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: 5cc557a519ad1
Sample: 5cc557a519ad1

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Summary
ID: 5cc557a519ad1
Date: Sun Apr 28 08:36:27 2019
Strain: lineage4.3;lineage4.1.1.1
Drug-resistance: Sensitive

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
Streptomycin
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage4.3Euro-American (LAM)mainly-LAMNone
lineage4.1.1.1Euro-American (X-type)X2RD183

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6142c.903G>A0.714
gyrB6145c.906C>T0.267
gyrB6178c.939C>T0.318
gyrB6184c.945C>T0.304
gyrB6196c.957C>T0.318
gyrB6208c.969G>C1.000
gyrB6214c.975G>C1.000
gyrB6223c.984G>C0.389
gyrB6700c.1461T>C1.000
gyrB6703c.1464G>C1.000
gyrB6709c.1470A>G0.500
gyrB6712c.1473G>C1.000
gyrB6724c.1485G>C1.000
gyrB6730c.1491A>G1.000
gyrB6745c.1506T>C1.000
gyrB6751c.1512G>C1.000
gyrB6760c.1521G>C1.000
gyrB6775c.1536G>C1.000
gyrB6793c.1554T>C1.000
gyrB6841c.1602T>C1.000
gyrB6844c.1605T>G1.000
gyrB6853c.1614A>G1.000
gyrB6856c.1617T>C1.000
gyrB6859c.1620T>C1.000
gyrB6869c.1630T>C1.000
gyrB6872c.1633T>C1.000
gyrB6877c.1638G>C1.000
gyrB6878c.1639T>C1.000
gyrB6881c.1642T>C1.000
gyrB7165c.1926C>G0.450
gyrB7168c.1929C>G1.000
gyrB7178c.1939T>C1.000
gyrB7201c.1962G>A1.000
gyrB7213c.1974G>C1.000
gyrB7216c.1977G>C1.000
gyrB7225c.1986T>C1.000
gyrB7243c.2004G>A1.000
gyrB7246c.2007T>C1.000
gyrB7252c.2013G>C1.000
gyrA7391c.90C>T1.000
gyrA7394c.93T>C1.000
gyrA7415c.114C>G1.000
gyrA7427c.126G>T1.000
gyrA7442c.141G>C1.000
gyrA7451c.150C>G1.000
gyrA7457c.156T>C1.000
gyrA7463c.162G>C1.000
gyrA7475c.174A>G1.000
gyrA7480p.Phe60Tyr1.000
gyrA7484c.183T>C1.000
gyrA7490c.189C>G1.000
gyrA7523c.222C>G0.955
gyrA7526c.225G>C0.955
gyrA7532c.231T>C0.955
gyrA7541c.240C>G0.947
gyrA7547c.246C>T0.960
gyrA7585p.Ser95Thr1.000
gyrA7587c.286C>T0.947
gyrA7607c.306C>G1.000
gyrA7619c.318C>A1.000
gyrA7628c.327G>C1.000
gyrA7631c.330G>C1.000
gyrA7652c.351C>T1.000
gyrA7728c.427A>C1.000
gyrA7742c.441G>A1.000
gyrA7763c.462T>C1.000
gyrA7784c.483A>G1.000
gyrA7787c.486G>A1.000
gyrA7799c.498A>G1.000
gyrA7832c.531G>C1.000
gyrA7835c.534A>C1.000
gyrA7859c.558A>G1.000
gyrA7865c.564T>C1.000
gyrA8294c.993T>C1.000
gyrA8306c.1005C>T1.000
gyrA8324c.1023T>C1.000
gyrA8337c.1036C>T1.000
gyrA8342c.1041G>C1.000
gyrA8375c.1074G>C1.000
gyrA8382p.Leu361Met1.000
gyrA8391p.Tyr364His1.000
gyrA8396c.1095C>T1.000
gyrA8399c.1098T>G1.000
gyrA8401p.Asp367Ala1.000
gyrA8543c.1242C>G1.000
gyrA8546c.1245T>C1.000
gyrA8552c.1251C>A0.900
gyrA8555c.1254G>C1.000
gyrA8558c.1257C>T1.000
gyrA8588c.1287G>A1.000
gyrA8597c.1296C>G1.000
gyrA8603c.1302A>G1.000
gyrA8624c.1323G>T1.000
gyrA8633c.1332C>G1.000
gyrA8636c.1335A>C1.000
gyrA8645c.1344C>T1.000
gyrA8672c.1371A>G1.000
gyrA8675c.1374C>T1.000
gyrA8693c.1392T>C1.000
gyrA8711c.1410A>C1.000
gyrA9119c.1818A>G1.000
gyrA9527c.2226A>G1.000
gyrA9542c.2241T>C1.000
gyrA9545c.2244A>G1.000
gyrA9560c.2259C>G1.000
gyrA9572c.2271C>G1.000
gyrA9583p.Arg761Lys1.000
gyrA9590c.2289T>G1.000
gyrA9593c.2292G>C1.000
gyrA9597c.2296T>C1.000
gyrA9602c.2301T>C1.000
rpoB759573c.-234T>C1.000
rpoB759577c.-230G>A1.000
rpoB759629c.-178T>C1.000
