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: 5d2736c4c2d6d
Sample: 5d2736c4c2d6d

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Summary
ID: 5d2736c4c2d6d
Date: Thu Jul 11 14:19:34 2019
Strain: lineage2
Drug-resistance: Sensitive

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

Lineage2FamilyMain SpoligotypeRDS
lineage2East-AsianBeijingRD105

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6100c.861G>A0.920
gyrB6115c.876A>G0.926
gyrB6121c.882C>T0.926
gyrB6127c.888G>C0.926
gyrB6133c.894G>C0.926
gyrB6136c.897G>A0.926
gyrB6151c.912C>T0.926
gyrB6172c.933C>T0.926
gyrB6184c.945C>T0.926
gyrB6193c.954G>A0.857
gyrB6196c.957C>T0.818
gyrB6616c.1377A>G1.000
gyrB6634c.1395T>C1.000
gyrB6637c.1398T>G1.000
gyrB6640c.1401A>C1.000
gyrB6643c.1404A>G1.000
gyrB6646c.1407C>T1.000
gyrB6655c.1416T>C1.000
gyrB6673c.1434A>C1.000
gyrB6676c.1437T>G1.000
gyrB6700c.1461T>C1.000
gyrB6703c.1464G>C1.000
gyrB6706c.1467G>A1.000
gyrB6709c.1470A>G1.000
gyrB6712c.1473G>C1.000
gyrB6727c.1488G>T1.000
gyrB6728c.1489C>T1.000
gyrB6745c.1506T>C1.000
gyrB6754c.1515C>T1.000
gyrB6763c.1524G>C0.984
gyrB6772c.1533C>G0.952
gyrB6775c.1536G>C0.948
gyrB6793c.1554T>C0.984
gyrB6798p.Gly520Ala0.984
gyrB6808c.1569C>G0.981
gyrB6824c.1585C>T0.978
gyrB6841c.1602T>C0.976
gyrB6862c.1623C>G0.975
gyrB6869c.1630T>C0.966
gyrB6872c.1633T>C0.964
gyrB6878c.1639T>C0.964
gyrB6889c.1650G>A0.963
gyrB6898c.1659G>T0.955
gyrA7499c.198G>C1.000
gyrA7511c.210C>T1.000
gyrA7523c.222C>G0.975
gyrA7526c.225G>C0.976
gyrA7547c.246C>T0.979
gyrA7553c.252C>T0.982
gyrA7559c.258G>C0.983
gyrA7565c.264C>T0.983
gyrA7574c.273G>C0.984
gyrA7585p.Ser95Thr1.000
gyrA7589c.288G>C0.985
gyrA7595c.294C>T0.985
gyrA7607c.306C>T0.984
gyrA7637c.336C>A1.000
gyrA8121c.820T>C1.000
gyrA8129c.828T>C1.000
gyrA8156c.855T>C1.000
gyrA8159c.858G>C0.933
gyrA8168c.867A>G1.000
gyrA8174c.873C>G0.933
gyrA8177c.876A>C1.000
gyrA8187p.Leu296Ile0.933
gyrA8192c.891C>G0.933
gyrA8198c.897T>C1.000
gyrA8207c.906T>C1.000
gyrA8267c.966G>C1.000
gyrA8283p.Ile328Leu1.000
gyrA8288c.987T>C1.000
gyrA8294c.993T>C1.000
gyrA8327c.1026C>T0.973
gyrA8330c.1029C>G1.000
gyrA8339c.1038A>G1.000
gyrA8340p.Ala347Ser1.000
gyrA8354c.1053G>C0.968
gyrA8372c.1071G>T1.000
gyrA8382c.1081C>T1.000
gyrA8840c.1539C>T1.000
gyrA8852c.1551T>C1.000
gyrA8858c.1557T>C0.971
gyrA8870c.1569G>C1.000
gyrA8873c.1572A>G1.000
gyrA8897c.1596T>C1.000
gyrA8903c.1602T>C1.000
gyrA8915c.1614A>G1.000
gyrA8921c.1620C>T1.000
gyrA8942c.1641G>C1.000
gyrA8945c.1644G>C1.000
gyrA8946c.1645T>C1.000
gyrA8957c.1656C>T1.000
gyrA8967p.Ala556Lys0.964
gyrA8978c.1677C>T1.000
gyrA8987c.1686C>G1.000
gyrA8990c.1689C>G1.000
gyrA8993c.1692C>T1.000
gyrA8996c.1695T>C1.000
gyrA8998p.Leu566Trp1.000
rpoB760079c.273G>A0.962
rpoB760091c.285G>C0.969
rpoB760101c.295T>C0.970
rpoB760110c.304T>A0.970
rpoB760118c.312T>G1.000
rpoB760121c.315T>C1.000
rpoB760130p.Asp108Glu1.000
rpoB760139c.333A>G1.000
rpoB760181c.375T>C1.000
rpoB760184c.378A>G1.000
rpoB760196c.390C>G1.000
rpoB760235c.429T>C1.000
rpoB760244c.438G>C1.000
rpoB760256c.450C>T1.000
rpoB760274p.Glu156Asp1.000
rpoB760276p.Lys157Met1.000
rpoB760283c.477G>C1.000
rpoB760298c.492G>C1.000
rpoB760307c.501T>C1.000
rpoB760357p.Thr184Ser1.000
