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: 5cc556ab08bec
Sample: 5cc556ab08bec

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Summary
ID: 5cc556ab08bec
Date: Sun Apr 28 08:32:49 2019
Strain: lineage4.3;lineage4.2.1
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
StreptomycinRrrs r.462c>t (1.00)
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage4.3Euro-American (LAM)mainly-LAMNone
lineage4.2.1Euro-American (TUR)H3;H4None

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7331c.30C>T1.000
gyrA7337c.36C>G1.000
gyrA7355c.54T>C1.000
gyrA7362p.Glu21Gln1.000
gyrA7394c.93T>C1.000
gyrA7412c.111C>G0.944
gyrA7427c.126G>C0.950
gyrA7451c.150C>G0.952
gyrA7457c.156T>C0.947
gyrA7472c.171T>C1.000
gyrA7475c.174A>G1.000
gyrA7484c.183T>C1.000
gyrA7490c.189C>G1.000
gyrA7502c.201C>T1.000
gyrA7506p.Ser69Gly1.000
gyrA7514c.213C>G1.000
gyrA7517c.216G>A1.000
gyrA7523c.222C>G1.000
gyrA7526c.225G>C1.000
gyrA7532c.231T>C1.000
gyrA7547c.246C>T1.000
gyrA7569p.Ala90Ser1.000
gyrA7585p.Ser95Thr1.000
gyrA7607c.306C>G1.000
gyrA7763c.462T>G1.000
gyrA7787c.486G>A1.000
gyrA7790c.489G>C1.000
gyrA7797c.496C>T1.000
gyrA7821c.520C>T1.000
gyrA7832c.531G>T1.000
gyrA7835c.534A>C1.000
gyrA7841c.540C>A1.000
gyrA7847c.546G>C1.000
gyrA7859c.558A>G1.000
gyrA7865c.564T>C1.000
gyrA7886c.585T>C1.000
gyrA8915c.1614A>G1.000
gyrA8918c.1617C>G0.917
gyrA8930c.1629C>T1.000
gyrA8939c.1638T>C1.000
gyrA8987c.1686C>G1.000
gyrA8996c.1695T>C1.000
gyrA8998p.Leu566Trp1.000
gyrA9017c.1716C>G1.000
gyrA9023c.1722A>C1.000
gyrA9029c.1728T>G1.000
gyrA9051c.1750T>C1.000
gyrA9056c.1755C>G0.917
gyrA9089c.1788G>C0.900
gyrA9119c.1818A>G0.900
gyrA9167c.1866C>T0.900
gyrA9191c.1890G>C1.000
gyrA9200c.1899A>G1.000
rpoB760199c.393C>G0.900
rpoB760235c.429T>C0.933
rpoB760253c.447T>C0.941
rpoB760283c.477G>C0.923
rpoB760298c.492G>C0.857
rpoB760310c.504G>C0.800
rpoB760313c.507G>C0.800
rpoB760317c.511A>T0.800
rpoB760331c.525G>C0.800
rpoB760611c.805T>C1.000
rpoB760649c.843G>C1.000
rpoB760655c.849A>G1.000
rpoB760661c.855A>C1.000
rpoB760931c.1125C>G1.000
rpoB760934c.1128C>T1.000
rpoB760946c.1140A>G1.000
rpoB760965p.Met387Leu1.000
rpoB760982c.1176G>C1.000
rpoB760988c.1182C>G1.000
rpoB760991c.1185G>C1.000
rpoB761015c.1209G>C1.000
rpoB761021c.1215G>C1.000
rpoB761027c.1221A>G1.000
rpoB761037c.1231T>C1.000
rpoB761051c.1245G>C1.000
rpoB761066c.1260G>C1.000
rpoB761132c.1326G>T0.818
rpoB761133c.1327T>C0.818
rpoB761150c.1344A>G0.818
rpoB761153c.1347G>C0.818
rpoB761156c.1350G>A0.800