rpoB760091c.285G>C1.000
rpoB760101c.295T>C1.000
rpoB760112c.306T>C1.000
rpoB760118c.312T>C1.000
rpoB760130p.Asp108Glu1.000
rpoB760139c.333A>G1.000
rpoB760142c.336C>G1.000
rpoB760181c.375T>C1.000
rpoB760184c.378A>G1.000
rpoB760196c.390C>G1.000
rpoB760202c.396G>A1.000
rpoB760223c.417T>C1.000
rpoB760235c.429T>C1.000
rpoB760283c.477G>C1.000
rpoB760307c.501T>C1.000
rpoB760313c.507G>C1.000
rpoB760331c.525G>C1.000
rpoB760337c.531C>G1.000
rpoB760340c.534G>C1.000
rpoB760361c.555T>C1.000
rpoB760370c.564C>G1.000
rpoB760376p.Asp190Glu1.000
rpoB760380p.Thr192Leu1.000
rpoB760406c.600G>C1.000
rpoB760415c.609C>T1.000
rpoB760424c.618C>G1.000
rpoB760430c.624T>C1.000
rpoB760475c.669A>G1.000
rpoB760481c.675G>C1.000
rpoB760484c.678A>G1.000
rpoB760522p.Ser239Asn0.955
rpoB760532c.726T>C0.947
rpoB760533p.Val243His0.947
rpoB760547c.741G>C1.000
rpoB760563253R>253*0.923
rpoB760566p.Ser254Ala0.923
rpoB760589c.783C>G0.944
rpoB760591p.Val262Ala0.944
rpoB760611c.805T>C0.950
rpoB760634c.828T>C1.000
rpoB760646c.840C>G1.000
rpoB760655c.849A>G1.000
rpoB760661c.855A>C1.000
rpoB760670c.864G>C1.000
rpoB760674c.868T>C1.000
rpoB760679c.873A>G1.000
rpoB760683c.877T>C1.000
rpoB760706c.900C>T1.000
rpoB760724c.918T>C1.000
rpoB760730c.924T>C1.000
rpoB760862c.1056G>C1.000
rpoB760869p.Val355Ile1.000
rpoB760886c.1080A>G1.000
rpoB760910c.1104C>T0.938
rpoB760925c.1119T>C1.000
rpoB760934c.1128C>T1.000
rpoB760938c.1132C>T1.000
rpoB760946c.1140A>G1.000
rpoB760982c.1176G>C1.000
rpoB760991c.1185G>C1.000
rpoB761006c.1200C>T1.000
rpoB761015c.1209G>C1.000
rpoB761027c.1221A>G1.000
rpoB761037c.1231T>C1.000
rpoB761132c.1326G>C1.000
rpoB761133c.1327T>C1.000
rpoB761150c.1344A>C1.000
rpoB761165c.1359G>C1.000
rpoB761180c.1374A>C1.000
rpoB761189c.1383T>G1.000
rpoB761249c.1443A>G1.000
rpoB761255c.1449T>G0.952
rpoB761264c.1458C>G1.000
rpoB761300c.1494G>C1.000
rpoB761318c.1512G>C1.000
rpoB761327c.1521A>G1.000
rpoB761354c.1548C>T1.000
rpoB761360c.1554T>C1.000
rpoB761362p.Ser519Thr1.000
rpoB761373p.Val523His1.000
rpoB761465c.1659G>C1.000
rpoB761477c.1671C>G1.000
rpoB761486c.1680C>T1.000
rpoB761492c.1686G>C1.000
rpoB761504c.1698C>G1.000
rpoB761510c.1704T>C1.000
rpoB761531c.1725C>G1.000
rpoB761537c.1731C>G1.000
rpoB761564c.1758G>C1.000
rpoB761570c.1764T>C1.000
rpoB761573c.1767C>G1.000
rpoB761579c.1773G>C1.000
rpoB761606c.1800C>G1.000
rpoB761612c.1806G>C1.000
rpoB761615c.1809A>C1.000
rpoB761627c.1821C>T1.000
rpoB761636c.1830G>T1.000
rpoB761645c.1839C>G1.000
rpoB761648c.1842T>C1.000
rpoB761954c.2148C>G1.000
rpoB762014c.2208C>T1.000
rpoB762017c.2211A>G1.000
rpoB762053c.2247T>C0.952
rpoB762062c.2256T>C0.944
rpoB762083c.2277T>C0.944
rpoB762086c.2280G>C0.944
rpoB762101c.2295C>G0.952
rpoB762114p.Ile770Val0.955
rpoB762131c.2325C>G0.947
rpoB762140c.2334G>C0.944
rpoB762143c.2337T>C0.944
rpoB762149c.2343G>C0.941
rpoB762158c.2352G>C0.944
rpoB762167c.2361T>C0.944
rpoB762176c.2370T>C1.000
rpoB762185c.2379G>C1.000
rpoB762233c.2427G>C1.000
rpoB762254c.2448T>C1.000
rpoB762257c.2451C>G1.000
rpoB762266c.2460T>C1.000
rpoB762275c.2469C>G1.000
rpoB762278c.2472C>T1.000
rpoB762284c.2478G>C1.000
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
rpoB762395c.2589G>C1.000
