747r.90c>t0.235
rrl1473751r.94c>t0.267
rrl1473753r.96a>g0.267
rrl1473756r.99g>t0.267
rrl1473757r.100t>g0.261
rrl1473758r.101g>t0.261
rrl1473862r.205c>t0.215
rrl1473871r.214t>c0.316
rrl1473876r.219g>a0.300
rrl1473916r.259c>a0.147
rrl1473923r.266c>g0.139
rrl1474130r.473c>t0.143
rrl1474140r.483c>t0.135
rrl1474141r.484g>c0.135
rrl1474142r.485c>g0.135
rrl1474151r.494c>t0.298
rrl1474155r.498g>a0.298
rrl1474164r.507c>t0.320
rrl1474171r.514c>t0.304
rrl1474181r.524c>t0.333
rrl1474184r.527c>t0.345
rrl1474185r.528g>a0.328
rrl1474197r.540c>t0.230
rrl1474199r.542g>a0.179
rrl1474202r.545t>a0.484
rrl1474218r.561t>a0.213
rrl1474228r.571t>a0.201
rrl1474249r.592g>t0.557
rrl1474252r.595t>a0.195
rrl1474269r.612c>t0.547
rrl1474275r.618t>g0.317
rrl1474282r.625g>a0.121
rrl1474308r.651g>t0.128
rrl1474310r.653t>g0.259
rrl1474326r.669t>a0.352
rrl1474330r.673a>t0.132
rrl1474348r.691c>t0.600
rrl1474351r.694g>t0.657
rrl1474353r.696a>g0.518
rrl1474354r.697c>t0.236
rrl1474355r.698a>g0.361
rrl1474362r.705a>g0.655
rrl1474381r.724t>g0.348
rrl1474383r.726g>t0.614
rrl1474387r.730c>t0.644
rrl1474454r.797g>a0.413
rrl1474467r.810a>g0.309
rrl1474476r.819c>t0.192
rrl1474488r.831g>t0.702
rrl1474495r.838g>a0.330
rrl1474496r.839c>a0.306
rrl1474497r.840g>c0.273
rrl1474498r.841g>t0.290
rrl1474505r.848c>g0.287
rrl1474506r.849c>g0.286
rrl1474507r.850g>t0.289
rrl1474508r.851c>t0.326
rrl1474516r.859c>a0.637
rrl1474529r.872a>c0.519
rrl1474530r.873g>a0.482
rrl1474537r.880g>a0.529
rrl1474539r.882c>t0.471
rrl1474540r.883t>g0.488
rrl1474558r.901g>a0.252
rrl1474584r.927c>t0.203
rrl1474627r.970g>a0.133
rrl1474632r.975g>t0.133
rrl1474636r.979a>c0.511
rrl1474637r.980c>g0.422
rrl1474638r.981c>g0.565
rrl1474639r.982g>c0.130
rrl1474643r.986a>g0.298
rrl1474663r.1006c>t0.333
rrl1474672r.1015c>t0.467
rrl1474674r.1017a>c0.170
rrl1474675r.1018c>a0.170
rrl1474676r.1019t>a0.394
rrl1474677r.1020a>g0.600
rrl1474692r.1035g>a0.360
rrl1474694r.1037c>t0.182
rrl1474706r.1049g>a0.321
rrl1474709r.1052g>a0.134
rrl1474713r.1056t>g0.152
rrl1474717r.1060a>t0.412
rrl1474734r.1077g>a0.613
rrl1474749r.1092c>t0.248
rrl1474754r.1097c>t0.541
rrl1474760r.1103a>g0.594
rrl1474777r.1120t>c0.316
rrl1474779r.1122g>a0.279
rrl1474782r.1125g>a0.392
rrl1474783r.1126g>a0.189
rrl1474794r.1137c>t0.731
rrl1474823r.1166c>g0.435
rrl1474824r.1167a>g0.287
rrl1474827r.1170c>t0.316
rrl1474830r.1173a>g0.524
rrl1474831r.1174a>t0.636
rrl1474832r.1175a>t0.321
rrl1474844r.1187g>t0.133
rrl1474864r.1207c>t0.647
rrl1474866r.1209c>a0.129
rrl1474869r.1212g>t0.128
rrl1474903r.1246t>c0.312
rrl1474904r.1247g>c0.459
rrl1474913r.1256t>c0.476
rrl1474932r.1275c>t0.261
rrl1474933r.1276a>g0.162
rrl1474934r.1277c>t0.155
rrl1475062r.1405a>t0.393