rpoB761207c.1401C>T0.900
rpoB761375c.1569G>C1.000
rpoB761930c.2124G>C1.000
rpoB761948c.2142G>C1.000
rpoB761954c.2148C>G1.000
rpoB761955p.Ile717Val1.000
rpoB762006c.2200C>A1.000
rpoB762017c.2211A>G1.000
rpoB762024p.Val740Thr1.000
rpoB762029c.2223C>G1.000
rpoB762053c.2247T>C1.000
rpoB762062c.2256T>C1.000
rpoB762065c.2259T>C1.000
rpoB762083c.2277T>C1.000
rpoB762086c.2280G>C1.000
rpoB762101c.2295C>G1.000
rpoB762114p.Ile770Val1.000
rpoB762122c.2316C>T1.000
rpoB762131c.2325C>G1.000
rpoB762134c.2328C>A1.000
rpoB762158c.2352G>C1.000
rpoB762167c.2361T>C1.000
rpoB762176c.2370T>C1.000
rpoB762185c.2379G>C1.000
rpoB762209c.2403C>G1.000
rpoB762233c.2427G>C1.000
rpoB762236c.2430G>C1.000
rpoB762249c.2443C>T1.000
rpoB762254c.2448T>C1.000
rpoB762266c.2460T>C1.000
rpoB762281c.2475G>A1.000
rpoB762284c.2478G>C1.000
rpoB762287c.2481C>G1.000
rpoB762293c.2487T>C1.000
rpoB762317c.2511A>G1.000
rpoB762329c.2523G>C1.000
rpoB762338c.2532T>C1.000
rpoB762347c.2541T>C1.000
rpoB762362p.Glu852Asp1.000
rpoB762369c.2563T>C1.000
rpoB762374c.2568G>C1.000
rpoB762380c.2574T>G1.000
rpoB762416c.2610A>G0.929
rpoB762452c.2646G>C0.950
rpoB762490p.Val895Ala0.947
rpoB762509c.2703T>G0.923
rpoB762510p.Ala902Pro0.923
rpoB762521c.2715C>G0.923
rpoB762527c.2721G>C0.923
rpoB762533c.2727T>C1.000
rpoB762536c.2730T>C1.000
rpoB762857c.3051C>G1.000
rpoB762860c.3054G>C1.000
rpoB762863c.3057T>C1.000
rpoB762911c.3105C>T1.000
rpoB762929c.3123G>T0.962
rpoB762989c.3183G>C1.000
rpoB762995c.3189G>T1.000
rpoB763031c.3225T>C1.000
rpoB763034c.3228C>G1.000
rpoB763040c.3234C>G1.000
rpoB763053c.3247T>C1.000
rpoB763058c.3252C>G1.000
rpoB763070c.3264T>C1.000
rpoB763094c.3288G>C1.000
rpoB763115c.3309T>C1.000
rpoB763127c.3321G>C1.000
rpoC763468c.99G>C1.000
rpoC763486c.117T>C1.000
rpoC763492c.123G>C1.000
rpoC763528c.159G>A1.000
rpoC763546c.177A>G1.000
rpoC763594c.225C>T1.000
rpoC763603c.234C>T1.000
rpoC763639c.270G>A1.000
rpoC763660c.291T>G1.000
rpoC763669c.300C>G1.000
rpoC763696c.327T>C1.000
rpoC764083c.714A>G1.000
rpoC764085p.Asn239Thr1.000
rpoC764087p.Leu240Val1.000
rpoC764098c.729A>G1.000
rpoC764101c.732C>G1.000
rpoC764131c.762T>C1.000
rpoC764134c.765C>G1.000
rpoC764188c.819A>G1.000
rpoC764257c.888G>C0.909
rpoC764266c.897T>C1.000
rpoC764278c.909A>G1.000
rpoC764293c.924G>C1.000
rpoC764317c.948C>G1.000
rpoC764320c.951C>G1.000
rpoC764344c.975C>T1.000
rpoC764365c.996C>T1.000
rpoC764387c.1018T>C1.000
rpoC764405c.1036A>C1.000
rpoC764446c.1077T>C1.000
rpoC764449c.1080G>C1.000
rpoC764458c.1089G>C1.000