rpoB760361c.555T>C1.000
rpoB760370c.564C>G1.000
rpoB760376p.Asp190Glu1.000
rpoB760382c.576G>C1.000
rpoB760388c.582C>T1.000
rpoB760400c.594G>C1.000
rpoB760406c.600G>C0.944
rpoB760406r.600ga>g1.000
rpoB760407p.Ser201Gly1.000
rpoB760415c.609C>T1.000
rpoB760418c.612G>C1.000
rpoB760430c.624T>C1.000
rpoB760460c.654G>C1.000
rpoB760475c.669A>G1.000
rpoB760481c.675G>C1.000
rpoB760484c.678A>G1.000
rpoB760502c.696C>G1.000
rpoB760522p.Ser239Asn1.000
rpoB760532c.726T>C1.000
rpoB760541c.735G>C1.000
rpoB760561252MRS>252MMG1.000
rpoB760571c.765G>C1.000
rpoB760588p.Thr261Ile1.000
rpoB760591p.Val262Ala1.000
rpoB760595c.789C>T1.000
rpoB760596p.Thr264Pro1.000
rpoB760608c.802C>T1.000
rpoB760611c.805T>C1.000
rpoB760634c.828T>C0.985
rpoB760646c.840C>G1.000
rpoB760655c.849A>G1.000
rpoB760661c.855A>G1.000
rpoB760668p.Thr288Ala0.980
rpoB760674c.868T>C1.000
rpoB760679c.873A>G1.000
rpoB760683c.877T>C1.000
rpoB760703c.897C>T1.000
rpoB760721c.915C>G1.000
rpoB760727c.921C>G0.962
rpoB760730c.924T>C1.000
rpoB760736c.930C>G0.952
rpoB760793c.987A>G1.000
rpoB760805c.999G>C1.000
rpoB760817c.1011A>G0.955
rpoB760820c.1014T>C1.000
rpoB760826c.1020C>G1.000
rpoB760830c.1024T>C1.000
rpoB760841c.1035T>C1.000
rpoB760858p.Val351Ala0.972
rpoB760862c.1056G>C1.000
rpoB760865c.1059C>T0.973
rpoB760886p.Glu360Asp1.000
rpoB760887p.Thr361Val0.975
rpoB760910c.1104C>T0.981
rpoB760916c.1110C>T0.962
rpoB760928c.1122G>C0.980
rpoB760943c.1137C>T0.977
rpoB760946c.1140A>G0.978
rpoB760965p.Met387Leu0.974
rpoB760970c.1164G>C0.973
rpoB760973c.1167G>T0.971
rpoB760982c.1176G>C1.000
rpoB760985c.1179G>C1.000
rpoB760988c.1182C>G1.000
rpoB760991c.1185G>T1.000
rpoB760997c.1191G>C1.000
rpoB761006c.1200C>G1.000
rpoB761015c.1209G>C1.000
rpoB761027c.1221A>C1.000
rpoB761036c.1230G>C1.000
rpoB761037c.1231T>C1.000
rpoB761051c.1245G>T1.000
rpoB761054c.1248G>C1.000
rpoB761057c.1251G>C0.975
rpoB761060c.1254C>G1.000
rpoB761063c.1257C>G1.000
rpoB761084c.1278C>A1.000
rpoB761097c.1291A>T1.000
rpoB761102c.1296A>G1.000
rpoB761132c.1326G>C1.000
rpoB761133c.1327T>C1.000
rpoB761147c.1341C>T1.000
rpoB761150c.1344A>T1.000
rpoB761165c.1359G>C1.000
rpoB761171c.1365C>T1.000
rpoB761178p.Ser458Thr1.000
rpoB761186p.Glu460Asp1.000
rpoB761189c.1383T>C1.000
rpoB761195c.1389G>C1.000
rpoB761198c.1392G>C1.000
rpoB761219c.1413G>C0.985
rpoB761234c.1428G>C0.982
rpoB761249c.1443A>G0.982
rpoB761255c.1449T>G0.977
rpoB761258c.1452G>A0.977
rpoB761261c.1455G>C0.956
rpoB761264c.1458C>G0.957
rpoB761273c.1467T>C0.982
rpoB761318c.1512G>T0.976
rpoB761327c.1521A>G0.974
rpoB761333c.1527G>T0.971
rpoB761339c.1533C>G1.000
rpoB761516c.1710G>C1.000
rpoB761528c.1722C>T1.000
rpoB761537c.1731C>G1.000
rpoB761555c.1749G>C1.000
rpoB761558c.1752C>G1.000
rpoB761564c.1758G>C1.000
rpoB761570c.1764T>C0.971
rpoB761573c.1767C>G0.972
rpoB761579c.1773G>C1.000
rpoB761612c.1806G>T0.979
rpoB761615c.1809A>C0.978
rpoB761636c.1830G>T0.974
rpoB761645c.1839C>G0.972
rpoB761657c.1851C>T0.971
rpoB761666c.1860G>C0.955
rpoB761669c.1863C>T0.955
rpoB761675c.1869G>T0.947
rpoB761681c.1875G>A0.944
rpoB761682c.1876C>T0.944
rpoB761687c.1881C>T0.941
rpoB761690c.1884G>C0.941
rpoB761693c.1887G>C0.941
rpoB761705c.1899C>A0.938
rpoB761891c.2085G>C1.000
