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: 5d2c39de1fe58
Sample: 5d2c39de1fe58

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Summary
ID: 5d2c39de1fe58
Date: Mon Jul 15 09:34:03 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>A1.000
gyrB6115c.876A>G1.000
gyrB6121c.882C>T1.000
gyrB6127c.888G>C1.000
gyrB6133c.894G>C1.000
gyrB6136c.897G>A1.000
gyrB6151c.912C>T1.000
gyrB6172c.933C>T1.000
gyrB6184c.945C>T1.000
gyrB6655c.1416T>C0.941
gyrB6673c.1434A>C0.950
gyrB6676c.1437T>G0.950
gyrB6703c.1464G>C0.955
gyrB6706c.1467G>A0.955
gyrB6709c.1470A>G0.955
gyrB6712c.1473G>C0.958
gyrB6727c.1488G>T0.962
gyrB6728c.1489C>T0.962
gyrB6739c.1500C>T0.929
gyrB6745c.1506T>C1.000
gyrB6754c.1515C>T0.963
gyrB6763c.1524G>C0.962
gyrB6772c.1533C>G0.880
gyrB6775c.1536G>C0.917
gyrB6793c.1554T>C0.957
gyrB6798p.Gly520Ala0.957
gyrB6808c.1569C>G0.938
gyrB6824c.1585C>T0.867
gyrB6841c.1602T>C0.929
gyrB6862c.1623C>G0.833
gyrA7499c.198G>C0.952
gyrA7511c.210C>T0.862
gyrA7523c.222C>G0.906
gyrA7526c.225G>A0.969
gyrA7547c.246C>T1.000
gyrA7553c.252C>T0.936
gyrA7559c.258G>C0.938
gyrA7565c.264C>T0.981
gyrA7574c.273G>C0.948
gyrA7585p.Ser95Thr1.000
gyrA7589c.288G>C0.951
gyrA7595c.294C>T0.983
gyrA7607c.306C>T0.982
gyrA7637c.336C>A0.978
gyrA8156c.855T>C0.900
gyrA8159c.858G>C0.800
gyrA8168c.867A>G0.900
gyrA8174c.873C>G0.900
gyrA8177c.876A>C0.889
gyrA8187p.Leu296Ile0.800
gyrA8192c.891C>G0.800
gyrA8198c.897T>C0.900
gyrA8207c.906T>C0.900
gyrA8267c.966G>C0.929
gyrA8283p.Ile328Leu1.000
gyrA8288c.987T>C1.000
gyrA8294c.993T>C1.000
gyrA8324c.1023T>C0.167
gyrA8327c.1026C>T0.857
gyrA8330c.1029C>G0.875
gyrA8339c.1038A>G1.000
gyrA8340p.Ala347Ser1.000
gyrA8354c.1053G>C0.944
gyrA8372c.1071G>T0.250
gyrA8382c.1081C>T0.818
gyrA8603c.1302A>C0.900
gyrA8609c.1308G>C0.700
gyrA8792c.1491G>C0.833
gyrA8799p.Ala500Ser0.867
gyrA8810c.1509A>G0.867
gyrA8817p.Ser506Ala0.812
gyrA8828c.1527T>C0.875
gyrA8829c.1528T>C0.875
gyrA8837c.1536C>G0.917
gyrA8846c.1545C>T0.885
gyrA8852c.1551T>C0.933
gyrA8858c.1557T>C0.938
gyrA8870c.1569G>C0.919
gyrA8873c.1572A>G0.950
gyrA8897c.1596T>C0.980
gyrA8903c.1602T>C0.981
gyrA8915c.1614A>G0.982
gyrA8942c.1641G>T1.000
gyrA8945c.1644G>C1.000
gyrA8946c.1645T>C1.000
gyrA8957c.1656C>T1.000
gyrA8967p.Ala556Lys1.000
gyrA8978c.1677C>T1.000
gyrA8987c.1686C>G1.000
gyrA8990c.1689C>G1.000
gyrA8993c.1692C>T1.000
gyrA8996c.1695T>C1.000
gyrA8998p.Leu566Trp1.000
gyrA9018p.Gln573Lys1.000
rpoB760079c.273G>A1.000
rpoB760091c.285G>C1.000
rpoB760101c.295T>C1.000
rpoB760110c.304T>A1.000
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>T0.973
rpoB760274p.Glu156Asp0.958
