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: 5d2588c75c9ad
Sample: 5d2588c75c9ad

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Summary
ID: 5d2588c75c9ad
Date: Wed Jul 10 07:44:50 2019
Strain: lineage2.2.1;lineage4.4.2
Drug-resistance: Sensitive

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

Lineage2FamilyMain SpoligotypeRDS
lineage2East-AsianBeijingRD105
lineage2.2East-Asian (Beijing)Beijing-RD207RD105;RD207
lineage4.4.2Euro-AmericanT1;T2None
lineage2.2.1East-Asian (Beijing)Beijing-RD181RD105;RD207;RD181

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>C1.000
gyrB6673c.1434A>C1.000
gyrB6676c.1437T>G1.000
gyrB6703c.1464G>C1.000
gyrB6706c.1467G>A1.000
gyrB6709c.1470A>G1.000
gyrB6712c.1473G>C1.000
gyrB6727c.1488G>T1.000
gyrB6728c.1489C>T1.000
gyrB6739c.1500C>T1.000
gyrB6745c.1506T>C1.000
gyrB6754c.1515C>T1.000
gyrB6763c.1524G>C1.000
gyrB6772c.1533C>G1.000
gyrB6775c.1536G>C1.000
gyrB6793c.1554T>C1.000
gyrB6798p.Gly520Ala1.000
gyrB6808c.1569C>G1.000
gyrB6824c.1585C>T1.000
gyrB6841c.1602T>C1.000
gyrB6862c.1623C>G1.000
gyrB6869c.1630T>C1.000
gyrB6872c.1633T>C1.000
gyrB6878c.1639T>C1.000
gyrB6889c.1650G>A1.000
gyrB6898c.1659G>T1.000
gyrA7499c.198G>C1.000
gyrA7511c.210C>T0.970
gyrA7523c.222C>G1.000
gyrA7526c.225G>A1.000
gyrA7547c.246C>T1.000
gyrA7553c.252C>T1.000
gyrA7559c.258G>C1.000
gyrA7565c.264C>T1.000
gyrA7574c.273G>C1.000
gyrA7585p.Ser95Thr1.000
gyrA7589c.288G>C1.000
gyrA7595c.294C>T1.000
gyrA7607c.306C>T1.000
gyrA7637c.336C>A1.000
gyrA8121c.820T>C1.000
gyrA8129c.828T>C1.000
gyrA8156c.855T>C1.000
gyrA8159c.858G>C1.000
gyrA8168c.867A>G1.000
gyrA8174c.873C>G1.000
gyrA8177c.876A>C1.000
gyrA8187p.Leu296Ile1.000
gyrA8192c.891C>G1.000
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>T1.000
gyrA8330c.1029C>G1.000
gyrA8339c.1038A>G1.000
gyrA8340p.Ala347Ser1.000
gyrA8354c.1053G>C1.000
gyrA8382c.1081C>T1.000
gyrA8783c.1482G>C0.917
gyrA8786c.1485T>G0.929
gyrA8792c.1491G>C0.938
gyrA8799p.Ala500Ser0.944
gyrA8810c.1509A>G0.958
gyrA8817p.Ser506Ala0.958
gyrA8828c.1527T>C0.958
gyrA8829c.1528T>C0.958
gyrA8837c.1536C>G0.969
gyrA8846c.1545C>T0.972
gyrA8852c.1551T>C0.977
gyrA8858c.1557T>C0.977
gyrA8870c.1569G>C1.000
gyrA8873c.1572A>G1.000
gyrA8897c.1596T>C1.000
gyrA8903c.1602T>C1.000
gyrA8915c.1614A>G1.000
gyrA8942c.1641G>T1.000
gyrA8945c.1644G>C1.000
gyrA8946c.1645T>C0.981
gyrA8957c.1656C>T0.979
gyrA8967p.Ala556Lys0.978
gyrA8978c.1677C>T0.976
gyrA8987c.1686C>G0.967
gyrA8990c.1689C>G0.964
gyrA8993c.1692C>T0.964
gyrA8996c.1695T>C0.964
gyrA8998p.Leu566Trp0.964
gyrA9018p.Gln573Lys0.941
gyrA9023c.1722A>C0.933
gyrA9026c.1725G>C0.933