rpoB761909c.2103T>C1.000
rpoB761912c.2106T>C1.000
rpoB761915p.Asp703Glu1.000
rpoB761916p.Asp704Asn1.000
rpoB761924c.2118G>A1.000
rpoB761930c.2124G>C1.000
rpoB761933c.2127G>C1.000
rpoB761936c.2130C>T1.000
rpoB761948c.2142G>C1.000
rpoB761954c.2148C>A1.000
rpoB761955p.Ile717Val1.000
rpoB761969c.2163G>A1.000
rpoB761990c.2184G>C1.000
rpoB762008c.2202C>T1.000
rpoB762014c.2208C>G1.000
rpoB762038c.2232C>T1.000
rpoB762047c.2241G>A1.000
rpoB762053c.2247T>C1.000
rpoB762056c.2250G>A1.000
rpoB762065c.2259T>G0.969
rpoB762083c.2277T>C0.971
rpoB762086c.2280G>C0.969
rpoB762101c.2295C>G0.971
rpoB762114p.Ile770Val0.970
rpoB762122c.2316C>T0.972
rpoB762131c.2325C>G0.968
rpoB762134c.2328C>A0.967
rpoB762137c.2331C>T0.967
rpoB762140c.2334G>C0.967
rpoB762143c.2337T>C0.968
rpoB762149c.2343G>T0.971
rpoB762158c.2352G>C0.976
rpoB762167c.2361T>C0.976
rpoB762176c.2370T>C0.977
rpoB762185c.2379G>C0.977
rpoB762194c.2388G>C0.978
rpoB762233c.2427G>C1.000
rpoB762236c.2430G>C1.000
rpoB762245c.2439G>C1.000
rpoB762275c.2469C>T1.000
rpoB762284c.2478G>C1.000
rpoB762293c.2487T>C1.000
rpoB762296c.2490G>C0.966
rpoB762317c.2511A>G0.955
rpoB762323c.2517C>A0.950
rpoB762329c.2523G>C1.000
rpoB762404c.2598T>C0.975
rpoB762410c.2604T>G0.975
rpoB762416c.2610A>G0.977
rpoB762449c.2643C>A0.980
rpoB762452c.2646G>C0.980
rpoB762470c.2664G>C0.980
rpoB762488c.2682G>C0.955
rpoB762491c.2685T>C0.955
rpoB762509c.2703T>G0.833
rpoB762510p.Ala902Pro0.833
rpoB762515c.2709C>T0.938
rpoB762533c.2727T>C0.944
rpoB762536c.2730T>C0.938
rpoB762537c.2731T>C0.938
rpoB762551c.2745C>T0.857
rpoB762827c.3021G>C0.889
rpoB762830c.3024C>G0.889
rpoB762857c.3051C>G0.963
rpoB762860c.3054G>C0.963
rpoB762863c.3057T>C0.964
rpoB762866c.3060C>T0.964
rpoB762879p.Met1025Leu1.000
rpoB762894c.3088C>T1.000
rpoB762899c.3093G>C1.000
rpoB762917c.3111C>G1.000
rpoB762920c.3114C>T1.000
rpoB762923c.3117C>G1.000
rpoB762929c.3123G>C1.000
rpoB762959c.3153G>C1.000
rpoB762962c.3156C>T1.000
rpoB762995c.3189G>T1.000
rpoB763031c.3225T>G1.000
rpoB763034c.3228C>G1.000
rpoB763040c.3234C>G1.000
rpoB763070c.3264T>C1.000
rpoB763082c.3276C>T0.979
rpoB763088c.3282C>G0.979
rpoB763094c.3288G>C0.978
rpoB763115c.3309T>C0.980
rpoB763127c.3321G>C0.979
rpoB763136c.3330C>T0.977
rpoB763145c.3339G>A0.976
rpoB763157c.3351G>T0.973
rpoB763166c.3360A>G0.971
rpoB763172c.3366G>C0.971
rpoB763193c.3387C>G0.963
rpoC763402c.33C>T1.000
rpoC763408c.39T>C0.929
rpoC763411c.42T>C1.000
rpoC763414c.45T>G1.000
rpoC763415p.Thr16Ser0.929
rpoC763423p.Glu18Asp0.929
rpoC763430c.61A>C0.929
rpoC763433p.Gln22Asn0.929
rpoC763443p.Tyr25Phe1.000
rpoC763450c.81G>A1.000
rpoC763456c.87A>G1.000
rpoC763468c.99G>C1.000
rpoC763486c.117T>C0.987
rpoC763492c.123G>C0.988
rpoC763528c.159G>A0.987
rpoC763531c.162G>T0.987
rpoC763546c.177A>G0.986
rpoC763570c.201G>C0.986
rpoC763594c.225C>T0.983
rpoC763633c.264T>C0.980
rpoC763657c.288G>A1.000
rpoC763660c.291T>G1.000
rpoC763666c.297G>C1.000
rpoC763669c.300C>G1.000
rpoC763675c.306C>G1.000
rpoC763696c.327T>C1.000
rpoC763699c.330G>T1.000
rpoC763702c.333C>G1.000
rpoC763708c.339G>C1.000
rpoC763711c.342G>C1.000
rpoC763714c.345G>C1.000
rpoC763717c.348T>C1.000
rpoC763723c.354G>C1.000
rpoC763732c.363C>A1.000