rpoC764461c.1092A>G1.000
rpoC764497c.1128A>G1.000
rpoC764503c.1134G>C1.000
rpoC764521c.1152T>C1.000
rpoC764611c.1242G>C1.000
rpoC764644c.1275G>C1.000
rpoC764650c.1281G>T1.000
rpoC764665c.1296C>G1.000
rpoC764713c.1344G>A1.000
rpoC764716c.1347G>C1.000
rpoC764752c.1383G>C1.000
rpoC764758c.1389C>G1.000
rpoC764764c.1395T>C1.000
rpoC764782c.1413C>T1.000
rpoC764791c.1422C>G1.000
rpoC764803c.1434C>G1.000
rpoC764809c.1440C>T1.000
rpoC764815c.1446A>G1.000
rpoC764824c.1455T>C1.000
rpoC764827c.1458G>C1.000
rpoC764869c.1500C>T1.000
rpoC764878c.1509C>G1.000
rpoC764888c.1519T>C1.000
rpoC764893c.1524T>C1.000
rpoC764896c.1527C>T1.000
rpoC764911c.1542A>G1.000
rpoC764912p.Met515Gln1.000
rpoC764923c.1554A>G1.000
rpoC764948c.1579T>C1.000
rpoC764962c.1593G>C1.000
rpoC764968c.1599T>C1.000
rpoC764995c.1626C>G1.000
rpoC765012p.Ser548Thr1.000
rpoC765019c.1650A>G1.000
rpoC765034c.1665T>C1.000
rpoC765040c.1671T>C1.000
rpoC765041c.1672T>C1.000
rpoC765047c.1678T>C1.000
rpoC765052c.1683C>T1.000
rpoC765076c.1707A>C1.000
rpoC765079c.1710T>G1.000
rpoC765082c.1713G>T1.000
rpoC765085c.1716T>C1.000
rpoC765089c.1720T>C1.000
rpoC765103c.1734G>A1.000
rpoC765121c.1752G>T1.000
rpoC765403c.2034G>C1.000
rpoC765404p.Leu679Val1.000
rpoC765409c.2040T>C1.000
rpoC765412c.2043T>C1.000
rpoC765421c.2052C>G1.000
rpoC765453p.Ala695Val1.000
rpoC765508c.2139C>G1.000
rpoC765548c.2179A>T1.000
rpoC765553c.2184C>G1.000
rpoC765556c.2187G>C1.000
rpoC765562c.2193G>C1.000
rpoC765607c.2238C>G1.000
rpoC765611p.His748Ser1.000
rpoC765628c.2259G>C1.000
rpoC765640c.2271A>G1.000
rpoC765662c.2293T>C1.000
rpoC765688c.2319G>A1.000
rpoC765787c.2418C>T1.000
rpoC765793c.2424C>G1.000
rpoC765796c.2427C>T1.000
rpoC765811c.2442T>C1.000
rpoC765814c.2445A>G1.000
rpoC765826c.2457T>C1.000
rpoC765835c.2466C>T1.000
rpoC765841c.2472G>C1.000
rpoC765850c.2481G>C1.000
rpoC765868c.2499G>A1.000
rpoC765871c.2502T>G1.000
rpoC765875p.Val836Ile1.000
rpoC765884c.2515T>A1.000
rpoC765904c.2535C>G1.000
rpoC765934c.2565C>T1.000
rpoC765937c.2568T>C1.000
rpoC765947c.2578T>C1.000
rpoC765961c.2592G>C1.000
rpoC765967c.2598C>T1.000
rpoC765979c.2610C>G1.000
rpoC765982c.2613C>T1.000
rpoC765994c.2625A>T1.000
rpoC766012c.2643C>G1.000
rpoC766288c.2919C>G1.000
rpoC766309c.2940G>C1.000
rpoC766312c.2943T>G1.000
rpoC766315c.2946C>G1.000
rpoC766345c.2976T>C1.000
rpoC766348c.2979A>G1.000
rpoC766357c.2988C>T1.000
rpoC766363c.2994G>C1.000
rpoC766366c.2997C>G1.000
rpoC766384c.3015A>G1.000
rpoC766390c.3021C>T1.000
rpoC766426c.3057C>T1.000