rpoB760276p.Lys157Met0.957
rpoB760283c.477G>C0.952
rpoB760298c.492G>C1.000
rpoB760307c.501T>C0.941
rpoB760357p.Thr184Ser1.000
rpoB760361c.555T>C1.000
rpoB760370c.564C>G0.938
rpoB760376p.Asp190Glu1.000
rpoB760382c.576G>C0.947
rpoB760388c.582C>T0.952
rpoB760400c.594G>C0.955
rpoB760406c.600G>C0.957
rpoB760406r.600ga>g1.000
rpoB760407p.Ser201Gly1.000
rpoB760415c.609C>T1.000
rpoB760418c.612G>C0.971
rpoB760430c.624T>C1.000
rpoB760460c.654G>C0.953
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.Thr261Ile0.969
rpoB760591p.Val262Ala1.000
rpoB760595c.789C>T1.000
rpoB760596p.Thr264Pro1.000
rpoB760608c.802C>T0.974
rpoB760611c.805T>C1.000
rpoB760634c.828T>C0.976
rpoB760646c.840C>G1.000
rpoB760655c.849A>G1.000
rpoB760661c.855A>G1.000
rpoB760668p.Thr288Ala0.935
rpoB760674c.868T>C1.000
rpoB760679c.873A>G1.000
rpoB760683c.877T>C1.000
rpoB760703c.897C>T1.000
rpoB760721c.915C>G1.000
rpoB760727c.921C>G0.938
rpoB760730c.924T>C1.000
rpoB760736c.930C>G0.923
rpoB760817c.1011A>G1.000
rpoB760820c.1014T>C1.000
rpoB760826c.1020C>G1.000
rpoB760830c.1024T>C1.000
rpoB760841c.1035T>C1.000
rpoB760858p.Val351Ala1.000
rpoB760862c.1056G>C1.000
rpoB760865c.1059C>T1.000
rpoB760886p.Glu360Asp1.000
rpoB760887p.Thr361Val1.000
rpoB760910c.1104C>T1.000
rpoB760916c.1110C>T1.000
rpoB760928c.1122G>C1.000
rpoB760943c.1137C>T0.966
rpoB760946c.1140A>G1.000
rpoB760965p.Met387Leu0.962
rpoB760970c.1164G>C0.960
rpoB760973c.1167G>T0.958
rpoB760982c.1176G>C1.000
rpoB760985c.1179G>C1.000
rpoB760988c.1182C>G0.944
rpoB760991c.1185G>T1.000
rpoB760997c.1191G>C0.957
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>C1.000
rpoB761060c.1254C>G1.000
rpoB761063c.1257C>G1.000
rpoB761084c.1278C>A1.000
rpoB761097c.1291A>T1.000
rpoB761102c.1296A>G1.000
rpoB761132c.1326G>C0.987
rpoB761133c.1327T>C0.987
rpoB761147c.1341C>T0.988
rpoB761150c.1344A>T0.988
rpoB761165c.1359G>C0.987
rpoB761171c.1365C>T0.958
rpoB761178p.Ser458Thr0.937
rpoB761186p.Glu460Asp0.934
rpoB761189c.1383T>C0.984
rpoB761195c.1389G>C0.983
rpoB761198c.1392G>C0.983
rpoB761219c.1413G>C0.933
rpoB761234c.1428G>C0.984
rpoB761246c.1440C>T0.875
rpoB761249c.1443A>G0.975
rpoB761255c.1449T>G0.850
rpoB761258c.1452G>A0.842
rpoB761261c.1455G>C0.108
rpoB761264c.1458C>G0.974
rpoB761273c.1467T>C0.923
rpoB761303c.1497G>C0.922
rpoB761318c.1512G>T0.979
rpoB761327c.1521A>G0.978
rpoB761333c.1527G>T0.907
rpoB761339c.1533C>G0.905
rpoB761345c.1539G>C0.933
rpoB761346p.Val514Ser0.733
rpoB761354c.1548C>A0.200
rpoB761357c.1551G>T0.733
rpoB761360c.1554T>C0.923
rpoB761362p.Ser519Thr0.923
rpoB761373p.Val523His0.846
rpoB761384c.1578C>G0.786