rpoB762398c.2592T>C1.000
rpoB762404c.2598T>C1.000
rpoB762410c.2604T>C1.000
rpoB762416c.2610A>G1.000
rpoB762443c.2637G>C1.000
rpoB762488c.2682G>C1.000
rpoB762491c.2685T>C1.000
rpoB762509c.2703T>G0.882
rpoB762510p.Ala902Pro0.882
rpoB762533c.2727T>C1.000
rpoB762536c.2730T>C1.000
rpoB762537c.2731T>C1.000
rpoB762551c.2745C>T1.000
rpoB762730p.Gln975Arg1.000
rpoB762737c.2931C>G1.000
rpoB762750c.2944C>T1.000
rpoB762753c.2947T>C1.000
rpoB762758c.2952G>C1.000
rpoB762827c.3021G>C1.000
rpoB762836c.3030C>T1.000
rpoB762839c.3033G>A1.000
rpoB762857c.3051C>G1.000
rpoB762868p.Tyr1021Phe1.000
rpoB762929c.3123G>C1.000
rpoB762962c.3156C>T1.000
rpoB762995c.3189G>T1.000
rpoB763028c.3222T>C1.000
rpoB763031c.3225T>G1.000
rpoB763034c.3228C>G1.000
rpoB763040c.3234C>G1.000
rpoB763070c.3264T>C1.000
rpoB763076c.3270C>G1.000
rpoB763085c.3279C>G1.000
rpoB763115c.3309T>C1.000
rpoB763127c.3321G>C1.000
rpoB763166c.3360A>G1.000
rpoB763169c.3363A>G1.000
rpoB763187c.3381C>G1.000
rpoB763202c.3396A>C1.000
rpoB763206c.3400A>T1.000
rpoB763214c.3408T>C1.000
rpoB763238c.3432T>C1.000
rpoB763262c.3456C>T1.000
rpoC763402c.33C>T1.000
rpoC763408c.39T>C1.000
rpoC763411c.42T>G1.000
rpoC763414c.45T>C1.000
rpoC763417c.48C>A1.000
rpoC763423c.54G>A1.000
rpoC763441c.72C>T1.000
rpoC763444c.75T>C1.000
rpoC763456c.87A>G1.000
rpoC763486c.117T>G1.000
rpoC763528c.159G>A1.000
rpoC763546c.177A>G1.000
rpoC763570c.201G>C1.000
rpoC763573c.204G>C1.000
rpoC763594c.225C>T0.964
rpoC763633c.264T>C1.000
rpoC763636c.267T>C1.000
rpoC763660c.291T>G1.000
rpoC763669c.300C>G1.000
rpoC763675c.306C>G1.000
rpoC763729c.360G>C1.000
rpoC763741c.372C>T1.000
rpoC763744c.375G>C1.000
rpoC763765c.396T>G1.000
rpoC763768c.399C>G1.000
rpoC763780c.411C>G1.000
rpoC763792p.Glu141Asp1.000
rpoC763801c.432C>G1.000
rpoC763807c.438T>C1.000
rpoC763813c.444C>G1.000
rpoC763835p.Ala156Met1.000
rpoC763855c.486C>T1.000
rpoC763858c.489A>G1.000
rpoC763872p.Gly168Ala1.000
rpoC763876p.Glu169Asp1.000
rpoC763879c.510A>G1.000
rpoC763888c.519G>C1.000
rpoC763894c.525A>G1.000
rpoC763945c.576T>C1.000
rpoC763948c.579G>C1.000
rpoC763951c.582G>C1.000
rpoC763960c.591T>G1.000
rpoC763978c.609C>G1.000
rpoC763991p.Ile208Leu1.000
rpoC763996c.627T>C1.000
rpoC764002c.633C>T1.000
rpoC764005c.636G>C1.000
rpoC764024c.655T>C1.000
rpoC764040p.Ser224Asn1.000
rpoC764044c.675T>C1.000
rpoC764059c.690G>C1.000
rpoC764083c.714A>G1.000
rpoC764089c.720C>T1.000
rpoC764098c.729A>G1.000
rpoC764131c.762T>C1.000
rpoC764152c.783C>T1.000
rpoC764161c.792G>C1.000
rpoC764188c.819A>G1.000
rpoC764194p.Glu275Asp1.000
rpoC764203c.834G>C1.000
rpoC764206c.837T>C1.000
rpoC764266c.897T>C1.000
rpoC764269c.900G>C1.000
rpoC764272c.903G>C1.000
rpoC764278c.909A>G1.000
rpoC764293c.924G>C1.000
rpoC764359c.990C>G1.000
rpoC764365c.996C>T1.000
rpoC764371c.1002G>C1.000
rpoC764405c.1036A>C1.000
rpoC764410c.1041G>C1.000
rpoC764428c.1059G>C0.909
rpoC764431c.1062G>C1.000
rpoC764434c.1065A>G1.000
rpoC764446c.1077T>C1.000
rpoC764449c.1080G>C1.000
rpoC764452c.1083T>C1.000
rpoC764458c.1089G>C1.000
rpoC764461c.1092A>G1.000
rpoC764497c.1128A>G1.000
rpoC764500c.1131C>G1.000
rpoC764503c.1134G>C1.000
rpoC764521c.1152T>C1.000