rpoC766484p.Val1039Ile1.000
rpoC766492c.3123T>C1.000
rpoC766517p.Thr1050Ala1.000
rpoC766522c.3153C>A1.000
rpoC766528c.3159T>C1.000
rpoC766531c.3162G>C1.000
rpoC766564c.3195C>G1.000
rpoC766570c.3201T>G1.000
rpoC766573c.3204T>G1.000
rpoC766582c.3213C>T1.000
rpoC766585c.3216T>C1.000
rpoC766607p.Ile1080Leu1.000
rpoC766610p.Ser1081Pro1.000
rpoC766618c.3249G>T1.000
rpoC766645c.3276A>G1.000
rpoC766657c.3288A>G1.000
rpoC766661p.Val1098Leu1.000
rpoC766666c.3297C>G1.000
rpoC766667p.Ser1100Ala1.000
rpoC766672c.3303T>C1.000
rpoC766687p.Glu1106Asp0.944
rpoC766690c.3321G>C0.944
rpoC766693c.3324C>G0.944
rpoC766702c.3333G>C0.947
rpoC766708c.3339A>G0.947
rpoC766726c.3357T>C0.941
rpoC766741c.3372G>T0.933
rpoC766765c.3396A>C0.909
rpoC767059c.3690T>C1.000
rpoC767098c.3729T>C1.000
rpoC767104c.3735C>G1.000
rpoC767105p.Asn1246Gln1.000
rpoC767110c.3741T>G1.000
rpoC767119c.3750A>G1.000
rpoC767152c.3783T>C1.000
rpoC767158c.3789T>C1.000
rpoC767167c.3798C>G1.000
rpoC767180p.Ala1271Thr1.000
rpoC767191c.3822C>G1.000
rpoC767206c.3837C>G1.000
rpoC767209c.3840T>C1.000
rpoC767212c.3843G>T1.000
rpoC767221c.3852C>G1.000
rpoC767263c.3894T>C1.000
rpoC767266c.3897G>C1.000
rpoC767278c.3909T>C1.000
rpoC767281c.3912C>G1.000
rpoC767284c.3915C>T0.950
rpoC767302c.3933C>G1.000
rpsL781571c.12C>T1.000
rpsL781589c.30G>A1.000
rpsL781592c.33T>C1.000
rpsL781595c.36T>C1.000
rpsL781598c.39G>C1.000
rpsL781608p.Ser17Gly1.000
rpsL781628c.69T>C1.000
rpsL781631c.72G>C1.000
rpsL781658c.99A>C1.000
rpsL781682c.123T>C1.000
rpsL781709c.150G>C0.947
rpsL781715c.156T>G0.947
rpsL781724c.165G>C0.947
rpsL781728c.169T>C0.950
rpsL781733c.174G>C0.952
rpsL781736c.177T>C0.952
rpsL781748c.189C>G0.938
rpsL781751c.192G>C0.929
rpsL781754c.195G>C0.944
rpsL781760c.201T>C0.944
rpsL781763c.204C>G0.944
rpsL781808c.249C>T0.947
rpsL781811c.252C>T0.944
rpsL781832c.273T>G0.944
rplC801220p.Ser138Gly1.000
rplC801228c.420T>C1.000
rplC801249c.441T>G1.000
rplC801255c.447C>T1.000
rplC801258c.450C>G1.000
rplC801267c.459A>C1.000
rplC801281p.Ala158Gly1.000
rrs1471923r.78t>c1.000
rrs1471925r.80t>c1.000
rrs1471926r.81c>t1.000
rrs1471932r.87a>g1.000
rrs1471934r.89a>g1.000
rrs1471936r.91a>g1.000
rrs1471985r.140t>c0.392
rrs1471986r.141c>t1.000
rrs1472029r.184c>t1.000
rrs1472053r.208agc>a1.000
rrs1472055r.210cgct>c1.000
rrs1472061r.216a>t0.981
rrs1472075r.230a>g1.000
rrs1472108r.263c>t1.000
rrs1472286r.441c>g1.000
rrs1472287r.442c>t1.000
rrs1472292r.447a>g1.000
rrs1472298r.453g>t1.000
rrs1472300r.455c>g1.000
