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: 5cc5521057e3f
Sample: 5cc5521057e3f

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Summary
ID: 5cc5521057e3f
Date: Sun Apr 28 08:12:35 2019
Strain: lineage1.2.1
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
EthambutolRembB p.His312Arg (0.23)
Pyrazinamide
StreptomycinRrrs r.462c>t (0.58)
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage1.2.1Indo-OceanicEAI2RD239

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7496c.195C>G0.538
gyrA7499c.198G>T0.308
gyrA7502c.201C>T0.538
gyrA7514c.213C>G0.615
gyrA7523c.222C>G0.417
gyrA7526c.225G>C0.417
gyrA7532c.231T>C1.000
gyrA7541c.240C>A0.462
gyrA7547c.246C>T1.000
gyrA7565c.264C>T0.429
gyrA7571c.270G>C0.500
gyrA7574c.273G>C0.500
gyrA7585p.Ser95Thr1.000
gyrA7587c.286C>T1.000
gyrA7784c.483A>G0.818
gyrA7787c.486G>A0.900
gyrA7799c.498A>G1.000
gyrA8324c.1023T>C1.000
gyrA8339c.1038A>G1.000
gyrA8342c.1041G>C1.000
gyrA8366c.1065G>C1.000
gyrA8382p.Leu361Met1.000
gyrA8391p.Tyr364His1.000
gyrA8420c.1119T>C1.000
gyrA8426c.1125G>C1.000
gyrA9248c.1947G>C0.700
gyrA9252p.Val651Ile0.700
rpoB759577c.-230G>A0.786
rpoB759606c.-201T>C0.786
rpoB759636c.-171C>T0.750
rpoB760181c.375T>C0.273
rpoB760184c.378A>G1.000
rpoB760196c.390C>G0.750
rpoB760223c.417T>C1.000
rpoB760235c.429T>C1.000
rpoB760241c.435G>C0.200
rpoB760298c.492G>C1.000
rpoB760508c.702G>C0.200
rpoB760520c.714C>G0.600
rpoB760547c.741G>C0.727
rpoB760561c.756 757del1.000
rpoC763486c.117T>G1.000
rpoC763528c.159G>A1.000
rpoC763546c.177A>G1.000
rpoC763570c.201G>C1.000
rpoC763573c.204G>C1.000
rpoC763633c.264T>C0.667
rpoC763636c.267T>C0.667
rpoC763660c.291T>C0.308
rpoC763666c.297G>T0.308
rpoC763669c.300C>G0.308
rpoC763675c.306C>G0.692
rpoC763696c.327T>C0.364
rpoC763702c.333C>T0.333
rpoC763705c.336G>A0.273
rpoC763708c.339G>C0.333
rpoC763709c.340C>T1.000
rpoC763714c.345G>C1.000
rpoC763717c.348T>C1.000
rpoC763723c.354G>C0.692
rpoC763732c.363C>G0.917
rpoC763735c.366G>C0.333
rpoC763741c.372C>T0.636
rpoC763744c.375G>C1.000
rpoC763765c.396T>G1.000
rpoC763768c.399C>G0.750
rpoC763780c.411C>G0.800
rpoC763792p.Glu141Asp0.800
rpoC763813c.444C>G0.900
rpoC764131c.762T>C1.000
rpoC764161c.792G>C0.769
rpoC764188c.819A>G1.000
rpoC764194p.Glu275Asp0.700
rpoC764195p.Ser276Thr0.333
rpoC764203c.834G>C0.300
rpoC764206c.837T>C0.273
rpoC764626c.1257C>T1.000
rpoC764632c.1263T>C0.714
rpoC764650c.1281G>T0.941
rpoC764656c.1287C>G0.278
rpoC764692c.1323C>T0.250
rpoC764695c.1326T>C0.714
rpoC764698c.1329G>A0.583
rpoC764713c.1344G>T0.286
rpoC764716c.1347G>C0.571
rpoC764731c.1362G>C0.643
rpoC764749c.1380G>C0.643
rpoC764752c.1383G>C1.000
rpoC764758c.1389C>G0.286
rpoC764764c.1395T>C1.000
rpoC764791c.1422C>G0.250
rpoC764803c.1434C>G0.727
rpoC764815c.1446A>G1.000
rpoC764824c.1455T>C0.923