gyrA9029c.1728T>C0.933
gyrA9035c.1734G>C0.933
gyrA9044c.1743C>G0.900
gyrA9047c.1746C>T0.900
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.Asp108Glu0.966
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.Thr184Ser0.923
rpoB760361c.555T>C0.933
rpoB760370c.564C>G0.941
rpoB760376p.Asp190Glu0.947
rpoB760382c.576G>C0.947
rpoB760388c.582C>T0.958
rpoB760400c.594G>C0.969
rpoB760406c.600G>C0.821
rpoB760407p.Ser201Gly0.970
rpoB760415c.609C>T0.976
rpoB760418c.612G>C0.976
rpoB760430c.624T>C0.979
rpoB760460c.654G>C0.983
rpoB760475c.669A>G0.982
rpoB760481c.675G>C0.982
rpoB760484c.678A>G0.982
rpoB760502c.696C>G1.000
rpoB760522p.Ser239Asn1.000
rpoB760532c.726T>C1.000
rpoB760541c.735G>C1.000
rpoB760567p.Ser254Trp1.000
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>C1.000
rpoB760646c.840C>G1.000
rpoB760655c.849A>G1.000
rpoB760661c.855A>G1.000
rpoB760668p.Thr288Ala1.000
rpoB760674c.868T>C1.000
rpoB760679c.873A>G1.000
rpoB760683c.877T>C1.000
rpoB760703c.897C>T1.000
rpoB760721c.915C>G1.000
rpoB760727c.921C>G1.000
rpoB760730c.924T>C1.000
rpoB760736c.930C>G1.000
rpoB760817c.1011A>G1.000
rpoB760820c.1014T>C1.000
rpoB760826c.1020C>G1.000
rpoB760830c.1024T>C1.000
rpoB760841c.1035T>C1.000
rpoB760858p.Val351Ala0.964
rpoB760862c.1056G>C0.964
rpoB760865c.1059C>T0.929
rpoB760886p.Glu360Asp0.975
rpoB760887p.Thr361Val0.976
rpoB760910c.1104C>T0.979
rpoB760916c.1110C>T0.979
rpoB760928c.1122G>C0.977
rpoB760943c.1137C>T0.953
rpoB760946c.1140A>G0.976
rpoB760965p.Met387Leu0.973
rpoB760970c.1164G>C0.971
rpoB760973c.1167G>T0.970
rpoB760982c.1176G>C0.962
rpoB760985c.1179G>C0.962
rpoB760988c.1182C>G0.960
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>C1.000
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>C1.000
rpoB761234c.1428G>C0.987
rpoB761249c.1443A>G0.987
rpoB761255c.1449T>G0.985
rpoB761258c.1452G>A0.985
rpoB761261c.1455G>C0.985
rpoB761264c.1458C>G0.985
rpoB761273c.1467T>C0.988
rpoB761303c.1497G>C0.986
rpoB761318c.1512G>T0.968
rpoB761327c.1521A>G0.983
rpoB761333c.1527G>T0.982
rpoB761339c.1533C>G0.982
rpoB761345c.1539G>C0.933
rpoB761346p.Val514Ser0.929
rpoB761354c.1548C>A0.929
rpoB761357c.1551G>T0.929
rpoB761360c.1554T>C0.929
rpoB761362p.Ser519Thr0.929
rpoB761373p.Val523His0.929
rpoB761384c.1578C>G0.929
rpoB761393c.1587G>A0.929
rpoB761414c.1608A>G0.909
rpoB761510c.1704T>C0.800
rpoB761516c.1710G>C0.926
rpoB761528c.1722C>T0.929
rpoB761531c.1725C>T0.964
rpoB761537c.1731C>G0.967
rpoB761555c.1749G>C0.973
rpoB761558c.1752C>G0.951
rpoB761564c.1758G>C0.952
rpoB761570c.1764T>C0.935
rpoB761573c.1767C>G0.896
rpoB761579c.1773G>C0.962
rpoB761612c.1806G>T0.967
