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: 5d2c3b25eb052
Sample: 5d2c3b25eb052

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Summary
ID: 5d2c3b25eb052
Date: Mon Jul 15 09:39:54 2019
Strain: lineage1
Drug-resistance: Sensitive

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

Lineage2FamilyMain SpoligotypeRDS
lineage1Indo-OceanicEAIRD239

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6097c.858G>A0.176
gyrB6100c.861G>A0.176
gyrB6109c.870G>C0.158
gyrB6115c.876A>G1.000
gyrB6121c.882C>T0.842
gyrB6123p.Ala295Gly0.158
gyrB6127c.888G>C0.158
gyrB6130c.891T>C0.158
gyrB6133c.894G>C1.000
gyrB6136c.897G>A0.842
gyrB6151c.912C>T0.842
gyrB6172c.933C>T0.842
gyrB6175c.936G>A0.158
gyrB6181c.942C>A0.158
gyrB6184c.945C>T1.000
gyrB6193c.954G>A0.800
gyrB6655c.1416T>C1.000
gyrB6673c.1434A>C1.000
gyrB6676c.1437T>G1.000
gyrB6703c.1464G>C1.000
gyrB6706c.1467G>A0.950
gyrB6709c.1470A>G1.000
gyrB6712c.1473G>C0.952
gyrB6727c.1488G>T0.909
gyrB6728c.1489C>T0.957
gyrB6739c.1500C>T0.821
gyrB6745c.1506T>C0.966
gyrB6754c.1515C>T0.857
gyrB6760c.1521G>C0.118
gyrB6763c.1524G>C0.886
gyrB6772c.1533C>G0.842
gyrB6775c.1536G>C0.919
gyrB6793c.1554T>C0.974
gyrB6798p.Gly520Ala0.974
gyrB6808c.1569C>G0.972
gyrB6824c.1585C>T0.886
gyrB6841c.1602T>C0.970
gyrB6862c.1623C>G0.906
gyrB6869c.1630T>C1.000
gyrB6872c.1633T>C1.000
gyrB6878c.1639T>C1.000
gyrB6889c.1650G>A1.000
gyrB6898c.1659G>T1.000
gyrB7006c.1767T>G0.600
gyrB7010p.Leu591Ile0.600
gyrB7015c.1776G>A0.600
gyrB7018c.1779G>C0.600
gyrB7024c.1785G>C0.900
gyrB7033c.1794G>C0.900
gyrB7051p.Glu604Asp0.900
gyrB7060c.1821T>C0.900
gyrB7066c.1827G>T0.900
gyrB7078c.1839A>G0.900
gyrB7081c.1842T>C0.900
gyrB7084c.1845A>G0.900
gyrB7090c.1851C>T0.900
gyrB7093c.1854T>C0.900
gyrB7100c.1861T>C0.900
gyrB7108c.1869G>A0.333
gyrA7433c.132G>A1.000
gyrA7442c.141G>C1.000
gyrA7457c.156T>C1.000
gyrA7463c.162G>C1.000
gyrA7472c.171T>C1.000
gyrA7475c.174A>G1.000
gyrA7480p.Phe60Tyr1.000
gyrA7484c.183T>C1.000
gyrA7499c.198G>C1.000
gyrA7511c.210C>T0.489
gyrA7523c.222C>G0.512
gyrA7526c.225G>A0.477
gyrA7532c.231T>G0.412
gyrA7541c.240C>G0.385
gyrA7547c.246C>T1.000
gyrA7553c.252C>T0.660
gyrA7559c.258G>C0.667
gyrA7565c.264C>T1.000
gyrA7569p.Ala90Ser0.283
gyrA7574c.273G>C0.745
gyrA7585p.Ser95Thr1.000
gyrA7589c.288G>C0.760
gyrA7592c.291G>C0.216
gyrA7595c.294C>T0.224
gyrA7601c.300C>T0.239
gyrA7607c.306C>T0.227
gyrA7613c.312G>A0.190