rpoB761393c.1587G>A0.786
rpoB761414c.1608A>G0.818
rpoB761482p.Ala559Gly0.900
rpoB761497p.Tyr564Phe0.909
rpoB761502p.Pro566Ser0.909
rpoB761505p.Ser567Ala0.909
rpoB761508p.Ser568Thr0.909
rpoB761516c.1710G>C0.962
rpoB761528c.1722C>T0.844
rpoB761531c.1725C>T0.848
rpoB761537c.1731C>G1.000
rpoB761552c.1746G>C0.146
rpoB761555c.1749G>C1.000
rpoB761558c.1752C>G1.000
rpoB761564c.1758G>C0.878
rpoB761570c.1764T>C1.000
rpoB761573c.1767C>G1.000
rpoB761579c.1773G>C1.000
rpoB761612c.1806G>T1.000
rpoB761615c.1809A>C1.000
rpoB761636c.1830G>T1.000
rpoB761645c.1839C>G1.000
rpoB761657c.1851C>T0.933
rpoB761666c.1860G>C1.000
rpoB761669c.1863C>T1.000
rpoB761675c.1869G>T1.000
rpoB761681c.1875G>A0.939
rpoB761682c.1876C>T1.000
rpoB761687c.1881C>T0.969
rpoB761690c.1884G>C1.000
rpoB761693c.1887G>C0.969
rpoB761705c.1899C>A0.960
rpoB761891c.2085G>C1.000
rpoB761909c.2103T>C1.000
rpoB761912c.2106T>C1.000
rpoB761915p.Asp703Glu1.000
rpoB761916p.Asp704Asn1.000
rpoB761924c.2118G>A0.905
rpoB761930c.2124G>C1.000
rpoB761933c.2127G>C0.905
rpoB761936c.2130C>T0.913
rpoB761948c.2142G>C1.000
rpoB761954c.2148C>A1.000
rpoB761955p.Ile717Val0.956
rpoB761969c.2163G>A1.000
rpoB761990c.2184G>C0.946
rpoB762008c.2202C>T0.983
rpoB762014c.2208C>G0.982
rpoB762038c.2232C>T0.960
rpoB762047c.2241G>A0.980
rpoB762053c.2247T>C0.976
rpoB762056c.2250G>A0.949
rpoB762065c.2259T>G0.971
rpoB762083c.2277T>C0.923
rpoB762086c.2280G>C0.920
rpoB762101c.2295C>G0.923
rpoB762114p.Ile770Val0.939
rpoB762122c.2316C>T0.818
rpoB762131c.2325C>G0.929
rpoB762134c.2328C>A0.769
rpoB762137c.2331C>T0.880
rpoB762140c.2334G>C0.923
rpoB762143c.2337T>C0.893
rpoB762149c.2343G>T0.935
rpoB762158c.2352G>C0.946
rpoB762167c.2361T>C0.977
rpoB762176c.2370T>C0.980
rpoB762185c.2379G>C1.000
rpoB762194c.2388G>C0.931
rpoB762233c.2427G>C1.000
rpoB762236c.2430G>C0.917
rpoB762245c.2439G>C0.986
rpoB762275c.2469C>T0.949
rpoB762284c.2478G>C1.000
rpoB762293c.2487T>C1.000
rpoB762296c.2490G>C0.938
rpoB762317c.2511A>G1.000
rpoB762323c.2517C>A0.914
rpoB762329c.2523G>C1.000
rpoB762404c.2598T>C1.000
rpoB762410c.2604T>G1.000
rpoB762416c.2610A>G1.000
rpoB762449c.2643C>A1.000
rpoB762452c.2646G>C1.000
rpoB762470c.2664G>C1.000
rpoB762488c.2682G>C1.000
rpoB762491c.2685T>C1.000
rpoB762509c.2703T>G0.913
rpoB762510p.Ala902Pro0.909
rpoB762515c.2709C>T0.952
rpoB762533c.2727T>C0.929
rpoB762536c.2730T>C0.923
rpoB762537c.2731T>C0.923
rpoB762551c.2745C>T0.900
rpoB762827c.3021G>C1.000
rpoB762830c.3024C>G0.889
rpoB762857c.3051C>G0.960
rpoB762860c.3054G>C0.920
rpoB762863c.3057T>C0.962
rpoB762866c.3060C>T0.926
rpoB762879p.Met1025Leu0.969