rpoB761615c.1809A>C0.967
rpoB761636c.1830G>T0.961
rpoB761645c.1839C>G0.959
rpoB761657c.1851C>T0.957
rpoB761666c.1860G>C0.969
rpoB761669c.1863C>T0.968
rpoB761675c.1869G>T0.967
rpoB761681c.1875G>A0.966
rpoB761682c.1876C>T0.966
rpoB761687c.1881C>T0.964
rpoB761690c.1884G>C0.964
rpoB761693c.1887G>C0.964
rpoB761705c.1899C>A1.000
rpoB761891c.2085G>C0.958
rpoB761909c.2103T>C0.929
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>G1.000
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
rpoB762137c.2331C>T1.000
rpoB762140c.2334G>C1.000
rpoB762143c.2337T>C1.000
rpoB762149c.2343G>T1.000
rpoB762158c.2352G>C1.000
rpoB762167c.2361T>C0.978
rpoB762176c.2370T>C0.979
rpoB762185c.2379G>C0.980
rpoB762194c.2388G>C0.982
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>C1.000
rpoB762317c.2511A>G1.000
rpoB762323c.2517C>A1.000
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>G0.909
rpoB762510p.Ala902Pro0.909
rpoB762515c.2709C>T0.952
rpoB762533c.2727T>C0.923
rpoB762536c.2730T>C0.917
rpoB762537c.2731T>C0.917
rpoB762551c.2745C>T0.900
rpoB762827c.3021G>C1.000
rpoB762830c.3024C>G1.000
rpoB762857c.3051C>G1.000
rpoB762860c.3054G>C1.000
rpoB762863c.3057T>C1.000
rpoB762866c.3060C>T1.000
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>T0.980
rpoB763031c.3225T>G1.000
rpoB763034c.3228C>G0.979
rpoB763040c.3234C>G0.979
rpoB763070c.3264T>C0.979
rpoB763082c.3276C>T0.976
rpoB763088c.3282C>G0.976
rpoB763094c.3288G>C0.977
rpoB763115c.3309T>C1.000
rpoB763127c.3321G>C1.000
rpoB763136c.3330C>T1.000
rpoB763145c.3339G>A1.000
rpoB763157c.3351G>T1.000
rpoB763166c.3360A>G1.000
rpoB763172c.3366G>C1.000
rpoB763193c.3387C>G1.000
rpoC763443p.Tyr25Phe0.800
rpoC763450c.81G>A0.947
rpoC763456c.87A>G0.913
rpoC763468c.99G>C0.923
rpoC763486c.117T>C0.947
rpoC763492c.123G>C0.949
rpoC763528c.159G>A0.977
rpoC763531c.162G>T0.976
rpoC763546c.177A>G0.977
rpoC763570c.201G>C0.977
rpoC763594c.225C>T0.976
rpoC763633c.264T>C0.971
rpoC763657c.288G>A0.964
rpoC763660c.291T>G0.963
rpoC763666c.297G>C0.960
rpoC763669c.300C>G0.960
rpoC763675c.306C>G0.957
rpoC763696c.327T>C0.857
rpoC763699c.330G>T0.857
rpoC763702c.333C>G0.846
rpoC763708c.339G>C0.846
rpoC763711c.342G>C0.846
rpoC763714c.345G>C0.846
rpoC763717c.348T>C0.846
rpoC763723c.354G>C0.917
rpoC763732c.363C>A0.917
rpoC763741c.372C>T0.917
rpoC763744c.375G>C0.917
rpoC763747c.378G>A0.917
rpoC763870c.501C>T0.909
rpoC763872p.Gly168Ala0.909
rpoC763876p.Glu169Asp0.917
rpoC763879c.510A>G0.917
rpoC763888c.519G>T0.923
rpoC763891c.522G>C0.929
rpoC763894c.525A>G0.929
rpoC763900c.531G>C0.970
rpoC763933c.564C>T0.974
rpoC763940p.Ala191Ser0.974