rpoC764536c.1167G>C0.955
rpoC764539c.1170C>G0.880
rpoC764575c.1206T>G1.000
rpoC764578c.1209C>G1.000
rpoC764585c.1216C>T1.000
rpoC764602c.1233C>T1.000
rpoC764611c.1242G>C0.966
rpoC764626c.1257C>T1.000
rpoC764632c.1263T>C1.000
rpoC764650c.1281G>T0.971
rpoC764695c.1326T>C1.000
rpoC764749c.1380G>C1.000
rpoC764752c.1383G>C1.000
rpoC764764c.1395T>C1.000
rpoC764803c.1434C>G1.000
rpoC764809c.1440C>T1.000
rpoC764815c.1446A>G1.000
rpoC764824c.1455T>C1.000
rpoC764830c.1461C>G1.000
rpoC764858c.1489T>C1.000
rpoC764888c.1519T>C1.000
rpoC764893c.1524T>C1.000
rpoC764923c.1554A>G1.000
rpoC764932c.1563C>G1.000
rpoC764968c.1599T>C1.000
rpoC764995c.1626C>G1.000
rpoC765007c.1638T>G1.000
rpoC765013c.1644C>T1.000
rpoC765019c.1650A>G1.000
rpoC765034c.1665T>G1.000
rpoC765070c.1701G>A1.000
rpoC765073c.1704G>C1.000
rpoC765079c.1710T>C1.000
rpoC765082c.1713G>C1.000
rpoC765089c.1720T>C1.000
rpoC765103c.1734G>A1.000
rpoC765129p.Tyr587Phe1.000
rpoC765349c.1980T>C1.000
rpoC765352c.1983G>C1.000
rpoC765379c.2010G>C1.000
rpoC765383p.Met672Leu1.000
rpoC765404p.Leu679Val1.000
rpoC765409c.2040T>C1.000
rpoC765412c.2043T>C1.000
rpoC765421c.2052C>G1.000
rpoC765454c.2085C>G1.000
rpoC765466c.2097C>T1.000
rpoC765469c.2100G>C1.000
rpoC765478c.2109T>G1.000
rpoC765499c.2130C>G1.000
rpoC765550c.2181C>T1.000
rpoC765553c.2184C>T1.000
rpoC765556c.2187G>C1.000
rpoC765559c.2190G>C1.000
rpoC765613p.His748Gln1.000
rpoC765625c.2256C>G1.000
rpoC765628c.2259G>C1.000
rpoC765631p.Asp754Glu1.000
rpoC765655c.2286T>C1.000
rpoC765689c.2320C>T1.000
rpoC765700c.2331T>C1.000
rpoC765734c.2365T>C1.000
rpoC765739c.2370G>C1.000
rpoC765772c.2403C>G1.000
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
rpoC765883c.2514C>G1.000
rpoC765886c.2517C>G1.000
rpoC765892c.2523T>C1.000
rpoC765928c.2559C>G1.000
rpoC765937c.2568T>C1.000
rpoC765946c.2577C>T1.000
rpoC765947c.2578T>C1.000
rpoC765967c.2598C>T1.000
rpoC765979c.2610C>G1.000
rpoC765982c.2613C>T1.000
rpoC765994c.2625A>T1.000
rpoC766010c.2641T>A1.000
rpoC766021c.2652G>C1.000
rpoC766027c.2658G>C1.000
rpoC766043p.Gln892Glu1.000
rpoC766061p.Val898Ile1.000
rpoC766072c.2703G>C1.000
rpoC766082p.Ala905Gln1.000
rpoC766096c.2727G>C1.000
rpoC766129c.2760C>G1.000
rpoC766162c.2793C>T1.000
rpoC766178p.Ile937Val1.000
rpoC766258c.2889T>C1.000
rpoC766315c.2946C>G1.000
rpoC766321c.2952C>G1.000
rpoC766345c.2976T>C1.000
rpoC766348c.2979A>G1.000
rpoC766363c.2994G>C1.000
rpoC766366c.2997C>G1.000
rpoC766381c.3012C>T0.947
rpoC766384c.3015A>G1.000
rpoC766387c.3018C>G1.000
rpoC766393c.3024C>G1.000
rpoC766408c.3039C>T1.000
rpoC766426c.3057C>T1.000
rpoC766447c.3078T>C1.000
rpoC766483c.3114G>T1.000
rpoC766486c.3117A>C1.000
rpoC766492c.3123T>G1.000
rpoC766495c.3126C>T1.000
rpoC766522c.3153C>G1.000
rpoC766528c.3159T>G1.000
rpoC766530p.Arg1054Gln1.000
rpoC766540p.Asp1057Glu1.000
rpoC766543c.3174C>T1.000
rpoC766549c.3180G>T1.000
rpoC766573c.3204T>C1.000
rpoC766607p.Ile1080Leu1.000
rpoC766618c.3249G>C1.000
rpoC766630c.3261G>C1.000
rpoC766645c.3276A>G1.000
rpoC766657c.3288A>G1.000
rpoC766666c.3297C>G1.000
rpoC766672c.3303T>C1.000
rpoC766711c.3342C>T1.000
rpoC766726c.3357T>C1.000
rpoC766738c.3369G>C1.000
rpoC766765c.3396A>C1.000