rpoB762894c.3088C>T0.912
rpoB762899c.3093G>C0.919
rpoB762917c.3111C>G0.976
rpoB762920c.3114C>T0.974
rpoB762923c.3117C>G0.854
rpoB762929c.3123G>C0.114
rpoB762959c.3153G>C1.000
rpoB762962c.3156C>T1.000
rpoB762995c.3189G>T1.000
rpoB763031c.3225T>G1.000
rpoB763034c.3228C>G0.930
rpoB763040c.3234C>G0.929
rpoB763070c.3264T>C1.000
rpoB763082c.3276C>T0.957
rpoB763088c.3282C>G0.957
rpoB763094c.3288G>C0.958
rpoB763115c.3309T>C1.000
rpoB763127c.3321G>C0.957
rpoB763136c.3330C>T1.000
rpoB763145c.3339G>A0.941
rpoB763157c.3351G>T0.938
rpoB763166c.3360A>G1.000
rpoB763172c.3366G>C1.000
rpoB763193c.3387C>G0.900
rpoC763450c.81G>A0.882
rpoC763456c.87A>G1.000
rpoC763468c.99G>C1.000
rpoC763486c.117T>C1.000
rpoC763492c.123G>C1.000
rpoC763528c.159G>A1.000
rpoC763531c.162G>T0.970
rpoC763546c.177A>G1.000
rpoC763570c.201G>C1.000
rpoC763594c.225C>T1.000
rpoC763633c.264T>C1.000
rpoC763657c.288G>A0.909
rpoC763660c.291T>G1.000
rpoC763666c.297G>C1.000
rpoC763669c.300C>G0.900
rpoC763675c.306C>G1.000
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>T0.952
rpoC763991p.Ile208Leu0.947
rpoC763996c.627T>C0.944
rpoC763999c.630C>T0.944
rpoC764002c.633C>G0.944
rpoC764003p.Ala212Ser0.944
rpoC764024c.655T>C0.958
rpoC764029p.Glu220Asp0.957
rpoC764032p.Asp221Glu0.958
rpoC764040p.Ser224Thr0.969
rpoC764044c.675T>C0.938
rpoC764054c.685C>T0.967
rpoC764059c.690G>T0.969
rpoC764083c.714A>G0.969
rpoC764084p.Asn239Val0.969
rpoC764095c.726C>T0.969
rpoC764098c.729A>G0.938
rpoC764143c.774G>C0.933
rpoC764147p.Ser260Ala0.929
rpoC764150p.Ile261Val0.929
rpoC764165p.Glu266Gln0.929
rpoC764311c.942C>G0.818
rpoC764317c.948C>G0.769
rpoC764320c.951C>G0.769
rpoC764332c.963G>A0.800
rpoC764338c.969G>A0.833
rpoC764353c.984G>T0.962
rpoC764365c.996C>T0.966
rpoC764371c.1002G>C0.938
rpoC764377c.1008C>G0.853
rpoC764380c.1011G>C0.971
rpoC764387c.1018T>C0.949
rpoC764405c.1036A>C0.930
rpoC764428c.1059G>C0.907
rpoC764431c.1062G>C0.907
rpoC764434c.1065A>G0.902
rpoC764435c.1066A>C0.878
rpoC764458c.1089G>C0.923
rpoC764461c.1092A>G0.925
rpoC764497c.1128A>G0.980
rpoC764510c.1141C>T0.943
rpoC764524c.1155C>G0.938
rpoC764530c.1161C>G0.911
rpoC764534c.1165C>A0.907
rpoC764539c.1170C>T0.974
rpoC764542c.1173C>T0.902
rpoC764545c.1176C>A0.902
rpoC764560c.1191T>C0.939
rpoC764575c.1206T>G1.000
rpoC764611c.1242G>T1.000
rpoC764626c.1257C>T1.000
rpoC764632c.1263T>C1.000
rpoC764650c.1281G>T1.000
rpoC764668c.1299C>T0.911
rpoC764692c.1323C>T0.936
rpoC764713c.1344G>T0.957
rpoC764716c.1347G>C0.978
rpoC764746c.1377G>T0.979
rpoC764752c.1383G>C0.979
rpoC764758c.1389C>G0.980
rpoC764764c.1395T>C0.980
rpoC764791c.1422C>G0.923