rrl1475079r.1422t>a0.407
rrl1475090r.1433a>t0.507
rrl1475104r.1447t>a0.556
rrl1475109r.1452c>t0.488
rrl1475114r.1457c>t0.562
rrl1475124r.1467a>t0.634
rrl1475129r.1472g>t0.200
rrl1475137r.1480a>t0.533
rrl1475171r.1514c>t0.540
rrl1475175r.1518g>c0.356
rrl1475176r.1519g>a0.144
rrl1475188r.1531c>g0.230
rrl1475499r.1842c>t0.524
rrl1475518r.1861a>g0.313
rrl1475521r.1864t>c0.307
rrl1475526r.1869c>t0.476
rrl1475529r.1872a>g0.333
rrl1475532r.1875a>t0.365
rrl1475538r.1881t>c0.405
rrl1475539r.1882a>t0.154
rrl1475545r.1888t>g0.204
rrl1475548r.1891c>t0.505
rrl1475549r.1892t>c0.561
rrl1475574r.1917c>a0.195
rrl1475649r.1992a>g0.287
rrl1475655r.1998t>g0.304
rrl1475659r.2002g>a0.329
rrl1475672r.2015c>t0.208
rrl1475673r.2016t>c0.222
rrl1475686r.2029c>g0.387
rrl1475696r.2039t>c0.377
rrl1475699r.2042c>t0.560
rrl1475703r.2046a>g0.393
rrl1475715r.2058g>c0.389
rrl1475722r.2065g>t0.151
rrl1475751r.2094c>a0.409
rrl1475752r.2095c>t0.165
rrl1475753r.2096c>g0.169
rrl1475756r.2099t>c0.141
rrl1475758r.2101a>g0.210
rrl1475760r.2103c>t0.171
rrl1475761r.2104c>a0.218
rrl1475762r.2105g>t0.244
rrl1475763r.2106c>t0.182
rrl1475764r.2107a>t0.420
rrl1475765r.2108a>g0.369
rrl1475769r.2112t>c0.165
rrl1475775r.2118g>t0.255
rrl1475777r.2120a>t0.380
rrl1475783r.2126t>g0.207
rrl1475803r.2146t>c0.222
rrl1475804r.2147g>c0.225
rrl1475816r.2159c>g0.245
rrl1475817r.2160a>g0.252
rrl1475858r.2201t>c0.161
rrl1475866r.2209t>a0.144
rrl1475869r.2212c>a0.219
rrl1475881r.2224t>c0.250
rrl1475883r.2226a>t0.636
rrl1475884r.2227a>g0.180
rrl1475896r.2239a>g0.130
rrl1475898r.2241a>g0.706
rrl1475899r.2242g>a0.701
rrl1475916r.2259c>g0.600
rrl1475937r.2280a>t0.416
rrl1475943r.2286g>a0.740
rrl1475945r.2288c>a0.458
rrl1475952r.2295a>g0.719
rrl1475963r.2306g>t0.268
rrl1475970r.2313c>t0.664
rrl1475975r.2318c>t0.627
rrl1475977r.2320a>g0.644
rrl1475978r.2321c>t0.231
rrl1475988r.2331a>g0.583
rrl1475991r.2334t>c0.195
rrl1475992r.2335t>g0.195
rrl1475993r.2336c>t0.280
rrl1475995r.2338g>t0.211
rrl1475997r.2340a>t0.321
rrl1475998r.2341c>t0.500
rrl1475999r.2342g>a0.203
rrl1476001r.2344t>c0.525
rrl1476030r.2373a>g0.408
rrl1476032r.2375c>a0.396
rrl1476034r.2377c>g0.404
rrl1476040r.2383c>t0.422
rrl1476045r.2388g>t0.442
rrl1476047r.2390g>t0.442
rrl1476049r.2392c>t0.452
rrl1476130r.2473g>a0.221
rrl1476131r.2474c>t0.785
rrl1476164r.2507a>t0.347
rrl1476179r.2522c>t0.555
rrl1476194r.2537a>t0.380
rrl1476200r.2543a>t0.786
rrl1476201r.2544c>t0.439
rrl1476204r.2547c>t0.412
rrl1476207r.2550t>c0.315
rrl1476214r.2557g>t0.654
rrl1476215r.2558c>t0.650
rrl1476224r.2567a>g0.667
rrl1476225r.2568t>g0.164
rrl1476245r.2588c>t0.489
rrl1476252r.2595t>g0.613
rrl1476253r.2596a>g0.282
rrl1476256r.2599a>g0.598