rpoC763741c.372C>T1.000
rpoC763744c.375G>C1.000
rpoC763747c.378G>A1.000
rpoC763891c.522G>C1.000
rpoC763894c.525A>G1.000
rpoC763900c.531G>C1.000
rpoC763933c.564C>T1.000
rpoC763940p.Ala191Ser1.000
rpoC763945c.576T>C1.000
rpoC763947p.Ala193Val1.000
rpoC763951c.582G>C1.000
rpoC763960c.591T>G1.000
rpoC763969c.600C>T1.000
rpoC763987c.618C>T1.000
rpoC763991p.Ile208Leu1.000
rpoC763996c.627T>C1.000
rpoC763999c.630C>T1.000
rpoC764002c.633C>G1.000
rpoC764003p.Ala212Ser1.000
rpoC764024c.655T>C1.000
rpoC764029p.Glu220Asp1.000
rpoC764032p.Asp221Glu1.000
rpoC764040p.Ser224Thr1.000
rpoC764044c.675T>C1.000
rpoC764054c.685C>T0.964
rpoC764059c.690G>T1.000
rpoC764083c.714A>G1.000
rpoC764084p.Asn239Val0.969
rpoC764095c.726C>T0.969
rpoC764098c.729A>G0.969
rpoC764143c.774G>C0.957
rpoC764147p.Ser260Ala0.955
rpoC764150p.Ile261Val0.952
rpoC764165p.Glu266Gln0.952
rpoC764311c.942C>G1.000
rpoC764317c.948C>G1.000
rpoC764320c.951C>G1.000
rpoC764332c.963G>A1.000
rpoC764338c.969G>A1.000
rpoC764353c.984G>T1.000
rpoC764365c.996C>T1.000
rpoC764371c.1002G>C0.976
rpoC764377c.1008C>G0.977
rpoC764380c.1011G>C1.000
rpoC764387c.1018T>C1.000
rpoC764405c.1036A>C1.000
rpoC764428c.1059G>C1.000
rpoC764431c.1062G>C1.000
rpoC764434c.1065A>G0.977
rpoC764435c.1066A>C0.977
rpoC764458c.1089G>C1.000
rpoC764461c.1092A>G1.000
rpoC764497c.1128A>G1.000
rpoC764510c.1141C>T1.000
rpoC764524c.1155C>G1.000
rpoC764530c.1161C>G1.000
rpoC764534c.1165C>A1.000
rpoC764539c.1170C>T1.000
rpoC764542c.1173C>T1.000
rpoC764545c.1176C>A1.000
rpoC764560c.1191T>C1.000
rpoC764575c.1206T>G0.967
rpoC764611c.1242G>T1.000
rpoC764626c.1257C>T1.000
rpoC764632c.1263T>C1.000
rpoC764650c.1281G>T1.000
rpoC764668c.1299C>T1.000
rpoC764692c.1323C>T1.000
rpoC764713c.1344G>T1.000
rpoC764716c.1347G>C1.000
rpoC764746c.1377G>T1.000
rpoC764752c.1383G>C0.981
rpoC764758c.1389C>G0.981
rpoC764764c.1395T>C0.981
rpoC764791c.1422C>G0.982
rpoC764803c.1434C>T0.981
rpoC764809c.1440C>T0.979
rpoC764810p.Pro481Ala0.980
rpoC764815c.1446A>G0.980
rpoC764824c.1455T>C0.981
rpoC764827c.1458G>C0.981
rpoC764858c.1489T>C0.981
rpoC764869c.1500C>T0.981
rpoC764875c.1506C>A1.000
rpoC764887c.1518G>C1.000
rpoC764888c.1519T>C1.000
rpoC764911c.1542A>G1.000
rpoC764912p.Met515Gln1.000
rpoC764932c.1563C>A1.000
rpoC764948c.1579T>C1.000
rpoC764968c.1599T>C1.000
rpoC765004c.1635G>C1.000
rpoC765007c.1638T>G1.000
rpoC765008c.1639T>C1.000
rpoC765011c.1642A>T1.000
rpoC765016c.1647C>G1.000
rpoC765019c.1650A>G1.000
rpoC765040c.1671T>C1.000
rpoC765041c.1672T>C1.000
rpoC765047c.1678T>C1.000
rpoC765055c.1686C>G1.000
rpoC765073c.1704G>C0.952
rpoC765076c.1707A>G0.950
rpoC765079c.1710T>G0.944
rpoC765082c.1713G>C0.944
rpoC765085c.1716T>C0.944
rpoC765089c.1720T>C0.944
rpoC765100c.1731G>C0.917
rpoC765103c.1734G>T0.917
rpoC765343c.1974G>A0.700
rpoC765356p.Met663Val0.800
rpoC765370c.2001G>C1.000
rpoC765379c.2010G>C1.000
rpoC765382c.2013G>T1.000
rpoC765383p.Met672Leu1.000
rpoC765403c.2034G>C1.000
rpoC765405p.Leu679His0.967
rpoC765409c.2040T>G1.000
rpoC765421c.2052C>G1.000
rpoC765449p.Ala694Ser1.000
rpoC765454c.2085C>G1.000
rpoC765469c.2100G>C1.000
rpoC765478c.2109T>G0.983
rpoC765480p.Tyr704Phe1.000
rpoC765499c.2130C>G1.000
rpoC765517c.2148C>G1.000