rpoC766774c.3405T>C1.000
rpoC766804c.3435A>G1.000
rpoC766843c.3474T>C1.000
rpoC766861c.3492G>C1.000
rpoC766864c.3495G>C1.000
rpoC766882c.3513C>T1.000
rpoC766883p.Ser1172Ala1.000
rpoC766894c.3525T>C1.000
rpoC766895c.3526T>C1.000
rpoC766900c.3531T>C1.000
rpoC766933c.3564A>G1.000
rpoC766942c.3573C>T1.000
rpoC766945c.3576A>G1.000
rpoC766963c.3594T>C1.000
rpoC766972c.3603G>C1.000
rpoC766978c.3609C>G1.000
rpoC766981c.3612T>C1.000
rpoC766996c.3627C>T0.947
rpoC767033c.3664T>A1.000
rpoC767059c.3690T>G1.000
rpoC767062c.3693C>A1.000
rpoC767080c.3711G>C1.000
rpoC767098c.3729T>C1.000
rpoC767119c.3750A>G1.000
rpoC767134c.3765C>A1.000
rpoC767158c.3789T>C1.000
rpoC767167c.3798C>G1.000
rpoC767180p.Ala1271Gln1.000
rpoC767191c.3822C>G1.000
rpoC767206c.3837C>G1.000
rpoC767209c.3840T>C1.000
rpoC767212c.3843G>C1.000
rpoC767221c.3852C>G1.000
rpsL781571c.12C>T1.000
rpsL781595c.36T>C0.938
rpsL781598c.39G>C0.938
rpsL781608p.Ser17Ala0.941
rpsL781628c.69T>C0.960
rpsL781649c.90T>C1.000
rpsL781655c.96T>C1.000
rpsL781664c.105C>T1.000
rpsL781682c.123T>C1.000
rpsL781715c.156T>C1.000
rpsL781718c.159C>T1.000
rpsL781728c.169T>C1.000
rpsL781736c.177T>C1.000
rpsL781751c.192G>C1.000
rpsL781754c.195G>C1.000
rpsL781760c.201T>C0.960
rpsL781763c.204C>G0.957
rpsL781811c.252C>T1.000
rpsL781817c.258G>A1.000
rpsL781820c.261G>C1.000
rpsL781832c.273T>C1.000
rpsL781835c.276T>C1.000
rpsL781865c.306G>C1.000
rpsL781868c.309T>C1.000
rpsL781871c.312G>C1.000
rpsL781877c.318T>G0.962
rpsL781880c.321C>G1.000
rpsL781892c.333A>G1.000
rpsL781898c.339A>T1.000
rpsL781913c.354C>T1.000
rpsL781916c.357T>C1.000
rpsL781929p.Gly124Ser1.000
rpsL781933374G>A1.000
rplC801171c.363A>G1.000
rplC801174c.366T>C1.000
rplC801195c.387G>C1.000
rplC801210c.402T>C1.000
rplC801222c.414T>C1.000
rplC801231c.423C>G1.000
rplC801240c.432G>C1.000
rplC801249c.441T>G1.000
rplC801252c.444G>C1.000
rplC801255c.447C>T1.000
rplC801267c.459A>C1.000
rplC801270c.462T>C1.000
rplC801276c.468G>C1.000
rplC801279c.471G>C1.000
rplC801357c.549T>C1.000
rplC801385c.577C>T1.000
rplC801396c.588T>C1.000
rplC801402c.594T>C1.000
rplC801405c.597T>C1.000
rrs1471922r.77gt>g1.000
rrs1471925r.80t>c1.000
rrs1471931r.86ga>g1.000
rrs1471934r.89a>g1.000
rrs1471969r.124t>c1.000
rrs1471970r.125g>a1.000
rrs1472030r.185g>t1.000
rrs1472031r.186g>t1.000
rrs1472033r.188a>g1.000
rrs1472034r.189t>c1.000
rrs1472040r.195t>c1.000
rrs1472053r.208agc>a1.000
rrs1472061r.216a>t1.000
rrs1472075r.230a>g1.000
rrs1472094r.249t>a1.000
rrs1472108r.263c>t1.000
rrs1472298r.453gtccgggtt>g1.000
rrs1472969r.1124a>g1.000
rrs1472970r.1125c>g1.000
rrs1472977r.1132g>c1.000
rrs1472978r.1133t>c1.000
rrs1473105r.1260g>a1.000
rrs1473120r.1275c>ct0.909
rrs1473123r.1278a>t1.000
rrs1473290r.1445c>t1.000
rrl1473756r.99g>a1.000
rrl1473758r.101g>t1.000
rrl1473806r.149c>t1.000
rrl1473813r.156c>t1.000
rrl1473815r.158t>c1.000
rrl1473839r.182g>t1.000
rrl1473877r.220g>a1.000
rrl1473898r.241c>t1.000
rrl1473899r.242a>c1.000
rrl1473934r.277g>t1.000
rrl1473937r.280c>t1.000
rrl1473944r.287g>a1.000
rrl1473981r.324g>t1.000
rrl1473995r.338g>t1.000
rrl1474001r.344c>t1.000
rrl1474009r.352a>g1.000
rrl1474012r.355c>t1.000
rrl1474051r.394t>c1.000