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>T1.000
rpoC764059c.690G>T1.000
rpoC764083c.714A>G1.000
rpoC764084p.Asn239Val1.000
rpoC764095c.726C>T1.000
rpoC764098c.729A>G1.000
rpoC764110c.741C>T1.000
rpoC764143c.774G>C1.000
rpoC764147p.Ser260Ala1.000
rpoC764150p.Ile261Val1.000
rpoC764165p.Glu266Gln1.000
rpoC764311c.942C>G0.909
rpoC764317c.948C>G0.923
rpoC764320c.951C>G0.929
rpoC764338c.969G>A1.000
rpoC764353c.984G>T1.000
rpoC764365c.996C>T1.000
rpoC764371c.1002G>C1.000
rpoC764377c.1008C>G1.000
rpoC764380c.1011G>C1.000
rpoC764387c.1018T>C1.000
rpoC764405c.1036A>C1.000
rpoC764428c.1059G>C1.000
rpoC764431c.1062G>C1.000
rpoC764434c.1065A>G1.000
rpoC764435c.1066A>C1.000
rpoC764458c.1089G>C1.000
rpoC764461c.1092A>G1.000
rpoC764470c.1101C>T0.979
rpoC764497c.1128A>G0.960
rpoC764510c.1141C>T0.959
rpoC764524c.1155C>G0.957
rpoC764530c.1161C>G0.950
rpoC764534c.1165C>A0.947
rpoC764539c.1170C>T0.946
rpoC764542c.1173C>T0.949
rpoC764545c.1176C>A0.950
rpoC764560c.1191T>C0.964
rpoC764575c.1206T>G0.964
rpoC764611c.1242G>T0.953
rpoC764626c.1257C>T0.966
rpoC764632c.1263T>C0.966
rpoC764650c.1281G>T0.985
rpoC764668c.1299C>T0.985
rpoC764692c.1323C>T0.985
rpoC764713c.1344G>T0.985
rpoC764716c.1347G>C0.968
rpoC764746c.1377G>T0.984
rpoC764752c.1383G>C0.984
rpoC764758c.1389C>G0.983
rpoC764764c.1395T>C1.000
rpoC764791c.1422C>G1.000
rpoC764803c.1434C>T1.000
rpoC764809c.1440C>T1.000
rpoC764810p.Pro481Ala1.000
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>A1.000
rpoC764948c.1579T>C1.000
rpoC764968c.1599T>C1.000
rpoC765004c.1635G>C0.950
rpoC765007c.1638T>G0.950
rpoC765008c.1639T>C0.950
rpoC765011c.1642A>T0.950
rpoC765016c.1647C>G0.952
rpoC765019c.1650A>G0.955
rpoC765040c.1671T>C0.966
rpoC765041c.1672T>C0.966
rpoC765047c.1678T>C0.966
rpoC765055c.1686C>G0.966
rpoC765073c.1704G>C0.941
rpoC765076c.1707A>G0.933
rpoC765079c.1710T>G0.923
rpoC765082c.1713G>C0.923
rpoC765085c.1716T>C0.923
rpoC765089c.1720T>C0.917
rpoC765100c.1731G>C0.923
rpoC765103c.1734G>T0.923
rpoC765121c.1752G>T0.909
rpoC765129p.Tyr587Phe0.909
rpoC765343c.1974G>A1.000
rpoC765352c.1983G>C1.000
rpoC765356p.Met663Val1.000
rpoC765370c.2001G>C1.000
rpoC765379c.2010G>C1.000
rpoC765382c.2013G>T1.000
rpoC765383p.Met672Leu1.000
rpoC765403c.2034G>C1.000
rpoC765405p.Leu679His0.971
rpoC765409c.2040T>G1.000
rpoC765421c.2052C>G1.000
rpoC765449p.Ala694Ser1.000
rpoC765454c.2085C>G1.000
rpoC765469c.2100G>C1.000
rpoC765478c.2109T>G1.000
rpoC765480p.Tyr704Phe1.000
rpoC765499c.2130C>G1.000
rpoC765517c.2148C>G1.000
rpoC765533p.Tyr722His1.000
rpoC765544c.2175C>G1.000
rpoC765547c.2178C>T1.000
rpoC765548c.2179A>T1.000
rpoC765553c.2184C>T1.000
