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: 5cf78513138c1
Sample: 5cf78513138c1

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Summary
ID: 5cf78513138c1
Date: Wed Jun 5 10:05:50 2019
Strain: lineage2
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
Streptomycin
Ethionamide
Fluoroquinolones
AmikacinRrrs r.1402c>a (0.54), rrs r.1484g>t (0.52)
CapreomycinRrrs r.1402c>a (0.54), rrs r.1484g>t (0.52)
KanamycinRrrs r.1402c>a (0.54), rrs r.1484g>t (0.52)

Lineage2FamilyMain SpoligotypeRDS
lineage2East-AsianBeijingRD105

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6700c.1461T>C1.000
gyrB6703c.1464G>C1.000
gyrB6709c.1470A>G1.000
gyrB6730c.1491A>G1.000
gyrB6742c.1503A>G1.000
gyrB6745c.1506T>C1.000
gyrB6749p.Ala504Ser1.000
gyrB6754p.Ile505Met1.000
gyrB6760c.1521G>C1.000
gyrB6763c.1524G>C0.750
gyrB6764p.Leu509Phe0.750
gyrB6775c.1536G>C1.000
gyrB6779p.His514Asn0.250
gyrB6793c.1554T>C0.250
gyrB6794p.Ile519Val0.750
gyrB6826c.1587G>C0.250
rpoB762197c.2391C>T0.926
rpoB762209c.2403C>T0.926
rpoB762218c.2412T>C0.926
rpoB762233c.2427G>C1.000
rpoB762236c.2430G>T0.926
rpoB762245c.2439G>T1.000
rpoB762254c.2448T>C1.000
rpoB762257c.2451C>G0.926
rpoB762863c.3057T>C1.000
rpoB762872p.Met1022Ile0.215
rpoB762878p.Ile1024Met1.000
rpoB762879p.Met1025Leu1.000
rpoB762899c.3093G>T0.211
rpoB762917c.3111C>G0.158
rpoB762920c.3114C>T0.842
rpoB762923c.3117C>G0.223
rpoB762925p.Thr1040Ile0.147
rpoB762929c.3123G>C0.232
rpoB762939p.Met1045Leu0.147
rpoB762942p.Ile1046Val0.171
rpoB762959c.3153G>T0.808
rpoB762965c.3159T>C0.222
rpoB762971c.3165G>C0.707
rpoB762983c.3177C>T0.842
rpoB762989c.3183G>A0.281
rpoB762995c.3189G>T0.368
rpoB763005p.Cys1067Gly0.474
rpoB763017p.Gln1071Glu1.000
rpoB763053c.3247T>C1.000
rpoB763067c.3261C>G0.389
rpoB763070c.3264T>C0.389
rpoB763074p.Thr1090Phe0.611
rpoB763077p.Val1091Leu0.389
rpoB763085c.3279C>T0.611
rpoB763094c.3288G>C0.611
rpoB763103c.3297G>C0.389
rpoB763115c.3309T>C1.000
rpoB763120p.Asn1105Ser0.611
rpoB763126p.Pro1107Gln0.389
rpoB763130c.3324G>A0.389
rpoB763136c.3330C>T0.389
rpoB763148c.3342G>C1.000
rpoC763456c.87A>G1.000
rpoC763465c.96G>A0.273
rpoC763468c.99G>C1.000
rpoC763483c.114G>C0.636
rpoC763486c.117T>G0.364
rpoC763492c.123G>C0.214
rpoC763495c.126G>A0.267
rpoC763528c.159G>A1.000
rpoC763534c.165T>C0.969
rpoC763537c.168C>G0.971
rpoC763546c.177A>G1.000
rpoC763570c.201G>C0.951