rrl1474054r.397t>c1.000
rrl1474056r.399t>c1.000
rrl1474071r.414g>a1.000
rrl1474103r.446a>t1.000
rrl1474140r.483c>t1.000
rrl1474151r.494c>t1.000
rrl1474181r.524c>t1.000
rrl1474291r.634tttcctctccggagga>t1.000
rrl1474308r.651g>t1.000
rrl1474310r.653t>g1.000
rrl1474356r.699t>c1.000
rrl1474362r.705a>g1.000
rrl1474376r.719t>c1.000
rrl1474627r.970g>a1.000
rrl1474632r.975g>t1.000
rrl1474639r.982g>a1.000
rrl1474717r.1060a>t1.000
rrl1474760r.1103a>g1.000
rrl1474794r.1137c>t1.000
rrl1474812r.1155g>a1.000
rrl1474831r.1174a>g1.000
rrl1474952r.1295acatcc>a1.000
rrl1474991r.1334t>c1.000
rrl1474995r.1338t>g1.000
rrl1475013r.1356g>a1.000
rrl1475017r.1360g>gt1.000
rrl1475027r.1370g>t1.000
rrl1475028r.1371g>t1.000
rrl1475061r.1404c>t1.000
rrl1475088r.1431a>t1.000
rrl1475206r.1549c>t1.000
rrl1475209r.1552g>c1.000
rrl1475249r.1592t>c1.000
rrl1475252r.1595c>t1.000
rrl1475266r.1609t>c1.000
rrl1475275r.1618c>t1.000
rrl1475276r.1619t>c1.000
rrl1475291r.1634a>c1.000
rrl1475313r.1656g>a1.000
rrl1475315r.1658a>t1.000
rrl1475355r.1698c>t1.000
rrl1475369r.1712g>t1.000
rrl1475402r.1745c>t1.000
rrl1475419r.1762c>t1.000
rrl1475436r.1779c>t1.000
rrl1475599r.1942a>g1.000
rrl1475608r.1951t>c1.000
rrl1475638r.1981c>t1.000
rrl1475642r.1985t>c1.000
rrl1475657r.2000a>g1.000
rrl1475659r.2002g>t1.000
rrl1475758r.2101ac>a0.962
rrl1475763r.2106c>t0.952
rrl1475765r.2108ag>a0.952
rrl1475881r.2224t>c1.000
rrl1475988r.2331a>g1.000
rrl1476033r.2376t>c1.000
rrl1476035r.2378g>a1.000
rrl1476086r.2429g>a1.000
rrl1476089r.2432t>c1.000
rrl1476095r.2438c>g1.000
rrl1476106r.2449a>t1.000
rrl1476115r.2458t>c1.000
rrl1476117r.2460g>c1.000
rrl1476214r.2557g>t1.000
rrl1476215r.2558c>t1.000
rrl1476224r.2567a>g1.000
rrl1476281r.2624t>c1.000
rrl1476583r.2926g>a1.000
rrl1476584r.2927c>t1.000
rrl1476597r.2940g>a1.000
rrl1476628r.2971t>a1.000
rrl1476689r.3032a>t1.000
rrl1476690r.3033c>t1.000
rrl1476693r.3036g>a1.000
rrl1476695r.3038t>a1.000
rrl1476716r.3059a>c1.000
rrl1476723r.3066t>a1.000
rrl1476725r.3068c>t1.000
rrl1476726r.3069a>g1.000
rrl1476732r.3075t>c1.000
inhA1674237c.36T>C1.000
inhA1674243c.42A>G1.000
inhA1674471c.270G>T1.000
inhA1674477c.276G>C1.000
inhA1674480c.279T>C1.000
inhA1674486c.285T>C1.000
inhA1674489c.288G>C1.000
inhA1674542p.Ala114Glu1.000
inhA1674549c.348G>C1.000
inhA1674570c.369G>C1.000
inhA1674576c.375T>C1.000
inhA1674585c.384T>C1.000
inhA1674589p.Met130Leu1.000
inhA1674618c.417C>T1.000
inhA1674624c.423A>C1.000
inhA1674627c.426T>G1.000
inhA1674654c.453G>C1.000
inhA1674663c.462G>C1.000
inhA1674675c.474C>T1.000
rpsA1833568c.27G>C1.000
rpsA1833589c.48A>T0.889
rpsA1833595c.54T>C1.000
rpsA1833610c.69C>T1.000
rpsA1833661c.120A>G1.000
rpsA1833664c.123C>G1.000
rpsA1833667c.126C>G1.000
rpsA1833721c.180A>G1.000
rpsA1833727c.186G>C1.000
rpsA1833742c.201A>G1.000
rpsA1833745c.204G>C1.000
rpsA1833760c.219C>T1.000
rpsA1833771p.Asn77Ser1.000
rpsA1833790c.249T>C1.000
rpsA1833793c.252C>T1.000
rpsA1833802c.261A>G1.000
rpsA1833811c.270G>T1.000
rpsA1833838c.297G>C1.000
rpsA1833841c.300C>G1.000
rpsA1833847c.306C>G1.000
rpsA1833856c.315A>G1.000
rpsA1833874c.333T>C1.000
rpsA1833928c.387G>C1.000
rpsA1833979c.438T>C1.000