gyrA7622c.321C>T0.154
gyrA7637c.336C>A1.000
gyrA7728c.427A>C0.909
gyrA7763c.462T>G0.941
gyrA7775c.474C>T0.944
gyrA7784c.483A>G0.952
gyrA7790c.489G>C0.952
gyrA7796c.495G>T0.950
gyrA7799c.498A>G0.950
gyrA7802c.501C>G0.952
gyrA7832c.531G>T1.000
gyrA7835c.534A>G1.000
gyrA7841c.540C>T1.000
gyrA7847c.546G>C1.000
gyrA7859c.558A>C1.000
gyrA7865c.564T>C1.000
gyrA7886c.585T>G1.000
gyrA8129c.828T>C1.000
gyrA8156c.855T>C1.000
gyrA8159c.858G>C0.571
gyrA8168c.867A>G1.000
gyrA8174c.873C>G1.000
gyrA8177c.876A>C1.000
gyrA8187p.Leu296Ile0.571
gyrA8191p.Ala297Gly0.429
gyrA8198c.897T>C1.000
gyrA8207c.906T>C1.000
gyrA8210c.909G>A0.429
gyrA8267c.966G>C1.000
gyrA8283p.Ile328Leu1.000
gyrA8288c.987T>C1.000
gyrA8294c.993T>C1.000
gyrA8324c.1023T>C0.277
gyrA8327c.1026C>T0.277
gyrA8330c.1029C>G0.723
gyrA8339c.1038A>G1.000
gyrA8340p.Ala347Ser1.000
gyrA8354c.1053G>C1.000
gyrA8366c.1065G>C0.250
gyrA8372c.1071G>T0.265
gyrA8382c.1081C>T0.714
gyrA8571c.1270C>T0.929
gyrA8576c.1275C>G0.429
gyrA8580p.Ile427Val0.611
gyrA8603c.1302A>C1.000
gyrA8609c.1308G>C0.688
gyrA8619c.1318T>C1.000
gyrA8624c.1323G>T1.000
gyrA8633c.1332C>G1.000
gyrA8636c.1335A>C1.000
gyrA8642c.1341A>G0.917
gyrA8645c.1344C>G1.000
gyrA8649p.Arg450Lys1.000
gyrA8666c.1365G>C0.917
gyrA8672c.1371A>G1.000
gyrA8693c.1392T>C0.917
gyrA8696c.1395G>C1.000
gyrA8699c.1398A>G1.000
gyrA8792c.1491G>C1.000
gyrA8799p.Ala500Ser1.000
gyrA8810c.1509A>G1.000
gyrA8817p.Ser506Ala0.913
gyrA8828c.1527T>C1.000
gyrA8829c.1528T>C1.000
gyrA8837c.1536C>G1.000
gyrA8846c.1545C>T0.909
gyrA8852c.1551T>C1.000
gyrA8858c.1557T>C1.000
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>C1.000
gyrA8957c.1656C>T0.942
gyrA8967p.Ala556Lys1.000
gyrA8978c.1677C>T0.952
gyrA8987c.1686C>G1.000
gyrA8990c.1689C>G0.938
gyrA8993c.1692C>T0.938
gyrA8996c.1695T>C0.938
gyrA8998p.Leu566Trp1.000
gyrA9018p.Gln573Lys0.941
gyrA9023c.1722A>C0.941
gyrA9026c.1725G>C1.000
gyrA9029c.1728T>C1.000
gyrA9035c.1734G>C1.000
rpoB760079c.273G>A0.900
rpoB760091c.285G>C1.000
rpoB760101c.295T>C1.000
rpoB760110c.304T>A0.913
rpoB760118c.312T>G1.000
rpoB760121c.315T>C0.960
rpoB760130p.Asp108Glu0.971
rpoB760136c.330G>A0.111
rpoB760139c.333A>G0.970
rpoB760181c.375T>C0.977
rpoB760184c.378A>G0.978
rpoB760196c.390C>G0.977
rpoB760235c.429T>C0.979
rpoB760244c.438G>C0.978
rpoB760256c.450C>T0.767
rpoB760274p.Glu156Asp0.757
rpoB760276p.Lys157Met0.737
rpoB760283c.477G>C1.000
rpoB760298c.492G>C1.000