rpoC763573c.204G>C0.900
rpoC763594c.225C>T0.894
rpoC763615c.246G>C0.132
rpoC763622p.Ala85Ser1.000
rpoC763627p.Lys86Asn0.868
rpoC763636c.267T>C0.132
rpoC763642c.273G>T1.000
rpoC763647c.279 280del0.875
rrs1471923r.78t>c1.000
rrs1471925r.80t>c0.444
rrs1471928r.83t>g0.852
rrs1471934r.89a>g1.000
rrs1471975r.130g>t0.348
rrs1471978r.133c>t0.579
rrs1471996r.151c>t0.579
rrs1472068r.223t>g0.154
rrs1472069r.224g>a0.654
rrs1472075r.230a>g0.184
rrs1472078r.233c>t0.306
rrs1472085r.240c>t0.156
rrs1472106r.261g>a0.833
rrs1472107r.262a>g0.248
rrs1472108r.263c>t0.832
rrs1472112r.267c>t0.289
rrs1472122r.277g>t0.187
rrs1472123r.278a>g0.281
rrs1472124r.279c>t0.204
rrs1472127r.282c>t0.175
rrs1472137r.292g>a0.153
rrs1472148r.303t>c0.302
rrs1472150r.305t>g0.219
rrs1472151r.306c>t0.287
rrs1472160r.315c>t0.403
rrs1472172r.327t>c0.715
rrs1472214r.369c>g0.256
rrs1472225r.380c>a0.506
rrs1472235r.390g>c0.268
rrs1472240r.395g>a0.548
rrs1472242r.397c>t0.305
rrs1472251r.406g>c0.320
rrs1472279r.434t>g0.408
rrs1472286r.441c>g1.000
rrs1472289r.444t>c0.217
rrs1472290r.445c>g1.000
rrs1472293r.448c>a0.783
rrs1472313r.468g>a1.000
rrs1472315r.470t>g0.767
rrs1472324r.479g>c0.767
rrs1472325r.480g>c0.833
rrs1472328r.483g>c0.767
rrs1472344r.499c>t1.000
rrs1472368r.523a>g0.339
rrs1472382r.537g>a0.215
rrs1472396r.551a>t0.374
rrs1472400r.555c>t0.651
rrs1472412r.567a>g0.554
rrs1472422r.577t>c0.417
rrs1472427r.582t>g0.157
rrs1472428r.583g>a0.157
rrs1472484r.639a>t0.333
rrs1472489r.644a>t0.333
rrs1472494r.649a>g0.667
rrs1472496r.651t>a0.292
rrs1472498r.653c>t0.526
rrs1472507r.662c>a0.397
rrs1472508r.663t>c0.253
rrs1472530r.685g>a0.772
rrs1472571r.726g>t0.425
rrs1472581r.736a>c0.772
rrs1472582r.737g>t0.443
rrs1472583r.738t>a0.422
rrs1472584r.739a>t0.610
rrs1472585r.740a>c0.407
rrs1472598r.753a>c0.317
rrs1472616r.771g>a0.299
rrs1472629r.784t>a0.463
rrs1472634r.789t>c0.407
rrs1472635r.790g>a0.278
rrs1472647r.802c>t0.531
rrs1472660r.815t>c0.238
rrs1472661r.816a>g0.182
rrs1472673r.828t>g0.857
rrs1472675r.830t>c0.769
rrs1472677r.832c>a0.846
rrs1472682r.837t>a1.000
rrs1472683r.838t>c1.000
rrs1472687r.842a>t0.857
rrs1472692r.847t>c0.194
rrs1472697r.852t>c0.327
rrs1472707r.862a>t0.228
rrs1472713r.868t>c0.271
rrs1472714r.869a>t0.290
rrs1472716r.871c>t0.378
rrs1472734r.889c>t0.253
rrs1472741r.896g>a0.249
rrs1472742r.897c>t0.515
rrs1472744r.899a>g0.228