rpoC764803c.1434C>T0.979
rpoC764809c.1440C>T0.975
rpoC764810p.Pro481Ala0.900
rpoC764815c.1446A>G1.000
rpoC764824c.1455T>C1.000
rpoC764827c.1458G>C1.000
rpoC764858c.1489T>C1.000
rpoC764869c.1500C>T1.000
rpoC764875c.1506C>A1.000
rpoC764887c.1518G>C1.000
rpoC764888c.1519T>C1.000
rpoC764911c.1542A>G1.000
rpoC764912p.Met515Gln1.000
rpoC764932c.1563C>A0.971
rpoC764948c.1579T>C0.985
rpoC764968c.1599T>C0.985
rpoC765004c.1635G>C0.905
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>C1.000
rpoC765076c.1707A>G1.000
rpoC765079c.1710T>G1.000
rpoC765082c.1713G>C1.000
rpoC765085c.1716T>C1.000
rpoC765089c.1720T>C1.000
rpoC765100c.1731G>C1.000
rpoC765103c.1734G>T1.000
rpoC765343c.1974G>A0.895
rpoC765352c.1983G>C1.000
rpoC765356p.Met663Val0.900
rpoC765370c.2001G>C0.867
rpoC765379c.2010G>C0.867
rpoC765382c.2013G>T0.839
rpoC765383p.Met672Leu1.000
rpoC765403c.2034G>C0.979
rpoC765405p.Leu679His1.000
rpoC765409c.2040T>G0.104
rpoC765421c.2052C>G0.914
rpoC765445c.2076G>C0.118
rpoC765449p.Ala694Ser0.855
rpoC765452p.Ala695Thr0.103
rpoC765469c.2100G>C0.877
rpoC765478c.2109T>G0.129
rpoC765480p.Tyr704Phe0.971
rpoC765496c.2127C>G0.108
rpoC765499c.2130C>G1.000
rpoC765517c.2148C>G0.849
rpoC765529c.2160C>T0.114
rpoC765533p.Tyr722His0.975
rpoC765544c.2175C>G0.826
rpoC765547c.2178C>T0.818
rpoC765548c.2179A>T1.000
rpoC765553c.2184C>T1.000
rpoC765556c.2187G>C1.000
rpoC765562c.2193G>T0.143
rpoC765826c.2457T>C0.963
rpoC765835c.2466C>T0.964
rpoC765841c.2472G>T0.903
rpoC765861p.Phe831Tyr0.923
rpoC765875p.Val836Ile0.952
rpoC765907c.2538G>T0.952
rpoC765910c.2541G>C0.950
rpoC765928c.2559C>G0.971
rpoC765940c.2571A>T0.970
rpoC765947c.2578T>C0.968
rpoC765962c.2593T>C0.947
rpoC765967c.2598C>T0.947
rpoC765973c.2604C>G0.947
rpoC765979c.2610C>G0.947
rpoC765982c.2613C>T0.947
rpoC765994c.2625A>T0.938
rpoC766003c.2634G>C0.857
rpoC766009c.2640G>C0.818
rpoC766012c.2643C>G0.800
rpoC766333c.2964G>T0.800
rpoC766345c.2976T>C1.000
rpoC766348c.2979A>G1.000
rpoC766351c.2982C>G0.800
rpoC766353p.Val995Ala0.800
rpoC766369c.3000C>G0.933
rpoC766375c.3006C>G0.933
rpoC766381c.3012C>T1.000
rpoC766384c.3015A>G1.000
rpoC766390c.3021C>T1.000
rpoC766393c.3024C>T0.950
rpoC766408c.3039C>T1.000
rpoC766435p.Glu1022Asp0.977
rpoC766501c.3132G>C0.929
rpoC766507c.3138C>T0.933
rpoC766513c.3144C>T0.933
rpoC766522c.3153C>A0.933
rpoC766528c.3159T>G0.933
rpoC766531c.3162G>C0.933
rpoC766534c.3165C>G0.933
rpoC766537c.3168G>A0.938
rpoC766540p.Asp1057Glu0.882
rpoC766549c.3180G>C0.923
rpoC766570c.3201T>C0.926
rpoC766573c.3204T>G0.962
rpoC766594c.3225G>T0.962
rpoC766607p.Ile1080Leu0.963
rpoC766618c.3249G>T0.923