rpoC765556c.2187G>C1.000
rpoC765562c.2193G>T1.000
rpoC765826c.2457T>C1.000
rpoC765835c.2466C>T1.000
rpoC765841c.2472G>T1.000
rpoC765861p.Phe831Tyr1.000
rpoC765875p.Val836Ile1.000
rpoC765886c.2517C>T1.000
rpoC765907c.2538G>T1.000
rpoC765910c.2541G>C1.000
rpoC765928c.2559C>G1.000
rpoC765940c.2571A>T0.970
rpoC765947c.2578T>C1.000
rpoC765962c.2593T>C1.000
rpoC765967c.2598C>T1.000
rpoC765973c.2604C>G1.000
rpoC765979c.2610C>G1.000
rpoC765982c.2613C>T1.000
rpoC765994c.2625A>T1.000
rpoC766003c.2634G>C1.000
rpoC766345c.2976T>C1.000
rpoC766348c.2979A>G1.000
rpoC766351c.2982C>G1.000
rpoC766353p.Val995Ala1.000
rpoC766369c.3000C>G1.000
rpoC766375c.3006C>G1.000
rpoC766381c.3012C>T1.000
rpoC766384c.3015A>G1.000
rpoC766390c.3021C>T1.000
rpoC766393c.3024C>T1.000
rpoC766408c.3039C>T1.000
rpoC766435p.Glu1022Asp1.000
rpoC766507c.3138C>T1.000
rpoC766513c.3144C>T0.923
rpoC766522c.3153C>A0.923
rpoC766528c.3159T>G0.923
rpoC766531c.3162G>C0.923
rpoC766534c.3165C>G0.923
rpoC766537c.3168G>A0.923
rpoC766540p.Asp1057Glu0.923
rpoC766549c.3180G>C0.950
rpoC766570c.3201T>C0.950
rpoC766573c.3204T>G0.950
rpoC766588c.3219G>A0.950
rpoC766594c.3225G>T0.950
rpoC766607p.Ile1080Leu0.950
rpoC766618c.3249G>T0.947
rpoC766624c.3255G>C0.933
rpoC766630c.3261G>C0.933
rpoC766633c.3264G>C0.933
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>T0.963
rpoC766861c.3492G>C0.963
rpoC766867c.3498C>G0.963
rpoC766876c.3507C>T0.963
rpoC766931p.Ala1188Ser0.923
rpoC766942c.3573C>T0.938
rpoC766945c.3576A>C0.938
rpoC766963c.3594T>C0.931
rpoC766996c.3627C>T0.940
rpoC767002c.3633G>C0.942
rpoC767008c.3639G>A0.957
rpoC767023c.3654C>T0.956
rpoC767044c.3675G>C0.969
rpoC767080c.3711G>C1.000
rpoC767098c.3729T>C1.000
rpoC767104c.3735C>G1.000
rpoC767107c.3738C>T1.000
rpoC767119c.3750A>G0.983
rpoC767125c.3756G>C0.982
rpoC767134c.3765C>T0.984
rpoC767138c.3769C>T0.985
rpoC767149c.3780C>T0.969
rpoC767158c.3789T>C0.968
rpoC767179c.3810C>T0.967
rpoC767180p.Ala1271Ser0.967
rpoC767191c.3822C>G0.971
rpoC767197c.3828G>A0.970
rpoC767203c.3834C>G0.966
rpoC767206c.3837C>G0.966
rpoC767209c.3840T>C0.950
rpoC767212c.3843G>C0.952
rpoC767221c.3852C>G0.960
rpoC767230c.3861G>C0.970
rpoC767233c.3864T>C0.969
rpoC767254c.3885G>C0.965
rpoC767264p.Ala1299Ser0.955
rpoC767267p.Ala1300Asn0.955
rpoC767281c.3912C>G0.950
rpoC767284c.3915C>G0.950
rpsL781559c.-1G>C0.964
rpsL781572p.Gln5Asn0.969
rpsL781586c.27C>T0.974
rpsL781595c.36T>C0.976
rpsL781608p.Ser17Ala0.978
rpsL781616c.57C>G0.981
rpsL781628c.69T>C0.982
rpsL781649c.90T>C0.984
rpsL781655c.96T>C0.983
rpsL781658c.99A>C0.983
rpsL781670c.111G>C0.982
rpsL781706c.147T>C1.000