rrs1472767r.922g>c0.300
rrs1472781r.936c>t0.552
rrs1472790r.945t>c0.358
rrs1472793r.948a>t0.558
rrs1472803r.958t>a0.457
rrs1472812r.967a>t0.352
rrs1472828r.983t>c0.211
rrs1472836r.991g>a0.200
rrs1472840r.995a>t0.286
rrs1472844r.999c>t0.286
rrs1472845r.1000g>c1.000
rrs1472846r.1001c>g1.000
rrs1472848r.1003t>g1.000
rrs1472850r.1005t>c0.714
rrs1472857r.1012a>g0.714
rrs1472859r.1014g>t1.000
rrs1472861r.1016g>t1.000
rrs1472873r.1028c>t0.714
rrs1472874r.1029c>t0.286
rrs1472875r.1030t>g1.000
rrs1472880r.1035g>a0.609
rrs1472887r.1042g>c0.295
rrs1472895r.1050c>t0.431
rrs1472956r.1111t>c0.360
rrs1472957r.1112c>t0.412
rrs1472973r.1128a>t0.975
rrs1472987r.1142g>a0.295
rrs1472990r.1145a>g0.610
rrs1472996r.1151t>c0.598
rrs1473035r.1190g>a0.329
rrs1473055r.1210c>t0.248
rrs1473056r.1211a>t0.248
rrs1473066r.1221a>g0.776
rrs1473080r.1235c>t0.254
rrs1473081r.1236c>t0.585
rrs1473088r.1243a>g0.382
rrs1473089r.1244a>t0.327
rrs1473091r.1246g>a0.196
rrs1473093r.1248c>t0.500
rrs1473094r.1249t>g0.157
rrs1473099r.1254t>c0.241
rrs1473100r.1255g>a0.444
rrs1473101r.1256c>t0.129
rrs1473102r.1257c>t0.306
rrs1473104r.1259c>t0.758
rrs1473109r.1264t>g0.157
rrs1473110r.1265t>g0.871
rrs1473111r.1266a>g1.000
rrs1473115r.1270g>t0.242
rrs1473120r.1275c>t0.217
rrs1473121r.1276t>c1.000
rrs1473122r.1277t>a0.549
rrs1473123r.1278a>g0.345
rrs1473132r.1287t>c0.168
rrs1473145r.1300c>t0.872
rrs1473163r.1318c>t0.220
rrs1473164r.1319c>t0.633
rrs1473166r.1321g>a0.807
rrs1473177r.1332g>a0.266
rrs1473192r.1347a>g0.172
rrs1473202r.1357c>t0.298
rrs1473226r.1381c>g0.604
rrs1473259r.1414c>t0.773
rrs1473276r.1431a>g0.932
rrs1473288r.1443c>g0.536
rrs1473289r.1444t>g0.357
rrs1473290r.1445c>a0.451
rrs1473292r.1447g>t0.549
rrs1473294r.1449a>g0.542
rrs1473295r.1450g>t0.352
rrs1473301r.1456t>c0.991
rrs1473315r.1470t>c0.990
rrs1473316r.1471c>t0.567
rrs1473317r.1472g>a0.433
rrs1473319r.1474c>t0.602
rrs1473324r.1479g>a0.620
rrl1473832r.175c>t1.000
rrl1473836r.179a>t1.000
rrl1473839r.182g>t1.000
rrl1473862r.205c>t1.000
rrl1473876r.219g>a1.000
rrl1473887r.230t>g1.000
rrl1473898r.241c>t1.000
rrl1473899r.242a>g1.000
rrl1473916r.259c>a1.000
rrl1473922r.265a>g1.000
rrl1473923r.266c>g1.000
rrl1474135r.478g>a1.000
rrl1474142r.485c>g1.000
rrl1474151r.494c>t1.000
rrl1474153r.496c>g0.417
rrl1474166r.509g>c0.192
rrl1474167r.510t>c0.595
rrl1474179r.522c>t0.161
rrl1474183r.526t>c0.198