rpoC766624c.3255G>C0.920
rpoC766630c.3261G>C0.955
rpoC766633c.3264G>C0.909
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.Ala1188Ser0.972
rpoC766942c.3573C>T0.977
rpoC766945c.3576A>C0.978
rpoC766963c.3594T>C0.981
rpoC766996c.3627C>T0.985
rpoC767002c.3633G>C0.986
rpoC767008c.3639G>A0.986
rpoC767023c.3654C>T0.985
rpoC767044c.3675G>C0.917
rpoC767080c.3711G>C0.911
rpoC767095c.3726C>T0.886
rpoC767098c.3729T>C0.977
rpoC767104c.3735C>G0.978
rpoC767107c.3738C>T0.977
rpoC767119c.3750A>G0.963
rpoC767125c.3756G>C0.920
rpoC767134c.3765C>T0.959
rpoC767138c.3769C>T0.960
rpoC767149c.3780C>T0.935
rpoC767158c.3789T>C0.956
rpoC767179c.3810C>T0.935
rpoC767180p.Ala1271Ser0.956
rpoC767191c.3822C>G0.957
rpoC767197c.3828G>A0.957
rpoC767203c.3834C>G0.927
rpoC767206c.3837C>G0.921
rpoC767209c.3840T>C0.921
rpoC767212c.3843G>C0.923
rpoC767221c.3852C>G0.962
rpoC767230c.3861G>C0.981
rpoC767233c.3864T>C0.981
rpoC767254c.3885G>C0.957
rpoC767264p.Ala1299Ser0.971
rpoC767267p.Ala1300Asn0.970
rpoC767281c.3912C>G1.000
rpoC767284c.3915C>G1.000
rpsL781559c.-1G>C0.955
rpsL781572p.Gln5Asn0.963
rpsL781586c.27C>T0.941
rpsL781595c.36T>C1.000
rpsL781608p.Ser17Ala1.000
rpsL781616c.57C>G0.957
rpsL781628c.69T>C1.000
rpsL781649c.90T>C1.000
rpsL781655c.96T>C1.000
rpsL781658c.99A>C1.000
rpsL781670c.111G>C0.961
rpsL781706c.147T>C0.952
rpsL781715c.156T>G1.000
rpsL781766c.207C>T0.636
rpsL781772c.213C>T1.000
rpsL781802c.243G>C0.884
rpsL781808c.249C>T0.111
rpsL781814c.255C>T0.975
rpsL781817c.258G>T0.976
rpsL781829c.270G>C0.976
rpsL781832c.273T>C1.000
rpsL781859c.300T>C0.943
rpsL781868c.309T>C0.969
rpsL781871c.312G>C0.967
rpsL781877c.318T>A0.889
rpsL781892c.333A>G0.957
rpsL781898c.339A>T0.950
rpsL781907c.348T>C0.950
rpsL781916c.357T>C1.000
rpsL781929p.Gly124Ser0.917
rpsL781933374G>A0.900
rrs1471922r.77gt>g0.909
rrs1471925r.80t>c0.900
rrs1471931r.86ga>g0.900
rrs1471934r.89a>g0.900
rrs1471985r.140t>c0.800
rrs1471986r.141c>t0.900
rrs1472106r.261g>a1.000
rrs1472108r.263c>t1.000
rrs1472113r.268t>c0.900
rrs1472150r.305t>a1.000
rrs1472380r.535g>c0.917
rrs1472446r.601t>a1.000
rrs1472452r.607g>a1.000
rrs1472464r.619a>g1.000
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
rrs1473166r.1321g>a0.636
rrl1473756r.99g>t1.000
rrl1473758r.101g>t1.000
rrl1473770r.113t>c1.000
rrl1474494r.837c>cg0.909
rrl1474496r.839c>g0.900
rrl1474497r.840g>c0.900
rrl1474722r.1065t>c1.000
rrl1474743r.1086t>g1.000
rrl1474760r.1103a>g1.000
rrl1474794r.1137c>t1.000
rrl1474803r.1146g>a1.000
rrl1474812r.1155g>a1.000
rrl1474830r.1173a>g1.000
rrl1475120r.1463g>t0.900
rrl1475129r.1472g>a0.909