rpoC764827c.1458G>C0.800
rpoC764843p.Ala492Ser0.188
rpoC764858c.1489T>C1.000
rpoC764888c.1519T>C0.760
rpoC764893c.1524T>C0.960
rpoC764911c.1542A>G0.964
rpoC764923c.1554A>G0.778
rpoC764932c.1563C>G0.250
rpoC764948c.1579T>C0.778
rpoC764968c.1599T>C1.000
rpoC765034c.1665T>C1.000
rpoC765040c.1671T>C1.000
rpoC765041c.1672T>C1.000
rpoC765052c.1683C>G0.929
rpoC765073c.1704G>C1.000
rpoC765076c.1707A>G1.000
rpoC765079c.1710T>C1.000
rpoC765089c.1720T>C1.000
rpoC765103c.1734G>A1.000
rpoC765129p.Tyr587Phe1.000
rpoC765370c.2001G>C0.818
rpoC765383p.Met672Leu1.000
rpoC765421c.2052C>G1.000
rpoC765451c.2082C>G0.882
rpoC765478c.2109T>C1.000
rpoC765499c.2130C>G1.000
rpoC765532c.2163C>T0.190
rpoC765541c.2172C>G0.278
rpoC765547c.2178C>A0.200
rpoC765550c.2181C>T0.588
rpoC765553c.2184C>T0.750
rpoC765556c.2187G>C0.733
rpoC765559c.2190G>C0.733
rpoC765562c.2193G>C0.222
rpoC765580c.2211G>C0.222
rpoC765583c.2214G>T0.778
rpoC765586c.2217G>C0.588
rpoC765592c.2223C>T0.200
rpoC765613p.His748Gln0.176
rpoC765625c.2256C>G0.800
rpoC765628c.2259G>C0.700
rpoC765631p.Asp754Glu1.000
rpoC765826c.2457T>C1.000
rpoC765835c.2466C>T0.158
rpoC765850c.2481G>C0.211
rpoC765871c.2502T>C0.778
rpoC765883c.2514C>G0.737
rpoC765886c.2517C>G1.000
rpoC765892c.2523T>C0.737
rpoC765937c.2568T>C0.833
rpoC765947c.2578T>C0.692
rpoC765967c.2598C>T1.000
rpoC765979c.2610C>G0.636
rpoC765982c.2613C>T0.273
rpoC766021c.2652G>C1.000
rpoC766027c.2658G>C0.727
rpoC766036c.2667C>T0.167
rpoC766043p.Gln892Glu0.750
rpoC766054c.2685C>G0.750
rpoC766061p.Val898Ile0.583
rpoC766081c.2712T>C0.818
rpoC766082p.Ala905Gln1.000
rpoC766087c.2718C>G0.900
rpoC766096c.2727G>C0.750
rpoC766105c.2736C>T0.231
rpoC766129c.2760C>G1.000
rpoC766135c.2766G>A0.200
rpoC766408c.3039C>T0.444
rpoC766426c.3057C>T0.667
rpoC766429c.3060C>G0.333
rpoC766447c.3078T>C1.000
rpoC766456c.3087C>G0.867
rpoC766459c.3090G>T0.400
rpoC766462c.3093G>C0.533
rpoC766483c.3114G>C1.000
rpoC766486c.3117A>G1.000
rpoC766492c.3123T>C0.571
rpoC766522c.3153C>G0.385
rpoC766525c.3156G>T0.250
rpoC766528c.3159T>G0.417
rpoC766530p.Arg1054His0.545
rpoC766540p.Asp1057Glu0.667
rpoC766549c.3180G>C1.000
rpoC766645c.3276A>G1.000
rpoC766651c.3282T>C0.222
rpoC766657c.3288A>G1.000
rpoC766666c.3297C>G0.688
rpoC766672c.3303T>C1.000
rpoC766708c.3339A>G0.737
rpoC766726c.3357T>C1.000
rpoC766738c.3369G>C0.227
rpoC766750c.3381C>G0.227
rpoC766765c.3396A>C1.000
rpoC766774c.3405T>C1.000
rpoC766777c.3408C>G0.211
rpoC766804c.3435A>G1.000
rpoC766837c.3468G>C0.250
rpoC766843c.3474T>C0.923
rpoC766861c.3492G>C1.000
rpoC766933c.3564A>G1.000
rpoC766972c.3603G>C1.000
rpoC766981c.3612T>C0.818
rpoC766996c.3627C>T1.000
rpoC767033c.3664T>A1.000
rpoC767059c.3690T>G1.000
rpoC767062c.3693C>A1.000
rpoC767098c.3729T>C1.000
rpoC767119c.3750A>G1.000
rpoC767134c.3765C>A1.000
rpoC767158c.3789T>C0.750