rpoB760307c.501T>C0.586
rpoB760310c.504G>C0.429
rpoB760316c.510C>G0.917
rpoB760325c.519G>C1.000
rpoB760331c.525G>C1.000
rpoB760334c.528G>T0.917
rpoB760340c.534G>T1.000
rpoB760343c.537G>C0.188
rpoB760357p.Thr184Ser1.000
rpoB760361c.555T>C1.000
rpoB760370c.564C>G0.548
rpoB760376p.Asp190Glu1.000
rpoB760382c.576G>C0.600
rpoB760388c.582C>T0.618
rpoB760400c.594G>C0.622
rpoB760406c.600G>C0.917
rpoB760407p.Ser201Gly1.000
rpoB760415c.609C>T1.000
rpoB760418c.612G>C0.733
rpoB760424c.618C>G0.286
rpoB760430c.624T>C1.000
rpoB760433c.627C>T0.235
rpoB760457c.651C>T0.185
rpoB760460c.654G>C0.808
rpoB760463c.657C>T0.180
rpoB760475c.669A>G1.000
rpoB760478c.672C>T0.140
rpoB760481c.675G>C0.143
rpoB760484c.678A>G1.000
rpoB760502c.696C>G1.000
rpoB760522p.Ser239Asn0.984
rpoB760532c.726T>C0.983
rpoB760541c.735G>C0.982
rpoB760547c.741G>C0.111
rpoB760567p.Ser254Trp0.964
rpoB760571c.765G>C0.966
rpoB760585p.Asn260Ser0.167
rpoB760588p.Thr261Ile0.792
rpoB760591p.Val262Ala0.958
rpoB760595c.789C>T0.958
rpoB760596p.Thr264Pro0.958
rpoB760608c.802C>T0.778
rpoB760611c.805T>C0.964
rpoB760634c.828T>C0.776
rpoB760646c.840C>G0.971
rpoB760655c.849A>G0.970
rpoB760661c.855A>G0.231
rpoB760668p.Thr288Ala0.722
rpoB760674c.868T>C0.980
rpoB760679c.873A>G0.980
rpoB760683c.877T>C0.980
rpoB760703c.897C>T0.979
rpoB760721c.915C>G1.000
rpoB760724c.918T>C0.286
rpoB760727c.921C>G0.697
rpoB760730c.924T>C1.000
rpoB760736c.930C>G0.677
rpoB760793c.987A>G0.938
rpoB760805c.999G>C0.952
rpoB760817c.1011A>G0.958
rpoB760820c.1014T>C0.960
rpoB760826c.1020C>G0.963
rpoB760830c.1024T>C0.962
rpoB760841c.1035T>C0.969
rpoB760858p.Val351Ala0.778
rpoB760862c.1056G>C0.944
rpoB760865c.1059C>T0.778
rpoB760877c.1071G>T0.140
rpoB760883c.1077G>C0.140
rpoB760886p.Glu360Asp0.140
rpoB760887p.Thr361Val0.953
rpoB760910c.1104C>T0.981
rpoB760916c.1110C>T0.981
rpoB760919c.1113C>T0.132
rpoB760925c.1119T>C0.132
rpoB760928c.1122G>C0.981
rpoB760931c.1125C>G0.137
rpoB760943c.1137C>T0.791
rpoB760946c.1140A>G1.000
rpoB760965p.Met387Leu1.000
rpoB760970c.1164G>C1.000
rpoB760973c.1167G>T0.171
rpoB760982c.1176G>C1.000
rpoB760985c.1179G>C1.000
rpoB760988c.1182C>G1.000
rpoB760991c.1185G>T1.000
rpoB760997c.1191G>C1.000
rpoB761006c.1200C>G0.907
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>T0.981
rpoB761150c.1344A>T0.980
rpoB761165c.1359G>C1.000
rpoB761171c.1365C>T0.909
rpoB761178p.Ser458Thr0.873
rpoB761186p.Glu460Asp0.873