rrs1472313r.468g>c1.000
rrs1472315r.470t>g1.000
rrs1472327r.482g>a1.000
rrs1472328r.483g>c1.000
rrs1472438r.593t>c1.000
rrs1472446r.601t>a1.000
rrs1472452r.607g>a1.000
rrs1472464r.619a>g1.000
rrs1472489r.644a>g1.000
rrs1472498r.653c>t1.000
rrs1472683r.838t>tta0.911
rrs1472847r.1002g>c1.000
rrs1472848r.1003t>g1.000
rrs1472849r.1004c>g1.000
rrs1472858r.1013g>t1.000
rrs1472859r.1014g>c1.000
rrs1472860r.1015c>g1.000
rrs1472973r.1128a>g0.984
rrs1473104r.1259c>t1.000
rrs1473111r.1266a>t1.000
rrs1473123r.1278a>t1.000
rrs1473276r.1431a>g1.000
rrs1473290r.1445c>t1.000
rrs1473301r.1456t>c1.000
rrl1473668r.11c>g1.000
rrl1473770r.113t>g1.000
rrl1473788r.131a>g1.000
rrl1473793r.136g>c1.000
rrl1473839r.182g>t0.957
rrl1473877r.220g>a1.000
rrl1473898r.241c>t1.000
rrl1473899r.242a>g1.000
rrl1473916r.259c>a1.000
rrl1474083r.426c>t1.000
rrl1474140r.483c>t1.000
rrl1474151r.494c>t1.000
rrl1474174r.517a>g1.000
rrl1474181r.524c>t1.000
rrl1474201r.544t>c0.982
rrl1474202r.545t>g0.982
rrl1474263r.606g>a0.962
rrl1474290r.633t>g0.900
rrl1474350r.693g>c0.952
rrl1474351r.694g>c0.952
rrl1474353r.696a>g0.952
rrl1474356r.699t>c0.952
rrl1474362r.705a>g0.955
rrl1474374r.717t>g0.955
rrl1474387r.730c>t0.952
rrl1474452r.795c>g1.000
rrl1474552r.895c>t1.000
rrl1474632r.975g>t1.000
rrl1474636r.979a>t1.000
rrl1474638r.981c>a1.000
rrl1474639r.982g>c1.000
rrl1474710r.1053t>g0.969
rrl1474711r.1054g>t0.484
rrl1474713r.1056t>a0.469
rrl1474753r.1096a>g0.980
rrl1474760r.1103a>g0.979
rrl1474794r.1137c>t0.980
rrl1474812r.1155g>a0.980
rrl1474830r.1173a>g0.980
rrl1474952r.1295ac>a1.000
rrl1475031r.1374g>t1.000
rrl1475037r.1380t>c1.000
rrl1475061r.1404c>t1.000
rrl1475062r.1405a>g1.000
rrl1475120r.1463g>t1.000
rrl1475315r.1658a>t1.000
rrl1475355r.1698c>t1.000
rrl1475375r.1718g>a1.000
rrl1475378r.1721a>t1.000
rrl1475379r.1722g>c1.000
rrl1475380r.1723c>a1.000
rrl1475419r.1762c>t1.000
rrl1475429r.1772g>a1.000
rrl1475430r.1773t>a1.000
rrl1475433r.1776a>c1.000
rrl1475436r.1779c>t1.000
rrl1475452r.1795c>a1.000
rrl1475460r.1803a>g1.000
rrl1475482r.1825a>g1.000
rrl1475505r.1848g>a1.000
rrl1475526r.1869c>a1.000
rrl1475544r.1887a>t1.000
rrl1475545r.1888t>g1.000
rrl1475573r.1916g>a1.000
rrl1475659r.2002g>a1.000
rrl1475753r.2096c>g1.000
rrl1475762r.2105g>t1.000
rrl1475763r.2106c>t1.000
rrl1475764r.2107a>c1.000
rrl1475765r.2108a>g1.000
rrl1475775r.2118g>t1.000
rrl1475916r.2259c>t1.000
rrl1475975r.2318c>t1.000
rrl1475977r.2320a>g1.000
rrl1475995r.2338g>a1.000
rrl1475997r.2340a>g1.000