rpoC765533p.Tyr722His1.000
rpoC765544c.2175C>G0.966
rpoC765547c.2178C>T0.963
rpoC765548c.2179A>T0.963
rpoC765553c.2184C>T0.963
rpoC765556c.2187G>C0.963
rpoC765562c.2193G>T0.929
rpoC765826c.2457T>C1.000
rpoC765835c.2466C>T1.000
rpoC765841c.2472G>T0.977
rpoC765861p.Phe831Tyr0.965
rpoC765875p.Val836Ile0.968
rpoC765907c.2538G>T0.965
rpoC765910c.2541G>C0.962
rpoC765928c.2559C>G0.955
rpoC765940c.2571A>T0.949
rpoC765947c.2578T>C1.000
rpoC765962c.2593T>C0.913
rpoC765967c.2598C>T0.952
rpoC765973c.2604C>G0.905
rpoC765979c.2610C>G0.905
rpoC765982c.2613C>T0.950
rpoC765994c.2625A>T0.947
rpoC766003c.2634G>C0.929
rpoC766321c.2952C>G0.917
rpoC766333c.2964G>T0.933
rpoC766345c.2976T>C0.933
rpoC766348c.2979A>G0.933
rpoC766351c.2982C>G0.933
rpoC766353p.Val995Ala0.933
rpoC766369c.3000C>G1.000
rpoC766375c.3006C>G1.000
rpoC766381c.3012C>T1.000
rpoC766384c.3015A>G1.000
rpoC766390c.3021C>T1.000
rpoC766393c.3024C>T0.976
rpoC766408c.3039C>T1.000
rpoC766435p.Glu1022Asp1.000
rpoC766501c.3132G>C1.000
rpoC766507c.3138C>T1.000
rpoC766513c.3144C>T1.000
rpoC766522c.3153C>A0.929
rpoC766528c.3159T>G0.929
rpoC766531c.3162G>C0.929
rpoC766534c.3165C>G0.929
rpoC766537c.3168G>A0.929
rpoC766540p.Asp1057Glu0.929
rpoC766549c.3180G>C0.971
rpoC766570c.3201T>C0.973
rpoC766573c.3204T>G0.973
rpoC766594c.3225G>T0.973
rpoC766607p.Ile1080Leu0.973
rpoC766618c.3249G>T0.970
rpoC766624c.3255G>C0.970
rpoC766630c.3261G>C0.966
rpoC766633c.3264G>C0.966
rpoC766792c.3423C>G1.000
rpoC766799p.Ala1144Ser1.000
rpoC766804c.3435A>G1.000
rpoC766837c.3468G>C1.000
rpoC766843c.3474T>G1.000
rpoC766846c.3477C>A1.000
rpoC766858c.3489C>T1.000
rpoC766861c.3492G>C1.000
rpoC766867c.3498C>G1.000
rpoC766876c.3507C>T1.000
rpoC766931p.Ala1188Ser1.000
rpoC766942c.3573C>T1.000
rpoC766945c.3576A>C1.000
rpoC766963c.3594T>C1.000
rpoC766996c.3627C>T1.000
rpoC767002c.3633G>C1.000
rpoC767008c.3639G>A1.000
rpoC767023c.3654C>T1.000
rpoC767044c.3675G>C1.000
rpoC767080c.3711G>C0.985
rpoC767098c.3729T>C0.986
rpoC767104c.3735C>G0.985
rpoC767107c.3738C>T0.985
rpoC767119c.3750A>G0.986
rpoC767125c.3756G>C0.985
rpoC767134c.3765C>T0.984
rpoC767138c.3769C>T0.983
rpoC767149c.3780C>T0.983
rpoC767158c.3789T>C0.983
rpoC767179c.3810C>T0.980
rpoC767180p.Ala1271Ser0.980
rpoC767191c.3822C>G0.981
rpoC767197c.3828G>A0.962
rpoC767203c.3834C>G0.978
rpoC767206c.3837C>G0.978
rpoC767209c.3840T>C0.978
rpoC767212c.3843G>C0.978
rpoC767221c.3852C>G0.984
rpoC767230c.3861G>C1.000
rpoC767233c.3864T>C1.000
rpoC767254c.3885G>C1.000
rpoC767264p.Ala1299Ser1.000
rpoC767267p.Ala1300Asn1.000
rpoC767281c.3912C>G1.000
rpoC767284c.3915C>G1.000
rpsL781559c.-1G>C1.000
rpsL781572p.Gln5Asn1.000
rpsL781586c.27C>T1.000
rpsL781595c.36T>C1.000
rpsL781608p.Ser17Ala1.000
rpsL781616c.57C>G1.000
rpsL781628c.69T>C1.000
rpsL781649c.90T>C1.000
rpsL781655c.96T>C1.000
rpsL781658c.99A>C1.000
rpsL781670c.111G>C1.000
rpsL781706c.147T>C1.000
rpsL781715c.156T>G1.000
rpsL781772c.213C>T0.966
rpsL781802c.243G>C1.000
rpsL781814c.255C>T1.000
rpsL781817c.258G>T1.000
rpsL781829c.270G>C1.000
rpsL781832c.273T>C1.000
rpsL781859c.300T>C1.000
rpsL781868c.309T>C1.000
rpsL781871c.312G>C1.000
rpsL781877c.318T>A1.000
rpsL781892c.333A>G1.000
rpsL781898c.339A>T1.000