rpsL781715c.156T>G0.971
rpsL781772c.213C>T0.968
rpsL781802c.243G>C0.971
rpsL781814c.255C>T0.971
rpsL781817c.258G>T0.972
rpsL781829c.270G>C0.977
rpsL781832c.273T>C0.977
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
rrs1472251r.406g>a1.000
rrs1472337r.492c>g1.000
rrs1472380r.535g>c1.000
rrs1472446r.601t>a1.000
rrs1472452r.607g>a1.000
rrs1472464r.619a>g1.000
rrs1472734r.889c>t1.000
rrs1472741r.896g>a1.000
rrs1472989r.1144g>a0.900
rrs1472990r.1145a>g0.900
rrs1473121r.1276t>c0.800
rrs1473145r.1300c>t1.000
rrs1473166r.1321g>a1.000
rrl1473876r.219g>a1.000
rrl1473887r.230t>c1.000
rrl1473888r.231t>c1.000
rrl1474151r.494c>t1.000
rrl1474181r.524c>ct0.923
rrl1474184r.527c>a1.000
rrl1474185r.528ga>g1.000
rrl1474249r.592g>t1.000
rrl1474263r.606g>a1.000
rrl1474626r.969t>c1.000
rrl1474632r.975g>t1.000
rrl1474636r.979a>t1.000
rrl1474637r.980c>t1.000
rrl1474638r.981c>g1.000
rrl1474639r.982g>t1.000
rrl1474640r.983c>t1.000
rrl1474812r.1155g>a1.000
rrl1474830r.1173a>g1.000
rrl1475061r.1404ca>c1.000
rrl1475076r.1419c>a1.000
rrl1475090r.1433a>t1.000
rrl1475114r.1457c>t1.000
rrl1475120r.1463g>t1.000
rrl1475129r.1472g>a1.000
rrl1476221r.2564t>c1.000
rrl1476224r.2567a>g1.000
rrl1476251r.2594t>c1.000
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
inhA1674876c.675C>T1.000
inhA1674879c.678T>C1.000
inhA1674892p.Asn231Asp1.000
inhA1674903c.702T>C1.000
inhA1674904p.Ala235Pro1.000
inhA1674909c.708G>A1.000
inhA1674912c.711G>C1.000
inhA1674915c.714C>G1.000
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>T1.000
inhA1674977p.Tyr259Phe1.000
inhA1674993c.792G>T1.000
rpsA1833536c.-6A>C1.000
rpsA1833538c.-4CA>C1.000
rpsA1833541c.-1T>C0.909
rpsA1833547c.6G>A1.000
rpsA1833589c.48A>C0.950
rpsA1833595c.54T>G0.950
rpsA1833596p.Ser19Ala0.950
rpsA1833604c.63C>T0.962
rpsA1833616c.75A>T0.966
rpsA1833619c.78A>C0.967
rpsA1833625c.84A>G0.971
rpsA1833664c.123C>G0.971
rpsA1833676c.135A>G0.969
rpsA1833679c.138G>T0.967
rpsA1833685c.144G>C0.935
rpsA1833691c.150G>A0.935
rpsA1833694c.153G>T0.933
rpsA1833697c.156C>T0.931
rpsA1833700c.159C>T0.931
rpsA1833709c.168C>T0.949
rpsA1833724c.183C>T0.941
rpsA1833727c.186G>C0.968
rpsA1833733c.192C>G0.966
rpsA1833734p.Ala65Ser0.966
rpsA1833742c.201A>G0.968
rpsA1833745c.204G>C0.968
rpsA1833748c.207C>G0.968
rpsA1833760c.219C>T0.971
rpsA1833787c.246C>G0.974
rpsA1833790c.249T>C0.974
rpsA1833802c.261A>G0.977
rpsA1833811c.270G>T0.978
rpsA1833823c.282G>A0.980
rpsA1833832c.291G>A1.000
rpsA1833838c.297G>C1.000
rpsA1833841c.300C>G1.000
rpsA1833847c.306C>G1.000
rpsA1833856c.315A>G1.000
rpsA1833862c.321G>T1.000
rpsA1833874c.333T>G0.982