rrl1474184r.527c>t1.000
rrl1474186r.529a>g0.800
rrl1474197r.540c>t0.689
rrl1474201r.544t>c0.241
rrl1474202r.545t>g0.702
rrl1474218r.561t>g0.623
rrl1474249r.592g>t0.547
rrl1474253r.596a>t0.725
rrl1474263r.606g>a0.221
rrl1474266r.609t>c0.343
rrl1474269r.612c>t0.675
rrl1474275r.618t>g0.239
rrl1474281r.624a>g0.211
rrl1474287r.630t>a0.308
rrl1474288r.631c>t0.216
rrl1474308r.651g>t0.846
rrl1474310r.653t>g0.217
rrl1474316r.659t>c0.186
rrl1474348r.691c>t0.529
rrl1474351r.694g>c0.667
rrl1474353r.696a>g0.765
rrl1474354r.697c>t0.529
rrl1474355r.698a>g0.235
rrl1474359r.702c>g0.235
rrl1474362r.705a>g1.000
rrl1474381r.724t>a0.294
rrl1474384r.727c>t0.235
rrl1474387r.730c>t0.444
rrl1474402r.745t>c0.556
rrl1474406r.749t>g0.444
rrl1474444r.787g>c0.438
rrl1474447r.790g>a0.273
rrl1474451r.794t>c0.209
rrl1474454r.797g>a0.714
rrl1474467r.810a>g0.409
rrl1474476r.819c>t0.565
rrl1474487r.830g>t0.375
rrl1474488r.831g>a0.603
rrl1474495r.838g>a0.262
rrl1474496r.839c>g0.319
rrl1474497r.840g>c0.952
rrl1474498r.841g>t0.262
rrl1474505r.848c>g0.262
rrl1474506r.849c>g0.952
rrl1474507r.850g>t0.952
rrl1474508r.851c>t0.310
rrl1474516r.859c>t0.570
rrl1474517r.860c>g0.381
rrl1474527r.870t>g0.220
rrl1474529r.872a>c0.620
rrl1474530r.873g>a0.596
rrl1474537r.880g>a1.000
rrl1474539r.882c>t0.590
rrl1474540r.883t>g0.590
rrl1474542r.885a>c0.218
rrl1474552r.895c>t0.612
rrl1474558r.901g>a0.628
rrl1474582r.925t>a0.662
rrl1474734r.1077g>t0.258
rrl1474736r.1079c>t0.258
rrl1474749r.1092c>t0.967
rrl1474751r.1094g>a0.175
rrl1474752r.1095ta>t1.000
rrl1474753r.1096ac>a1.000
rrl1474760r.1103a>g1.000
rrl1474779r.1122g>a0.903
rrl1474780r.1123c>t0.738
rrl1474782r.1125g>a0.738
rrl1474794r.1137c>t1.000
rrl1474798r.1141c>t0.817
rrl1474806r.1149a>c0.738
rrl1474823r.1166c>g1.000
rrl1474827r.1170c>t0.769
rrl1474830r.1173a>g0.865
rrl1474831r.1174a>t0.889
rrl1474853r.1196a>g0.774
rrl1474864r.1207c>t0.879
rrl1474904r.1247g>c1.000
rrl1474905r.1248t>c0.866
rrl1474913r.1256t>c0.358
rrl1474921r.1264c>t0.169
rrl1474932r.1275c>t0.579
rrl1474934r.1277c>t0.211
rrl1474938r.1281g>a0.211
rrl1475499r.1842c>t0.889
rrl1475500r.1843a>t0.182
rrl1475515r.1858g>a0.727
rrl1475525r.1868g>a0.182
rrl1475526r.1869c>a1.000
rrl1475531r.1874c>t0.909
rrl1475532r.1875a>g0.273
rrl1475538r.1881t>a0.182
rrl1475539r.1882a>g0.182
rrl1475542r.1885a>g0.273
rrl1475544r.1887a>t0.273
rrl1475545r.1888t>g1.000