rrl1476214r.2557g>t1.000
rrl1476215r.2558c>t1.000
rrl1476221r.2564t>c0.900
rrl1476224r.2567a>g1.000
rrl1476251r.2594t>c0.900
rrl1476260r.2603a>g0.182
rrl1476281r.2624t>c0.909
rrl1476529r.2872a>g0.300
rrl1476540r.2883c>t0.308
rrl1476608r.2951c>g0.800
rrl1476619r.2962c>t0.800
rrl1476628r.2971t>a0.900
inhA1674855c.654C>G1.000
inhA1674858c.657G>A1.000
inhA1674876c.675C>T1.000
inhA1674879c.678T>C1.000
inhA1674892p.Asn231Asp0.895
inhA1674903c.702T>C0.895
inhA1674904p.Ala235Pro1.000
inhA1674909c.708G>A0.895
inhA1674912c.711G>C0.895
inhA1674915c.714C>G0.895
inhA1674942c.741T>C1.000
inhA1674949c.748C>T1.000
inhA1674954c.753G>C1.000
inhA1674957c.756G>C1.000
inhA1674963c.762G>C1.000
inhA1674966c.765T>C1.000
inhA1674975c.774C>T0.895
inhA1674977p.Tyr259Phe0.895
inhA1674993c.792G>T1.000
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.Ser19Ala0.952
rpsA1833604c.63C>T0.958
rpsA1833616c.75A>T0.958
rpsA1833619c.78A>C0.960
rpsA1833625c.84A>G0.929
rpsA1833664c.123C>G0.960
rpsA1833676c.135A>G0.958
rpsA1833679c.138G>T0.950
rpsA1833685c.144G>C0.938
rpsA1833691c.150G>A0.833
rpsA1833694c.153G>T0.133
rpsA1833697c.156C>T1.000
rpsA1833700c.159C>T0.875
rpsA1833709c.168C>T0.900
rpsA1833724c.183C>T1.000
rpsA1833727c.186G>C1.000
rpsA1833733c.192C>G1.000
rpsA1833734p.Ala65Ser1.000
rpsA1833742c.201A>G0.938
rpsA1833745c.204G>C1.000
rpsA1833748c.207C>G0.938
rpsA1833760c.219C>T1.000
rpsA1833787c.246C>G1.000
rpsA1833790c.249T>C1.000
rpsA1833802c.261A>G1.000
rpsA1833811c.270G>T1.000
rpsA1833823c.282G>A0.962
rpsA1833832c.291G>A1.000
rpsA1833838c.297G>C0.957
rpsA1833841c.300C>G1.000
rpsA1833847c.306C>G1.000
rpsA1833856c.315A>G1.000
rpsA1833862c.321G>T1.000
rpsA1833874c.333T>G0.931
rpsA1833886c.345C>G0.909
rpsA1833894p.Ala118Glu1.000
rpsA1833928c.387G>C1.000
rpsA1833949c.408T>C1.000
rpsA1833961c.420C>G0.935
rpsA1833970c.429G>T1.000
rpsA1833979c.438T>C1.000
rpsA1833991c.450C>G1.000
rpsA1834000c.459G>C1.000
rpsA1834009c.468C>T1.000
rpsA1834012c.471G>C1.000
rpsA1834015c.474G>C1.000
rpsA1834021c.480C>T1.000
rpsA1834030c.489C>G1.000
rpsA1834033c.492C>T0.875
rpsA1834073p.Lys178Arg0.867
rpsA1834096c.555G>C0.808
rpsA1834097p.Ser186Arg0.192
rpsA1834102c.561T>C0.208
rpsA1834108c.567C>G0.739
rpsA1834114c.573G>C0.727
rpsA1834177c.636A>C1.000
rpsA1834189c.648G>C0.226
rpsA1834213c.672G>C0.171
rpsA1834228c.687C>A0.769
rpsA1834231c.690T>G0.792
rpsA1834234c.693G>T0.200
rpsA1834240c.699T>C0.920
rpsA1834246c.705G>T0.120
rpsA1834249c.708T>C0.960
rpsA1834252c.711C>G0.923
rpsA1834261c.720A>G0.939
rpsA1834264c.723G>C0.943
rpsA1834279c.738C>T0.939
rpsA1834294c.753G>T0.871