rpsA1833991c.450C>G1.000
rpsA1833994c.453G>C1.000
rpsA1834000c.459G>C1.000
rpsA1834015c.474G>C1.000
rpsA1834021c.480C>T1.000
rpsA1834022c.481C>T1.000
rpsA1834030c.489C>G1.000
rpsA1834102c.561T>C1.000
rpsA1834105c.564C>G1.000
rpsA1834177c.636A>C1.000
rpsA1834189c.648G>C1.000
rpsA1834195c.654G>C1.000
rpsA1834222c.681T>C1.000
rpsA1834249c.708T>C1.000
rpsA1834261c.720A>G1.000
rpsA1834262c.721T>A1.000
rpsA1834294c.753G>C1.000
rpsA1834303c.762T>G1.000
rpsA1834306c.765T>C1.000
rpsA1834345c.804C>T1.000
rpsA1834348c.807T>C1.000
rpsA1834366c.825A>G1.000
rpsA1834375c.834G>C1.000
rpsA1834411c.870T>C1.000
rpsA1834417c.876G>C1.000
rpsA1834423c.882G>C1.000
rpsA1834435c.894G>C1.000
rpsA1834451c.910T>C1.000
rpsA1834465c.924T>C0.950
rpsA1834468c.927A>G0.950
rpsA1834489c.948T>C0.955
rpsA1834498c.957C>T0.947
rpsA1834528c.987T>C0.944
rpsA1834546c.1005T>C0.952
rpsA1834555c.1014T>C0.952
rpsA1834573c.1032G>C0.958
rpsA1834606c.1065C>G1.000
rpsA1834609c.1068T>C1.000
rpsA1834633c.1092A>G1.000
rpsA1834639c.1098T>C1.000
rpsA1834690c.1149T>C0.917
rpsA1834732c.1191T>C0.857
rpsA1834747c.1206A>G0.846
rpsA1834753c.1212T>C0.833
rpsA1834759c.1218A>C0.833
rpsA1834765p.Glu408Asp0.818
rpsA1834767p.Lys409Thr0.818
rpsA1834780c.1239A>G0.867
rpsA1834786c.1245A>G0.867
rpsA1834789c.1248T>C0.867
rpsA1834792c.1251G>C0.867
rpsA1834852c.1311C>G1.000
kasA2518174c.60A>G1.000
kasA2518190p.Ser26Ala1.000
kasA2518220c.106C>T1.000
kasA2518234c.120G>A1.000
kasA2518248p.Ala45Val1.000
kasA2518255c.141A>G1.000
kasA2518459c.345T>G1.000
kasA2518462c.348A>C1.000
kasA2518468c.354A>C1.000
kasA2518475c.361A>C1.000
kasA2518480c.366T>C1.000
kasA2518504c.390T>C1.000
kasA2518506p.Ala131Glu1.000
kasA2518513c.399C>T1.000
kasA2518519c.405G>C1.000
kasA2518528c.414C>G1.000
kasA2518534c.420G>C1.000
kasA2518540c.426T>C1.000
kasA2518561c.447T>C1.000
kasA2518642c.528A>G1.000
kasA2518651c.537C>G1.000
kasA2518663c.549T>C1.000
kasA2518671p.Val186Ala1.000
kasA2518678c.564C>T1.000
kasA2518688p.Val192Phe1.000
kasA2518711c.597A>G1.000
kasA2518714c.600A>T1.000
kasA2518747c.633C>G1.000
kasA2518765c.651G>C1.000
kasA2518768c.654C>T1.000
kasA2518777c.663C>T1.000
kasA2518783c.669T>C1.000
kasA2518786c.672G>A1.000
kasA2518789c.675G>C1.000
kasA2518795c.681C>G1.000
kasA2518816c.702C>T1.000
kasA2518825c.711T>C1.000
folC2747302c.297T>C1.000
folC2747314c.285T>C1.000
folC2747317c.282G>C1.000
folC2747341c.258G>C1.000
folC2747365c.234C>G1.000
folC2747389c.210C>G1.000
folC2747404c.195C>G1.000
thyX3067349c.597C>T0.909
thyX3067367c.579C>G0.900
thyX3067457c.489G>C1.000
thyX3067465p.Ile161Val1.000
thyX3067733c.213C>G1.000
thyX3067742c.204T>C1.000
thyX3067745c.201G>C1.000
thyX3067762p.Arg62Lys1.000
thyX3067765p.Leu61Ile1.000
thyX3067781c.165G>C1.000
thyX3067802c.144G>C1.000
thyX3067823c.123C>G1.000
thyX3067835c.111C>T1.000
thyX3067847c.99G>C1.000
thyX3067850c.96T>C1.000
thyX3067857p.Asp30Gly1.000
thyX3067874c.72G>C1.000
thyX3067883c.63G>C1.000
thyX3067886c.60T>C1.000
thyX3067889c.57G>T1.000
thyX3067894c.52A>G1.000
thyX3067898p.Asp16Glu1.000
thyA3073863c.609A>G1.000
thyA3073866c.606G>C1.000
thyA3073874p.Ile200Val1.000
thyA3073881c.591G>A1.000
thyA3073889p.Ser195Ala1.000