rrl1475548r.1891c>t0.727
rrl1475549r.1892t>c0.727
rrl1475550r.1893a>g0.182
rrl1475649r.1992a>g1.000
rrl1475652r.1995c>t0.273
rrl1475655r.1998t>c0.171
rrl1475657r.2000a>g0.543
rrl1475659r.2002g>t0.257
rrl1475673r.2016t>c0.600
rrl1475696r.2039t>c0.147
rrl1475699r.2042c>t0.780
rrl1475703r.2046a>g0.147
rrl1475722r.2065g>t0.457
rrl1475740r.2083g>c0.273
rrl1475747r.2090a>g0.441
rrl1475753r.2096c>g0.958
rrl1475759r.2102c>g0.500
rrl1475760r.2103c>t0.500
rrl1475762r.2105g>t0.178
rrl1475763r.2106c>t0.644
rrl1475764r.2107a>c0.400
rrl1475765r.2108a>t0.256
rrl1475766r.2109g>t0.333
rrl1475767r.2110g>t0.229
rrl1475769r.2112t>c0.593
rrl1475775r.2118g>t0.662
rrl1475777r.2120a>t0.287
rrl1475781r.2124t>c0.422
rrl1475783r.2126t>g0.148
rrl1475803r.2146t>c0.482
rrl1475804r.2147g>c0.482
rrl1475816r.2159c>g0.498
rrl1475817r.2160a>g0.498
rrl1475858r.2201t>c0.183
rrl1475869r.2212c>a0.452
rrl1475877r.2220c>t0.430
rrl1475881r.2224t>c0.895
rrl1475883r.2226a>c0.322
rrl1475884r.2227a>g0.177
rrl1475892r.2235a>c0.789
rrl1475898r.2241a>g0.970
rrl1475899r.2242g>a0.929
rrl1475906r.2249c>t0.897
rrl1475916r.2259c>t0.927
rrl1475943r.2286g>a0.871
rrl1475952r.2295a>g0.831
rrl1475970r.2313c>t0.770
rrl1475975r.2318c>t1.000
rrl1475977r.2320a>g1.000
rrl1475978r.2321c>t0.754
rrl1475988r.2331a>g1.000
rrl1475991r.2334t>a0.656
rrl1475993r.2336c>t0.836
rrl1475996r.2339t>g0.727
rrl1475997r.2340a>t0.273
rrl1476024r.2367t>g0.516
rrl1476028r.2371a>g0.700
rrl1476031r.2374c>g0.727
rrl1476032r.2375c>a0.273
rrl1476034r.2377c>g0.273
rrl1476040r.2383c>t0.727
rrl1476044r.2387t>g1.000
rrl1476045r.2388g>t0.364
rrl1476046r.2389g>t0.636
rrl1476047r.2390g>t0.273
rrl1476049r.2392c>t1.000
rrl1476080r.2423t>g1.000
rrl1476085r.2428g>a0.842
rrl1476116r.2459a>g0.196
rrl1476126r.2469c>t0.257
rrl1476130r.2473g>a0.554
rrl1476131r.2474c>t1.000
rrl1476141r.2484a>g0.425
rrl1476153r.2496t>c0.440
rrl1476160r.2503t>c0.275
rrl1476164r.2507a>g0.725
rrl1476165r.2508t>g0.694
rrl1476194r.2537a>g1.000
rrl1476200r.2543a>t1.000
rrl1476201r.2544c>t1.000
rrl1476204r.2547c>t0.549
rrl1476214r.2557g>t0.215
rrl1476215r.2558c>t1.000
rrl1476224r.2567a>g1.000
rrl1476235r.2578a>g0.431
rrl1476245r.2588c>t0.754
rrl1476251r.2594t>a0.265
rrl1476252r.2595t>g0.769
rrl1476256r.2599a>t0.333
rrl1476260r.2603a>g1.000
rrl1476261r.2604a>g0.154
rrl1476267r.2610g>a0.154
rrl1476268r.2611a>g0.154