rpoC767167c.3798C>G0.917
rpoC767185c.3816G>T0.400
rpoC767206c.3837C>G0.500
rpoC767209c.3840T>C1.000
rpoC767212c.3843G>C0.417
rpoC767221c.3852C>G0.300
rpoC767239c.3870T>C0.700
rpoC767264p.Ala1299Gln1.000
rpoC767302c.3933C>G0.818
rpsL781628c.69T>C0.333
rpsL781649c.90T>C1.000
rpsL781655c.96T>C1.000
rpsL781658c.99A>G0.353
rpsL781682c.123T>C0.450
rpsL781700c.141G>C0.150
rpsL781703c.144G>C0.529
rpsL781715c.156T>C1.000
rpsL781718c.159C>G0.353
rpsL781721c.162C>T0.529
rpsL781728c.169T>C1.000
rpsL781733c.174G>C0.444
rpsL781736c.177T>C1.000
rpsL781742c.183C>T0.611
rpsL781748c.189C>G0.176
rpsL781751c.192G>C0.400
rpsL781754c.195G>C1.000
rpsL781760c.201T>C0.875
rpsL781763c.204C>G0.643
rpsL781787c.228G>A0.600
rpsL781808c.249C>T0.308
rpsL781811c.252C>T1.000
rpsL781817c.258G>A0.692
rpsL781820c.261G>C0.667
rpsL781832c.273T>C1.000
rpsL781841c.282C>T0.214
rpsL781865c.306G>C1.000
rpsL781868c.309T>C1.000
rpsL781871c.312G>C1.000
rpsL781877c.318T>G0.385
rpsL781880c.321C>G0.308
rpsL781892c.333A>G1.000
rpsL781898c.339A>T1.000
rpsL781916c.357T>C1.000
rpsL781929p.Gly124Ser1.000
rpsL781933c.374G>A0.455
rplC801162c.354C>G0.250
rplC801171c.363A>G1.000
rplC801174c.366T>C1.000
rplC801204c.396C>T0.267
rplC801210c.402T>A0.267
rplC801228c.420T>C0.733
rplC801231c.423C>G0.267
rplC801249c.441T>C0.273
rplC801255c.447C>T0.667
rrs1471923r.78t>c1.000
rrs1471925r.80t>c1.000
rrs1471932r.87a>g1.000
rrs1471934r.89a>g1.000
rrs1471969r.124t>c0.762
rrs1471970r.125g>a0.762
rrs1472030r.185g>t0.684
rrs1472031r.186g>t0.650
rrs1472033r.188a>g0.684
rrs1472034r.189t>c0.684
rrs1472040r.195t>c0.737
rrs1472042r.197t>c0.263
rrs1472053r.208agc>a1.000
rrs1472061r.216a>t1.000
rrs1472075r.230a>g1.000
rrs1472108r.263c>t0.714
rrs1472489r.644a>g0.217
rrs1472847r.1002g>c0.190
rrs1472848r.1003t>g0.238
rrs1472849r.1004c>g0.190
rrs1472850r.1005t>c0.200
rrs1472857r.1012a>g0.235
rrs1472858r.1013g>t0.235
rrs1472859r.1014g>c0.235
rrs1472860r.1015c>g0.235
rrs1472969r.1124a>g1.000
rrs1472970r.1125c>g1.000
rrs1472977r.1132g>c1.000
rrs1472978r.1133t>c1.000
rrs1473104r.1259c>t0.632
rrs1473105r.1260g>a0.737
rrs1473120r.1275c>ct0.889
rrs1473123r.1278a>t1.000
rrs1473290r.1445c>t1.000
rrl1473756r.99g>a0.762
rrl1473758r.101g>t1.000
rrl1473806r.149c>t1.000
rrl1473813r.156c>t0.174
rrl1473815r.158t>c0.889
rrl1473839r.182g>t0.857
rrl1473877r.220g>a0.895
rrl1473898r.241c>t0.889
rrl1473899r.242a>t1.000
rrl1473937r.280c>t1.000
rrl1473944r.287g>a0.917
rrl1474018r.361g>t0.833
rrl1474051r.394t>c0.625
rrl1474054r.397t>c0.588
rrl1474056r.399t>c0.588
rrl1474060r.403g>a0.556
rrl1474071r.414g>a0.611
rrl1474093r.436g>t0.294
rrl1474099r.442g>a0.875
rrl1474103r.446a>t1.000
rrl1474111r.454t>c0.692
rrl1474112r.455t>a0.583
rrl1474140r.483c>t1.000
rrl1474151r.494c>t1.000
rrl1474181r.524c>t1.000