rpsL781907c.348T>C1.000
rpsL781916c.357T>C1.000
rpsL781929p.Gly124Ser1.000
rpsL781933374G>A1.000
rplC800796c.-13ATTGG>A1.000
rrs1471922r.77gt>g1.000
rrs1471925r.80t>c1.000
rrs1471931r.86ga>g1.000
rrs1471934r.89a>g1.000
rrs1471985r.140t>c1.000
rrs1471986r.141c>t1.000
rrs1472030r.185g>a0.944
rrs1472031r.186g>c0.941
rrs1472032r.187g>a0.941
rrs1472033r.188a>c1.000
rrs1472035r.190g>t1.000
rrs1472040r.195t>g1.000
rrs1472041r.196c>t1.000
rrs1472042r.197t>g1.000
rrs1472043r.198t>a1.000
rrs1472050r.205g>c1.000
rrs1472053r.208agc>a1.000
rrs1472061r.216a>t1.000
rrs1472106r.261g>a0.978
rrs1472108r.263c>t1.000
rrs1472113r.268t>c0.980
rrs1472150r.305t>a0.980
rrs1472251r.406g>a1.000
rrs1472337r.492c>g1.000
rrs1472380r.535g>c1.000
rrs1472446r.601t>a1.000
rrs1472452r.607g>a1.000
rrs1472464r.619a>g1.000
rrs1472612r.767g>t1.000
rrs1472734r.889c>t1.000
rrs1472741r.896g>a1.000
rrs1472846r.1001c>t1.000
rrs1472847r.1002g>a1.000
rrs1472848r.1003t>c1.000
rrs1472860r.1015c>t1.000
rrs1472861r.1016g>a1.000
rrs1472956r.1111t>c1.000
rrs1472957r.1112c>t1.000
rrs1472969r.1124a>g1.000
rrs1472970r.1125c>g1.000
rrs1472977r.1132g>c1.000
rrs1472978r.1133t>c1.000
rrs1472989r.1144g>a1.000
rrs1472990r.1145a>g1.000
rrs1473082r.1237g>a0.956
rrs1473088r.1243a>g0.953
rrs1473099r.1254t>a0.926
rrs1473104r.1259c>t0.889
rrs1473105r.1260g>a0.923
rrs1473110r.1265t>g0.885
rrs1473111r.1266a>g0.885
rrs1473121r.1276t>c0.917
rrs1473123r.1278a>t0.946
rrs1473129r.1284c>t0.923
rrs1473145r.1300c>t0.953
rrs1473166r.1321g>a0.956
rrs1473288r.1443c>t1.000
rrs1473290r.1445c>t1.000
rrs1473291r.1446g>t1.000
rrl1473684r.27g>a0.923
rrl1473697r.40c>a0.923
rrl1473707r.50t>a0.947
rrl1473717r.60g>a0.958
rrl1473731r.74t>a0.963
rrl1473746r.89t>c0.967
rrl1473756r.99g>t0.971
rrl1473758r.101g>t0.971
rrl1473770r.113t>c0.973
rrl1473806r.149c>t1.000
rrl1473812r.155g>a1.000
rrl1473814r.157a>t1.000
rrl1473815r.158t>g1.000
rrl1473829r.172g>c1.000
rrl1473831r.174g>t1.000
rrl1473832r.175c>t1.000
rrl1473839r.182g>a1.000
rrl1473876r.219g>a1.000
rrl1473887r.230t>c1.000
rrl1473888r.231t>c1.000
rrl1473898r.241c>t1.000
rrl1473899r.242a>g1.000
rrl1473916r.259c>a1.000
rrl1473923r.266c>g1.000
rrl1473937r.280c>t1.000
rrl1473943r.286g>t1.000
rrl1473945r.288t>a1.000
rrl1473946r.289a>t1.000
rrl1473950r.293g>t1.000
rrl1474056r.399t>c1.000
rrl1474061r.404t>c1.000
rrl1474074r.417c>t1.000
rrl1474089r.432c>t0.955
rrl1474093r.436g>a0.955
rrl1474100r.443c>t0.955
rrl1474103r.446a>c0.955
rrl1474130r.473c>t0.971
rrl1474140r.483c>t0.971
rrl1474151r.494c>t0.974
rrl1474181r.524c>ct0.884
rrl1474184r.527c>a0.974
rrl1474249r.592g>t1.000
rrl1474263r.606g>a1.000
rrl1474282r.625g>a0.939
rrl1474306r.649a>c0.909
rrl1474308r.651g>t0.909
rrl1474310r.653t>g0.909
rrl1474356r.699t>c0.976
rrl1474362r.705a>g0.977
rrl1474387r.730c>t0.952
rrl1474413r.756a>c0.967
rrl1474414r.757cccacacgcgcatacgcgcgtgtg>c0.935
rrl1474415r.758ccacacgcgcatacgcgcgtgtga>c0.967
rrl1474435r.778gtgaa>g1.000
rrl1474496r.839c>g0.978
rrl1474497r.840g>c0.978
rrl1474506r.849c>g0.980
rrl1474507r.850g>c0.980
rrl1474626r.969t>c1.000
rrl1474632r.975g>t1.000
rrl1474636r.979a>t0.962
rrl1474637r.980c>t0.962
rrl1474638r.981c>g0.962
rrl1474639r.982g>t1.000