thyA3073892c.580A>G1.000
thyA3073920c.552G>C1.000
thyA3073925c.547A>G1.000
thyA3073929c.543A>G1.000
thyA3073956c.516C>G1.000
thyA3073977c.495T>C1.000
thyA3073983c.489G>C1.000
thyA3073989c.483A>G1.000
thyA3074028c.444C>G1.000
thyA3074031c.441A>G1.000
thyA3074037c.435G>C1.000
thyA3074053p.Arg140Gln1.000
thyA3074057p.Glu139Pro1.000
thyA3074061c.411T>C1.000
thyA3074064c.408G>C1.000
thyA3074091c.381G>C1.000
thyA3074097c.375G>C1.000
thyA3074102p.Asp124Asn1.000
thyA3074103c.369G>C1.000
thyA3074106c.366A>G1.000
thyA3074121p.Asp117Glu1.000
fbiA3640347c.-196A>G1.000
fbiA3640365c.-178C>G1.000
fbiA3640378c.-165A>T1.000
panD4044120c.162T>G1.000
panD4044123c.159A>G1.000
panD4044126c.156A>G1.000
panD4044138c.144A>G1.000
panD4044141c.141G>C1.000
panD4044150c.132T>C1.000
panD4044156c.126T>C1.000
panD4044162c.120T>C1.000
panD4044174c.108G>A1.000
panD4044180p.Asp34Glu1.000
panD4044188c.94A>G1.000
panD4044195c.87A>G1.000
panD4044225c.57G>A1.000
embC4240066c.204C>A1.000
embC4240069c.207T>C1.000
embC4240075p.Glu71Asp1.000
embC4240078c.216A>T1.000
embC4240087c.225T>C1.000
embC4240090c.228C>T1.000
embC4240099c.237C>G1.000
embC4240120c.258C>G1.000
embC4240123c.261C>G1.000
embC4240126c.264C>T1.000
embC4240141c.279A>G1.000
embC4240151p.Ser97Pro1.000
embC4240160p.Thr100Ala1.000
embC4240175c.313T>C1.000
embC4240183c.321A>C1.000
embC4240717p.His285Gln1.000
embC4240726c.864G>C1.000
embC4240771c.909G>A1.000
embC4240780c.918T>C1.000
embC4240783c.921G>C1.000
embC4240789c.927T>C1.000
embC4240819c.957A>G1.000
embC4240822c.960C>G1.000
embC4240831c.969T>C1.000
embC4240843c.981C>T1.000
embC4240855c.993G>C1.000
embC4240859p.Leu333Val1.000
embC4240867c.1005T>C1.000
embC4241086c.1224G>C1.000
embC4241095c.1233C>T1.000
embC4241104c.1242G>A1.000
embC4241107c.1245G>C1.000
embC4241110c.1248G>C1.000
embC4241140c.1278A>C1.000
embC4241141p.Ile427Val1.000
embC4241162c.1300T>C1.000
embC4241167c.1305C>G1.000
embC4241425c.1563G>C1.000
embC4241453p.Ile531Val1.000
embC4242844c.2982A>G1.000
embC4242859c.2997C>T1.000
embC4242862c.3000A>G1.000
embC4242863p.Tyr1001Asn1.000
embC4242880c.3018A>G1.000
embC4242883c.3021C>G1.000
embC4242886c.3024G>A1.000
embC4242907c.3045G>T1.000
embA4245131c.1899G>C1.000
embA4245137c.1905T>C1.000
embA4245149c.1917C>G1.000
embA4245152c.1920C>G1.000
embA4245158c.1926C>G1.000
embA4245182c.1950T>C1.000
embA4245189c.1957C>T1.000
embB4248097c.1584C>G1.000
embB4248100c.1587C>T1.000
embB4248124c.1611G>C1.000
embB4248127c.1614G>C1.000
embB4248130c.1617G>C1.000
embB4248142c.1629T>C1.000
embB4248143c.1630T>C1.000
embB4248157c.1644A>G0.947
embB4248172c.1659G>C1.000
embB4248175c.1662G>A1.000
embB4248199c.1686A>G1.000
embB4248200p.Ile563Val1.000
embB4248205c.1692C>G1.000
embB4248206p.Ser565Gly1.000
embB4248220c.1707A>G1.000
embB4248232c.1719G>C1.000
embB4248241c.1728C>T1.000
embB4248253c.1740C>A1.000
embB4248266c.1753C>T1.000
embB4248277c.1764G>C1.000
embB4248316c.1803C>G1.000
embB4248319c.1806A>G1.000
embB4248322c.1809G>C1.000
embB4248337c.1824G>T1.000
embB4248350c.1837T>C1.000
embB4248355c.1842A>G0.909
embB4249469p.Leu986Met1.000
embB4249486c.2973T>G1.000

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;