rrl1474290r.633ttttcctctccggagg>t0.625
rrl1474291r.634tttcctctccggagga>t1.000
rrl1474308r.651g>t1.000
rrl1474310r.653t>g1.000
rrl1474356r.699t>c0.688
rrl1474362r.705a>g1.000
rrl1474376r.719t>c0.714
rrl1474447r.790g>a0.200
rrl1474627r.970g>a0.905
rrl1474632r.975g>t0.909
rrl1474639r.982g>a1.000
rrl1474716r.1059a>c0.161
rrl1474717r.1060a>t0.733
rrl1474760r.1103a>g0.778
rrl1474794r.1137c>t1.000
rrl1474812r.1155g>a1.000
rrl1474831r.1174a>g1.000
rrl1474956r.1299c>t0.300
rrl1474963r.1306g>a0.750
rrl1474964r.1307t>a0.727
rrl1474965r.1308g>c0.333
rrl1474991r.1334t>c0.400
rrl1474995r.1338t>g0.400
rrl1475006r.1349a>g0.467
rrl1475007r.1350c>t0.650
rrl1475013r.1356g>a0.800
rrl1475018r.1361g>c0.333
rrl1475019r.1362t>c0.333
rrl1475027r.1370g>t0.571
rrl1475028r.1371g>t0.571
rrl1475061r.1404c>a0.240
rrl1475062r.1405a>t0.240
rrl1475088r.1431a>t0.792
rrl1475206r.1549c>t1.000
rrl1475209r.1552g>c0.933
rrl1475213r.1556c>t1.000
rrl1475249r.1592t>c1.000
rrl1475252r.1595c>t1.000
rrl1475266r.1609t>c1.000
rrl1475267r.1610g>a1.000
rrl1475275r.1618c>t1.000
rrl1475276r.1619t>c1.000
rrl1475291r.1634a>c1.000
rrl1475313r.1656g>a0.824
rrl1475315r.1658a>t0.765
rrl1475355r.1698c>t1.000
rrl1475369r.1712g>c1.000
rrl1475380r.1723c>t0.667
rrl1475387r.1730c>t0.588
rrl1475402r.1745c>t1.000
rrl1475419r.1762c>t0.632
rrl1475429r.1772g>a0.882
rrl1475479r.1822c>t0.273
rrl1475480r.1823a>t0.273
rrl1475505r.1848g>a0.950
rrl1475526r.1869c>a0.273
rrl1475573r.1916g>a0.167
rrl1475599r.1942a>g1.000
rrl1475604r.1947a>c0.190
rrl1475607r.1950a>g0.182
rrl1475608r.1951t>c0.818
rrl1475635r.1978g>a0.158
rrl1475637r.1980t>g0.158
rrl1475638r.1981c>t0.842
rrl1475642r.1985t>c0.842
rrl1475657r.2000a>g0.789
rrl1475659r.2002g>a0.200
rrl1475758r.2101ac>a0.846
rrl1475881r.2224t>c0.773
rrl1475977r.2320a>g0.182
rrl1475988r.2331a>t0.182
rrl1476033r.2376t>c1.000
rrl1476035r.2378g>a0.895
rrl1476086r.2429g>a1.000
rrl1476089r.2432t>c1.000
rrl1476095r.2438c>g1.000
rrl1476106r.2449a>t1.000
rrl1476115r.2458t>c1.000
rrl1476117r.2460g>c1.000
rrl1476131r.2474c>t0.150
rrl1476214r.2557g>t0.929
rrl1476215r.2558c>t0.929
rrl1476224r.2567a>g0.875
rrl1476281r.2624t>c0.800
rrl1476583r.2926g>c0.318
rrl1476584r.2927c>t0.667
rrl1476594r.2937c>t0.318
rrl1476597r.2940g>a1.000
rrl1476603r.2946g>a0.368
rrl1476628r.2971t>c0.389
rrl1476629r.2972c>a0.368
rrl1476675r.3018c>t0.316
rrl1476679r.3022t>c0.316
rrl1476689r.3032a>t1.000
rrl1476690r.3033c>t0.615
rrl1476692r.3035t>a0.385
rrl1476693r.3036g>a0.615
rrl1476695r.3038t>a1.000
rrl1476710r.3053c>t0.364
rrl1476716r.3059a>c0.700
inhA1674480c.279T>C1.000
inhA1674486c.285T>C1.000
inhA1674489c.288G>C0.778
inhA1674507c.306G>C0.200
inhA1674537c.336C>G0.692
inhA1674540c.339C>T0.692
inhA1674542p.Ala114Glu1.000
inhA1674546c.345T>C0.250
inhA1674549c.348G>C0.250
rpsA1833568c.27G>C0.400