rrl1476260r.2603a>g0.785
rrl1476267r.2610g>t0.382
rrl1476276r.2619c>a0.337
rrl1476279r.2622g>a0.327
rrl1476281r.2624t>c0.673
rrl1476294r.2637a>g0.522
rrl1476295r.2638c>a0.380
rrl1476296r.2639c>t0.530
rrl1476297r.2640c>a0.224
rrl1476299r.2642c>g0.221
rrl1476300r.2643g>t0.221
rrl1476301r.2644a>t0.507
rrl1476306r.2649a>g0.271
rrl1476307r.2650a>t0.275
rrl1476308r.2651g>c0.217
rrl1476311r.2654g>t0.345
rrl1476312r.2655t>c0.493
rrl1476337r.2680c>t0.253
rrl1476357r.2700t>c0.290
rrl1476358r.2701t>c0.134
rrl1476359r.2702c>g0.630
rrl1476372r.2715t>c0.144
rrl1476381r.2724g>c0.618
rrl1476382r.2725a>g0.145
rrl1476383r.2726t>a0.147
rrl1476408r.2751g>a0.170
rrl1476425r.2768g>t0.149
rrl1476428r.2771c>t0.479
rrl1476429r.2772a>c0.400
rrl1476466r.2809c>t0.768
rrl1476481r.2824t>c0.589
rrl1476506r.2849t>c0.698
rrl1476513r.2856g>t0.257
rrl1476515r.2858c>t0.553
rrl1476524r.2867c>t0.459
rrl1476525r.2868a>g0.531
rrl1476530r.2873c>t0.237
rrl1476536r.2879g>a0.521
rrl1476538r.2881a>g0.330
rrl1476539r.2882a>g0.474
rrl1476540r.2883c>g0.460
rrl1476547r.2890c>t0.254
rrl1476567r.2910c>t0.206
rrl1476584r.2927c>t0.505
rrl1476585r.2928a>g0.477
rrl1476592r.2935g>a0.231
rrl1476594r.2937c>a0.200
rrl1476596r.2939c>t0.220
rrl1476603r.2946g>t0.176
rrl1476605r.2948c>t0.152
rrl1476607r.2950c>t0.333
rrl1476608r.2951c>g0.354
rrl1476614r.2957a>t0.333
rrl1476616r.2959a>g0.232
rrl1476619r.2962c>t0.338
rrl1476628r.2971t>g0.297
rrl1476629r.2972c>a0.342
rrl1476630r.2973a>g0.191
rrl1476633r.2976a>g0.117
rrl1476661r.3004a>g0.123
rrl1476668r.3011c>t0.118
rpsA1833661c.120A>G0.169
rpsA1833668p.Ile43Val0.141
rpsA1833676c.135A>G0.148
rpsA1833694c.153G>C0.181
rpsA1833721c.180A>G0.133
rpsA1833732p.Pro64Leu0.128
rpsA1833734p.Ala65Ser0.125
rpsA1833742c.201A>G0.143
rpsA1833970c.429G>T0.162
rpsA1833976c.435C>T0.156
rpsA1833979c.438T>C0.198
rpsA1833991c.450C>A0.143
rpsA1833994c.453G>C0.155
rpsA1833997c.456G>C0.126
rpsA1834000c.459G>T0.160
rpsA1834012c.471G>C0.151
rpsA1834015c.474G>C0.136
rpsA1834030c.489C>T0.134
rpsA1834039c.498C>T0.129
rpsA1834040p.Lys167Gln0.155
rpsA1834043p.Glu168Gln0.126
rpsA1834051c.510G>A0.214
rpsA1834054c.513C>T0.187
rpsA1834093c.552G>T0.200
rpsA1834102c.561T>C0.178
rpsA1834108c.567C>T0.134
rpsA1834246c.705G>T0.167
rpsA1834249c.708T>C0.194
rpsA1834261c.720A>G0.191
rpsA1834264c.723G>C0.194
rpsA1834294c.753G>T0.133
rpsA1834298p.Gln253Glu0.169
tlyA1917972c.33A>G1.000
pncA2288937p.Ala102Val1.000
ahpC2726146c.-47G>GT0.985
ald3086788c.-32T>C1.000
alr3841652c.-232A>T0.234
alr3841654c.-234A>C0.295
alr3841662c.-242A>G0.318
alr3841663c.-243G>A0.293
embC4242643c.2781C>T1.000
gid4407997p.Gly69Asp1.000

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;