rrl1474640r.983c>t0.964
rrl1474717r.1060a>g0.968
rrl1474722r.1065t>c0.968
rrl1474743r.1086t>g0.977
rrl1474760r.1103a>g0.979
rrl1474794r.1137c>t1.000
rrl1474803r.1146g>a0.961
rrl1474812r.1155g>a1.000
rrl1474830r.1173a>g0.979
rrl1474913r.1256t>c0.970
rrl1474932r.1275c>t1.000
rrl1475031r.1374g>c1.000
rrl1475061r.1404ca>c1.000
rrl1475076r.1419c>a0.978
rrl1475090r.1433a>t0.980
rrl1475114r.1457c>t0.979
rrl1475120r.1463g>t1.000
rrl1475129r.1472g>a0.976
rrl1475202r.1545g>c1.000
rrl1475209r.1552g>a1.000
rrl1475213r.1556c>t1.000
rrl1475220r.1563g>t1.000
rrl1475429r.1772g>a0.955
rrl1475443r.1786g>a0.958
rrl1475452r.1795c>a0.960
rrl1475475r.1818c>t0.963
rrl1475479r.1822c>t0.960
rrl1475480r.1823a>t0.960
rrl1475505r.1848g>a0.963
rrl1475526r.1869c>a0.960
rrl1475531r.1874c>t0.962
rrl1475573r.1916g>a1.000
rrl1475649r.1992a>g1.000
rrl1475659r.2002g>a1.000
rrl1475760r.2103ccg>c1.000
rrl1475764r.2107a>t0.976
rrl1475765r.2108a>t0.976
rrl1475975r.2318c>t0.972
rrl1475977r.2320a>g0.972
rrl1475988r.2331a>g0.968
rrl1475989r.2332t>c0.967
rrl1475993r.2336c>t0.967
rrl1475997r.2340a>t0.967
rrl1476131r.2474c>t0.958
rrl1476160r.2503t>c0.972
rrl1476214r.2557g>t0.976
rrl1476215r.2558c>t0.976
rrl1476221r.2564t>c0.976
rrl1476224r.2567a>g0.976
rrl1476251r.2594t>c1.000
rrl1476281r.2624t>c1.000
rrl1476297r.2640c>t1.000
rrl1476299r.2642c>t0.977
rrl1476584r.2927c>t1.000
rrl1476594r.2937c>t1.000
rrl1476597r.2940g>a1.000
rrl1476603r.2946g>a1.000
rrl1476608r.2951c>g1.000
rrl1476619r.2962c>t1.000
rrl1476628r.2971t>a1.000
rrl1476665r.3008t>a1.000
rrl1476666r.3009c>t1.000
rrl1476674r.3017t>c1.000
inhA1674858c.657G>A1.000
inhA1674876c.675C>T0.944
inhA1674879c.678T>C1.000
inhA1674892p.Asn231Asp0.944
inhA1674903c.702T>C1.000
inhA1674904p.Ala235Pro1.000
inhA1674909c.708G>A1.000
inhA1674912c.711G>C0.944
inhA1674915c.714C>G0.944
inhA1674942c.741T>C1.000
inhA1674949c.748C>T0.944
inhA1674954c.753G>C0.944
inhA1674957c.756G>C0.944
inhA1674963c.762G>C0.944
inhA1674966c.765T>C1.000
inhA1674975c.774C>T0.944
inhA1674977p.Tyr259Phe0.944
inhA1674993c.792G>T0.917
rpsA1833536c.-6A>C1.000
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>T1.000
rpsA1833616c.75A>T1.000
rpsA1833619c.78A>C1.000
rpsA1833625c.84A>G1.000
rpsA1833664c.123C>G1.000
rpsA1833676c.135A>G1.000
rpsA1833679c.138G>T1.000
rpsA1833685c.144G>C1.000
rpsA1833691c.150G>A1.000
rpsA1833694c.153G>T1.000
rpsA1833697c.156C>T1.000
rpsA1833700c.159C>T1.000
rpsA1833709c.168C>T1.000
rpsA1833724c.183C>T0.979
rpsA1833727c.186G>C0.979
rpsA1833733c.192C>G0.957
rpsA1833734p.Ala65Ser0.957
rpsA1833742c.201A>G0.980
rpsA1833745c.204G>C0.980
rpsA1833748c.207C>G0.981
rpsA1833760c.219C>T0.984
rpsA1833787c.246C>G0.984
rpsA1833790c.249T>C0.984
rpsA1833802c.261A>G0.984
rpsA1833811c.270G>T0.985
rpsA1833823c.282G>A0.985
rpsA1833832c.291G>A0.985
rpsA1833838c.297G>C0.985
rpsA1833841c.300C>G0.985
rpsA1833847c.306C>G0.985
rpsA1833856c.315A>G0.986
rpsA1833862c.321G>T1.000
rpsA1833874c.333T>G1.000
rpsA1833886c.345C>G1.000
rpsA1833894p.Ala118Glu1.000
rpsA1833928c.387G>C1.000
rpsA1833949c.408T>C1.000
rpsA1833961c.420C>G1.000
rpsA1833970c.429G>T1.000
rpsA1833979c.438T>C1.000
rpsA1833991c.450C>G1.000
rpsA1834000c.459G>C1.000