rpsA1833589c.48A>T0.333
rpsA1833805c.264C>G1.000
rpsA1833808c.267G>C0.909
rpsA1833811c.270G>C1.000
rpsA1833832c.291G>A0.200
rpsA1833847c.306C>G1.000
rpsA1833856c.315A>G1.000
rpsA1833874c.333T>C1.000
rpsA1833928c.387G>C1.000
rpsA1833940c.399C>G0.200
rpsA1833949c.408T>C0.789
rpsA1833970c.429G>C0.722
rpsA1833971c.430C>T0.222
rpsA1833976c.435C>T0.737
rpsA1833979c.438T>C1.000
rpsA1833991c.450C>G0.778
rpsA1834000c.459G>C1.000
rpsA1834012c.471G>C0.727
rpsA1834015c.474G>C0.846
rpsA1834021c.480C>T1.000
rpsA1834030c.489C>G1.000
rpsA1834105c.564C>G1.000
rpsA1834210c.669C>T0.700
rpsA1834222c.681T>C1.000
rpsA1834225c.684C>G0.273
rpsA1834231c.690T>G0.364
rpsA1834240c.699T>C1.000
rpsA1834249c.708T>C1.000
rpsA1834252c.711C>G0.727
rpsA1834261c.720A>G1.000
rpsA1834264c.723G>C1.000
rpsA1834288c.747C>G0.733
rpsA1834294c.753G>C0.647
rpsA1834297c.756C>G0.188
rpsA1834303c.762T>C1.000
rpsA1834306c.765T>C1.000
rpsA1834333c.792C>T0.250
rpsA1834336c.795C>G0.571
rpsA1834348c.807T>C1.000
rpsA1834366c.825A>G1.000
rpsA1834396c.855G>C0.200
rpsA1834411c.870T>G1.000
rpsA1834417c.876G>C1.000
rpsA1834423c.882G>C0.786
rpsA1834435c.894G>C0.846
rpsA1834451c.910T>C1.000
rpsA1834465c.924T>C0.900
rpsA1834468c.927A>G1.000
rpsA1834489c.948T>C1.000
rpsA1834513c.972C>G0.833
rpsA1834528c.987T>C1.000
rpsA1834546c.1005T>C1.000
rpsA1834555c.1014T>C1.000
rpsA1834609c.1068T>C1.000
rpsA1834633c.1092A>G1.000
rpsA1834639c.1098T>C1.000
rpsA1834654p.Glu371Asp0.273
rpsA1834690c.1149T>C1.000
kasA2518183c.69G>A0.778
kasA2518190p.Ser26Ala1.000
kasA2518199p.Ile29Val0.200
kasA2518220c.106C>T1.000
kasA2518234c.120G>A1.000
kasA2518248p.Ala45Val1.000
kasA2518255c.141A>G0.700
kasA2518261p.Glu49Asp0.200
kasA2518265p.Val51Ile0.200
thyA3074079c.393C>T0.200
thyA3074097c.375G>C0.200
thyA3074100c.372A>G1.000
thyA3074103c.369G>C1.000
thyA3074106c.366A>G0.200
embC4240780c.918T>C1.000
embC4240783c.921G>C1.000
embC4240795c.933C>G0.455
embC4240819c.957A>C0.200
embC4240822c.960C>G0.400
embC4240828c.966G>A0.200
embC4240831c.969T>G0.400
embC4240859p.Leu333Val0.429
embC4240867c.1005T>G0.455
embC4241416c.1554C>T0.818
embC4241449c.1587C>T1.000
embC4241453p.Ile531Val1.000
embA4245110c.1878C>T0.800
embB4247437c.924A>G0.308
embB4247446c.933C>T0.286
embB4247452c.939C>G0.769
embB4247464c.951C>G0.833
embB4247470c.957T>C1.000
embB4247476c.963C>T1.000
embB4247491c.978G>C0.818
embB4247494c.981G>A1.000
embB4247512c.999T>C1.000
embB4248118c.1605T>C0.273
embB4248124c.1611G>C0.545
embB4248130c.1617G>C0.417
embB4248133c.1620C>A0.250
embB4248139c.1626C>G0.250
embB4248142c.1629T>C1.000
embB4248143p.Leu544Met0.417
embB4248157c.1644A>G0.231
embB4248163c.1650G>C0.692
embB4248169c.1656C>G0.231
embB4248172c.1659G>C0.750
embB4248173p.Val554Met0.667

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;