rrl1476275r.2618t>c0.188
rrl1476276r.2619c>t0.188
rrl1476279r.2622g>a0.188
rrl1476280r.2623a>c0.250
rrl1476281r.2624t>c0.750
rrl1476288r.2631t>c0.222
rrl1476293r.2636c>t0.500
rrl1476294r.2637a>g0.500
rrl1476295r.2638c>g0.500
rrl1476296r.2639c>t0.500
rrl1476297r.2640c>t0.737
rrl1476299r.2642c>a0.316
rrl1476300r.2643g>t0.316
rrl1476301r.2644a>c0.400
rrl1476302r.2645g>a0.308
rrl1476308r.2651g>t0.231
rrl1476311r.2654g>c0.769
rrl1476312r.2655t>c0.769
rrl1476313r.2656g>a0.571
rrl1476332r.2675g>c0.145
rrl1476336r.2679c>g0.216
rrl1476338r.2681c>t0.255
rrl1476358r.2701t>c0.377
rrl1476359r.2702c>g0.531
rrl1476363r.2706a>g0.435
rrl1476366r.2709a>c0.403
rrl1476368r.2711t>c0.507
rrl1476369r.2712c>t0.632
rrl1476372r.2715t>c0.215
rrl1476374r.2717t>g0.377
rrl1476381r.2724g>c0.498
rrl1476382r.2725a>g0.399
rrl1476383r.2726t>a0.193
rrl1476408r.2751g>a0.325
rrl1476411r.2754g>a0.340
rrl1476428r.2771c>a0.191
rrl1476429r.2772a>c0.546
rrl1476443r.2786g>c0.240
rrl1476455r.2798c>a0.215
rrl1476463r.2806c>t0.272
rrl1476466r.2809c>t0.409
rrl1476481r.2824t>c0.726
rrl1476506r.2849t>c0.702
rrl1476515r.2858c>t0.607
rrl1476517r.2860c>t0.202
rrl1476524r.2867c>a0.962
rrl1476525r.2868a>t0.288
rrl1476528r.2871a>g0.288
rrl1476529r.2872a>t0.373
rrl1476530r.2873c>g0.312
rrl1476535r.2878g>a0.510
rrl1476536r.2879g>a0.451
rrl1476538r.2881a>g0.451
rrl1476539r.2882a>g0.627
rrl1476540r.2883c>g0.980
rrl1476547r.2890c>t0.157
rrl1476573r.2916a>t0.568
rrl1476580r.2923g>a0.568
rrl1476584r.2927c>t1.000
rrl1476585r.2928a>g1.000
rrl1476592r.2935g>a0.560
rrl1476594r.2937c>t0.440
rpsA1833970c.429G>C1.000
rpsA1833976c.435C>T1.000
rpsA1833979c.438T>C1.000
rpsA1833985c.444G>T1.000
rpsA1833991c.450C>T0.190
rpsA1833994c.453G>T0.190
rpsA1833997c.456G>T1.000
rpsA1834000c.459G>T1.000
rpsA1834012c.471G>A1.000
rpsA1834015c.474G>C1.000
rpsA1834018c.477C>T1.000
rpsA1834024c.483G>C1.000
rpsA1834034p.Ile165Val1.000
rpsA1834039c.498C>T1.000
rpsA1834040p.Lys167Gln1.000
rpsA1834054c.513C>G0.364
rpsA1834069c.528G>C0.636
rpsA1834090c.549G>T0.364
rpsA1834093c.552G>C0.364
rpsA1834096c.555G>C0.632
rpsA1834099c.558C>G0.368
rpsA1834102c.561T>C0.632
rpsA1834105c.564C>T0.368
rpsA1834108c.567C>T0.200
rpsA1834114c.573G>C1.000
folC2746336c.1263G>A0.286
embA4245555p.Glu775Lys1.000
embB4249289p.Pro926Thr0.722
embB4249772p.Gly1087Ser0.267

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;