rpsA1834009c.468C>T0.979
rpsA1834012c.471G>C0.979
rpsA1834015c.474G>C0.979
rpsA1834021c.480C>T1.000
rpsA1834030c.489C>G1.000
rpsA1834033c.492C>T0.983
rpsA1834073p.Lys178Arg0.977
rpsA1834096c.555G>C0.974
rpsA1834099c.558C>G1.000
rpsA1834108c.567C>G1.000
rpsA1834114c.573G>C0.969
rpsA1834177c.636A>C1.000
rpsA1834228c.687C>A0.974
rpsA1834231c.690T>G1.000
rpsA1834234c.693G>T1.000
rpsA1834240c.699T>C0.973
rpsA1834246c.705G>T0.972
rpsA1834249c.708T>C1.000
rpsA1834252c.711C>G0.973
rpsA1834261c.720A>G1.000
rpsA1834264c.723G>C1.000
rpsA1834279c.738C>T0.977
rpsA1834294c.753G>T0.970
rpsA1834297c.756C>T0.970
rpsA1834303c.762T>G1.000
rpsA1834306c.765T>C1.000
rpsA1834327c.786G>T0.977
rpsA1834357c.816T>C1.000
rpsA1834366c.825A>G0.980
rpsA1834375c.834G>C1.000
rpsA1834396c.855G>C1.000
rpsA1834411c.870T>G1.000
rpsA1834414c.873C>T1.000
rpsA1834417c.876G>C1.000
rpsA1834423c.882G>C1.000
rpsA1834429c.888C>T1.000
rpsA1834438c.897C>T1.000
rpsA1834451c.910T>C1.000
rpsA1834456c.915T>G1.000
rpsA1834468c.927A>G1.000
rpsA1834477c.936C>T1.000
rpsA1834489c.948T>C1.000
rpsA1834519c.978G>C1.000
rpsA1834520p.Ala327Ser1.000
rpsA1834528c.987T>C1.000
rpsA1834534c.993C>T1.000
rpsA1834543c.1002C>G1.000
rpsA1834546c.1005T>C1.000
rpsA1834552c.1011G>T1.000
rpsA1834555c.1014T>G1.000
rpsA1834557p.Ala339Gly1.000
rpsA1834606c.1065C>T1.000
rpsA1834609c.1068T>C1.000
rpsA1834619c.1078T>C1.000
rpsA1834622c.1081T>A1.000
rpsA1834633c.1092A>G1.000
rpsA1834639c.1098T>C1.000
rpsA1834645c.1104C>T1.000
rpsA1834666c.1125G>C1.000
rpsA1834667p.Ala376Ser1.000
rpsA1834690c.1149T>C1.000
rpsA1834701p.Gln387Pro1.000
rpsA1834720c.1179C>G0.981
rpsA1834732c.1191T>C0.981
rpsA1834738c.1197A>G0.981
rpsA1834753c.1212T>C0.981
rpsA1834759c.1218A>C0.981
rpsA1834765p.Glu408Asp0.980
rpsA1834774c.1233C>T0.977
rpsA1834776p.Ala412Glu0.976
rpsA1834780c.1239A>G0.976
rpsA1834789c.1248T>C0.976
rpsA1834813c.1272G>T0.971
rpsA1834830p.Ala430Val0.957
kasA2518738c.624G>C1.000
kasA2518756c.642G>C0.964
kasA2518768c.654C>G0.967
kasA2518771c.657C>G0.967
kasA2518774c.660C>T0.967
kasA2518783c.669T>G0.967
kasA2518787p.Arg225Lys0.967
kasA2518792c.678C>T0.967
kasA2518795c.681C>T0.967
kasA2518798c.684G>C0.969
kasA2518822c.708C>A1.000
kasA2518825c.711T>C0.981
kasA2518846c.732G>T1.000
kasA2518849c.735G>C1.000
kasA2518853p.Leu247Val1.000
kasA2518864c.750G>C1.000
embC4240729c.867C>G1.000
embC4240735c.873C>G1.000
embC4240741c.879C>T1.000
embC4240756c.894G>C1.000
embC4240771c.909G>C1.000
embC4240772p.Ser304Ala1.000
embC4240778p.His306Gly1.000
embC4240781p.Ala307Ser1.000
embC4240789c.927T>C1.000
embC4240819c.957A>C1.000
embC4240826p.Ala322Ser1.000
embC4240831c.969T>G1.000
embC4240856p.Ala332Thr1.000
embC4240859p.Leu333Ile1.000
embC4240876c.1014C>T1.000
embC4240879c.1017G>T1.000
embC4240885c.1023T>C1.000
embC4240886p.Ile342Val1.000
embC4240897c.1035C>G0.964
embC4240900c.1038A>G1.000
embB4248220c.1707A>G1.000
embB4248226c.1713G>C1.000
embB4248232c.1719G>T1.000
embB4248233p.Leu574Val1.000
embB4248236p.Met575Leu1.000
embB4248245p.Ile578Val1.000
embB4248250c.1737C>T1.000
embB4248259p.Met582Ile1.000
embB4248275p.Thr588Ala1.000
embB4248292c.1779G>A1.000

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;