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>T1.000
rpsA1834012c.471G>C1.000
rpsA1834015c.474G>C1.000
rpsA1834021c.480C>T1.000
rpsA1834030c.489C>G1.000
rpsA1834033c.492C>T1.000
rpsA1834073p.Lys178Arg1.000
rpsA1834096c.555G>C1.000
rpsA1834099c.558C>G1.000
rpsA1834108c.567C>G1.000
rpsA1834114c.573G>C1.000
rpsA1834177c.636A>C1.000
rpsA1834228c.687C>A1.000
rpsA1834231c.690T>G1.000
rpsA1834234c.693G>T1.000
rpsA1834240c.699T>C1.000
rpsA1834246c.705G>T1.000
rpsA1834249c.708T>C1.000
rpsA1834252c.711C>G1.000
rpsA1834261c.720A>G1.000
rpsA1834264c.723G>C1.000
rpsA1834279c.738C>T1.000
rpsA1834294c.753G>T0.974
rpsA1834297c.756C>T1.000
rpsA1834303c.762T>G1.000
rpsA1834306c.765T>C0.976
rpsA1834327c.786G>T0.979
rpsA1834357c.816T>C0.978
rpsA1834366c.825A>G0.979
rpsA1834375c.834G>C1.000
rpsA1834396c.855G>C1.000
rpsA1834411c.870T>G1.000
rpsA1834414c.873C>T1.000
rpsA1834417c.876G>C1.000
rpsA1834420c.879C>T1.000
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>C0.972
rpsA1834520p.Ala327Ser0.972
rpsA1834528c.987T>C0.973
rpsA1834534c.993C>T0.973
rpsA1834543c.1002C>G0.973
rpsA1834546c.1005T>C0.973
rpsA1834552c.1011G>T0.971
rpsA1834555c.1014T>G0.971
rpsA1834557p.Ala339Gly0.971
rpsA1834606c.1065C>T0.980
rpsA1834609c.1068T>C0.978
rpsA1834619c.1078T>C0.972
rpsA1834622c.1081T>A0.971
rpsA1834633c.1092A>G0.978
rpsA1834639c.1098T>C0.980
rpsA1834645c.1104C>T0.980
rpsA1834666c.1125G>C0.980
rpsA1834667p.Ala376Ser1.000
rpsA1834690c.1149T>C1.000
rpsA1834700p.Gln387Ala0.956
rpsA1834705c.1164C>G0.978
rpsA1834720c.1179C>G0.982
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>T1.000
rpsA1834830p.Ala430Val1.000
kasA2518738c.624G>C1.000
kasA2518756c.642G>C1.000
kasA2518768c.654C>G1.000
kasA2518771c.657C>G1.000
kasA2518774c.660C>T1.000
kasA2518783c.669T>G1.000
kasA2518787p.Arg225Lys1.000
kasA2518792c.678C>T1.000
kasA2518795c.681C>T1.000
kasA2518798c.684G>C1.000
kasA2518822c.708C>A1.000
kasA2518825c.711T>C1.000
kasA2518846c.732G>T1.000
kasA2518849c.735G>C1.000
kasA2518853p.Leu247Val1.000
kasA2518864c.750G>C1.000
panD4044138c.144A>G1.000
panD4044150c.132T>G0.950
panD4044156c.126T>C1.000
panD4044167c.115G>A1.000
panD4044171c.111G>A1.000
panD4044174c.108G>A1.000
panD4044180p.Asp34Glu1.000
panD4044188c.94C>G1.000
panD4044189c.93G>A1.000
panD4044194p.Ala30Pro1.000
panD4044195c.87A>G1.000
panD4044233p.Cys17His1.000
panD4044234c.48G>C1.000
panD4044249c.33G>A1.000
panD4044266p.Leu6Met1.000
panD4044273c.9C>G1.000
panD4044276p.Leu2Phe1.000
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>G1.000
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
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