rrl1476033r.2376t>c1.000
rrl1476034r.2377c>g1.000
rrl1476035r.2378g>c1.000
rrl1476044r.2387t>g1.000
rrl1476045r.2388g>t1.000
rrl1476049r.2392c>t1.000
rrl1476086r.2429g>a1.000
rrl1476088r.2431a>c1.000
rrl1476103r.2446c>a1.000
rrl1476108r.2451t>g1.000
rrl1476110r.2453g>t1.000
rrl1476115r.2458t>c1.000
rrl1476131r.2474c>t1.000
rrl1476214r.2557g>t1.000
rrl1476215r.2558c>t1.000
rrl1476224r.2567a>g1.000
rrl1476245r.2588c>t1.000
rrl1476246r.2589g>a1.000
rrl1476252r.2595t>g1.000
rrl1476256r.2599a>c1.000
rrl1476262r.2605g>a1.000
rrl1476281r.2624t>c1.000
rrl1476529r.2872a>t1.000
rrl1476583r.2926g>a1.000
rrl1476584r.2927c>t1.000
rrl1476594r.2937c>t1.000
rrl1476597r.2940g>a1.000
rrl1476603r.2946g>a1.000
rrl1476608r.2951c>g1.000
rrl1476628r.2971t>a1.000
rrl1476664r.3007t>c1.000
rrl1476665r.3008t>a1.000
rrl1476674r.3017t>c1.000
rrl1476679r.3022t>a1.000
rrl1476689r.3032a>t0.556
rrl1476690r.3033c>t0.400
rrl1476692r.3035t>a1.000
rrl1476693r.3036g>a0.400
rrl1476695r.3038t>a0.600
rrl1476716r.3059a>c1.000
inhA1674624c.423A>C1.000
inhA1674627c.426T>G1.000
inhA1674630c.429C>G1.000
inhA1674639c.438C>G1.000
inhA1674656p.Ser152Thr1.000
inhA1674690c.489C>G1.000
rpsA1833538c.-4CA>C1.000
rpsA1833541c.-1T>C1.000
rpsA1833547c.6G>A1.000
rpsA1833589c.48A>C1.000
rpsA1833595c.54T>G1.000
rpsA1833596p.Ser19Ala1.000
rpsA1833604c.63C>T0.950
rpsA1833616c.75A>C0.950
rpsA1833619c.78A>C0.952
rpsA1833664c.123C>G0.944
rpsA1833676c.135A>G0.938
rpsA1833679c.138G>T0.938
rpsA1833694c.153G>C0.923
rpsA1833697c.156C>G0.923
rpsA1833709c.168C>T0.923
rpsA1833724c.183C>G0.900
rpsA1833727c.186G>C0.900
rpsA1833734p.Ala65Ser0.900
rpsA1833742c.201A>G0.917
rpsA1833770p.Asn77His1.000
rpsA1833778c.237C>G1.000
rpsA1833781c.240T>G1.000
rpsA1833790c.249T>C1.000
rpsA1833811c.270G>C1.000
rpsA1833814c.273C>G1.000
rpsA1833841c.300C>G1.000
rpsA1833847c.306C>G1.000
rpsA1833856c.315A>G1.000
rpsA1833862c.321G>C1.000
rpsA1833874c.333T>C1.000
rpsA1833892c.351G>A1.000
rpsA1833894p.Ala118Glu1.000
rpsA1833928c.387G>C1.000
rpsA1833949c.408T>C1.000
rpsA1833970c.429G>T1.000
rpsA1833979c.438T>C1.000
rpsA1834015c.474G>C1.000
rpsA1834042c.501G>A1.000
rpsA1834051c.510G>A1.000
rpsA1834096c.555G>T1.000
rpsA1834097c.556T>A1.000
rpsA1834186c.645C>G1.000
rpsA1834210c.669C>T1.000
rpsA1834222c.681T>C1.000
rpsA1834225c.684C>G1.000
rpsA1834231c.690T>C1.000
rpsA1834240c.699T>C1.000
rpsA1834249c.708T>C1.000
rpsA1834261c.720A>G1.000
rpsA1834264c.723G>C1.000
rpsA1834297c.756C>T0.941
rpsA1834303c.762T>G0.941
rpsA1834306c.765T>C0.938