rpsA1834297c.756C>T0.971
rpsA1834303c.762T>G0.970
rpsA1834306c.765T>C0.971
rpsA1834327c.786G>T0.911
rpsA1834357c.816T>C0.933
rpsA1834366c.825A>G0.977
rpsA1834375c.834G>C0.935
rpsA1834396c.855G>C0.977
rpsA1834411c.870T>G0.972
rpsA1834414c.873C>T0.944
rpsA1834417c.876G>C0.944
rpsA1834420c.879C>T0.944
rpsA1834423c.882G>C1.000
rpsA1834429c.888C>T0.950
rpsA1834438c.897C>T0.956
rpsA1834451c.910T>C1.000
rpsA1834456c.915T>G1.000
rpsA1834468c.927A>G1.000
rpsA1834477c.936C>T0.919
rpsA1834489c.948T>C1.000
rpsA1834519c.978G>C0.880
rpsA1834520p.Ala327Ser1.000
rpsA1834528c.987T>C1.000
rpsA1834534c.993C>T0.880
rpsA1834543c.1002C>G1.000
rpsA1834546c.1005T>C1.000
rpsA1834552c.1011G>T0.909
rpsA1834555c.1014T>G1.000
rpsA1834557p.Ala339Gly0.905
rpsA1834606c.1065C>T0.971
rpsA1834609c.1068T>C0.971
rpsA1834619c.1078T>C0.960
rpsA1834622c.1081T>A0.960
rpsA1834633c.1092A>G0.968
rpsA1834639c.1098T>C0.969
rpsA1834645c.1104C>T0.912
rpsA1834666c.1125G>C0.971
rpsA1834667p.Ala376Ser0.971
rpsA1834690c.1149T>C0.977
rpsA1834700p.Gln387Ala0.882
rpsA1834705c.1164C>G0.857
rpsA1834720c.1179C>G0.921
rpsA1834732c.1191T>C1.000
rpsA1834738c.1197A>G1.000
rpsA1834753c.1212T>C1.000
rpsA1834759c.1218A>C1.000
rpsA1834765p.Glu408Asp1.000
rpsA1834774c.1233C>T1.000
rpsA1834776p.Ala412Glu1.000
rpsA1834780c.1239A>G1.000
rpsA1834789c.1248T>C1.000
rpsA1834813c.1272G>T0.920
rpsA1834830p.Ala430Val1.000
kasA2518723c.609G>A0.727
kasA2518726c.612G>C0.167
kasA2518738c.624G>C0.926
kasA2518756c.642G>C1.000
kasA2518768c.654C>G0.946
kasA2518771c.657C>G0.946
kasA2518774c.660C>T0.946
kasA2518783c.669T>G1.000
kasA2518787p.Arg225Lys1.000
kasA2518792c.678C>T0.944
kasA2518795c.681C>T0.974
kasA2518798c.684G>C0.921
kasA2518822c.708C>A0.935
kasA2518825c.711T>C0.984
kasA2518846c.732G>T0.947
kasA2518849c.735G>C0.945
kasA2518853p.Leu247Val0.981
kasA2518864c.750G>C0.980
thyX3067376c.570C>G0.700
thyX3067403c.543G>C0.700
thyX3067406c.540T>C0.700
thyX3067415c.531G>A0.700
embC4240729c.867C>G0.965
embC4240735c.873C>G0.967
embC4240741c.879C>T0.969
embC4240756c.894G>C0.971
embC4240771c.909G>C0.965
embC4240772p.Ser304Ala0.965
embC4240778p.His306Gly0.982
embC4240781p.Ala307Ser0.982
embC4240789c.927T>C1.000
embC4240819c.957A>C0.986
embC4240826p.Ala322Ser0.971
embC4240831c.969T>G0.985
embC4240856p.Ala332Thr0.951
embC4240859p.Leu333Ile0.950
embC4240876c.1014C>T0.933
embC4240879c.1017G>T0.966
embC4240885c.1023T>C0.966
embC4240886p.Ile342Val0.966
embC4240897c.1035C>G0.962
embC4240900c.1038A>G0.960
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
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