rpsA1834333c.792C>T0.933
rpsA1834348c.807T>C0.929
rpsA1834364c.823T>A0.933
rpsA1834375c.834G>T0.941
rpsA1834411c.870T>C0.944
rpsA1834417c.876G>C0.941
rpsA1834423c.882G>C0.944
rpsA1834432c.891G>T0.947
rpsA1834451c.910T>C1.000
rpsA1834456c.915T>G1.000
rpsA1834468c.927A>G1.000
rpsA1834489c.948T>C1.000
rpsA1834495c.954G>A1.000
rpsA1834498c.957C>T1.000
rpsA1834527p.Arg329Gln1.000
rpsA1834543c.1002C>G1.000
rpsA1834546c.1005T>C1.000
rpsA1834555c.1014T>C1.000
rpsA1834558c.1017C>G1.000
rpsA1834567c.1026C>T1.000
rpsA1834573c.1032G>C1.000
rpsA1834603p.Glu354Asp1.000
rpsA1834606c.1065C>G1.000
rpsA1834609c.1068T>C1.000
rpsA1834619c.1078T>C1.000
rpsA1834622c.1081T>A1.000
rpsA1834633c.1092A>G1.000
rpsA1834639c.1098T>C1.000
rpsA1834667p.Ala376Ser1.000
rpsA1834690c.1149T>C1.000
rpsA1834732c.1191T>C1.000
rpsA1834738c.1197A>G1.000
rpsA1834747c.1206A>G1.000
rpsA1834751p.Leu404Ile1.000
rpsA1834759c.1218A>T1.000
rpsA1834765p.Glu408Asp1.000
rpsA1834780c.1239A>G1.000
rpsA1834786c.1245A>G1.000
rpsA1834789c.1248T>C1.000
rpsA1834792c.1251G>C1.000
rpsA1834837p.Met432Ile0.947
kasA2518234c.120G>A1.000
kasA2518240c.126C>A1.000
kasA2518248p.Ala45Val1.000
kasA2518279c.165T>C1.000
kasA2518816c.702C>G0.909
kasA2518825c.711T>C0.909
kasA2518843c.729T>C0.900
kasA2518847p.Leu245Met0.900
kasA2518853p.Leu247Ile0.900
kasA2518864c.750G>C0.900
ahpC2726633c.441C>G0.900
ahpC2726638p.Ala149Val0.900
ahpC2726657c.465A>C0.917
ahpC2726669c.477T>C0.917
ahpC2726675c.483A>G0.917
ahpC2726681c.489A>C1.000
thyA3074255p.His73Asn1.000
thyA3074263p.Gly70Ala1.000
thyA3074268c.204A>G1.000
thyA3074285c.187A>G1.000
embC4241039p.Asp393Asn1.000
embC4241047c.1185C>G1.000
embC4241050c.1188T>G1.000
embC4241053c.1191G>C1.000
embC4241056c.1194C>G1.000
embC4241071c.1209C>G1.000
embC4241084p.Leu408Ala1.000
embC4241135p.Val425Leu1.000
embC4241140c.1278A>G1.000
embC4241141p.Ile427Val1.000
embC4241146c.1284C>G1.000
embC4241155p.Ile431Met0.950
embC4241161c.1299C>G1.000
embC4241162c.1300T>C1.000
embC4241167c.1305C>G1.000
embB4247462c.949T>A1.000
embB4247470c.957T>C1.000
embB4247497c.984T>C1.000
embB4247500c.987C>G1.000
embB4247512c.999T>C1.000
embB4248064c.1551G>C1.000
embB4248070c.1557T>C1.000
embB4248085c.1572T>C1.000
embB4248097c.1584C>G1.000
embB4248118c.1605T>C1.000
embB4248133c.1620C>G1.000
embB4248157c.1644A>G1.000
embB4248173p.Val554Met1.000
embB4248215p.Arg568Ser1.000
embB4248220c.1707A>G1.000
embB4248225p.Ala571Val1.000

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;