rpoB761189c.1383T>C1.000
rpoB761195c.1389G>C1.000
rpoB761198c.1392G>C0.121
rpoB761213c.1407G>C0.145
rpoB761217p.Pro471Ser0.129
rpoB761234c.1428G>C0.986
rpoB761246c.1440C>T0.817
rpoB761249c.1443A>G0.982
rpoB761255c.1449T>G0.825
rpoB761258c.1452G>A0.810
rpoB761261c.1455G>C0.158
rpoB761264c.1458C>G0.935
rpoB761273c.1467T>C0.851
rpoB761282c.1476C>T0.160
rpoB761288c.1482G>T0.164
rpoB761303c.1497G>C0.762
rpoB761318c.1512G>T0.983
rpoB761327c.1521A>G0.980
rpoB761330c.1524G>C0.280
rpoB761333c.1527G>T0.688
rpoB761339c.1533C>G0.667
rpoB761345c.1539G>C0.958
rpoB761346p.Val514Ser0.417
rpoB761354c.1548C>T0.476
rpoB761357c.1551G>T0.500
rpoB761360c.1554T>C1.000
rpoB761362p.Ser519Thr1.000
rpoB761367p.Glu521Gln0.500
rpoB761373p.Val523His0.500
rpoB761384c.1578C>G0.500
rpoB761393c.1587G>A0.556
rpoB761408c.1602G>C0.444
rpoB761414c.1608A>G1.000
rpoB761423c.1617T>C1.000
rpoB761516c.1710G>C0.931
rpoB761528c.1722C>T0.702
rpoB761531c.1725C>T0.708
rpoB761537c.1731C>G0.942
rpoB761552c.1746G>C0.217
rpoB761555c.1749G>C0.917
rpoB761558c.1752C>G0.921
rpoB761564c.1758G>C0.696
rpoB761570c.1764T>C0.930
rpoB761573c.1767C>G0.893
rpoB761579c.1773G>C0.935
rpoB761606c.1800C>G0.267
rpoB761612c.1806G>T0.940
rpoB761615c.1809A>C0.939
rpoB761636c.1830G>T0.959
rpoB761645c.1839C>G0.937
rpoB761648c.1842T>C0.274
rpoB761657c.1851C>T0.667
rpoB761666c.1860G>C0.919
rpoB761669c.1863C>T0.912
rpoB761675c.1869G>T0.929
rpoB761681c.1875G>A0.429
rpoB761682c.1876C>T0.929
rpoB761687c.1881C>T0.414
rpoB761690c.1884G>C0.929
rpoB761693c.1887G>C0.429
rpoB761705c.1899C>A0.500
rpoB761708c.1902C>T0.286
rpoB761712p.Val636Ile0.308
rpoB761747c.1941G>C1.000
rpoB761765c.1959T>C1.000
rpoB761772p.His656Ala1.000
rpoB761778p.Asn658Asp1.000
rpoB761785p.Thr660Ser1.000
rpoB761791p.Arg662His1.000
rpoB761813c.2007T>C1.000
rpoB761834c.2028T>C1.000
rpoB761885c.2079T>C0.269
rpoB761891c.2085G>C1.000
rpoB761892p.Ile696Val0.269
rpoB761906c.2100C>G0.300
rpoB761909c.2103T>C1.000
rpoB761912c.2106T>C1.000
rpoB761915p.Asp703Glu1.000
rpoB761916p.Asp704Asn1.000
rpoB761921c.2115C>T0.294
rpoB761924c.2118G>A0.667
rpoB761930c.2124G>C1.000
rpoB761933c.2127G>C0.658
rpoB761936c.2130C>T0.667
rpoB761948c.2142G>C1.000
rpoB761954c.2148C>A0.275
rpoB761955p.Ile717Val0.725
rpoB761969c.2163G>A1.000
rpoB761990c.2184G>C0.676
rpoB762008c.2202C>T1.000
rpoB762014c.2208C>G0.299
rpoB762038c.2232C>T0.706
rpoB762047c.2241G>A1.000
rpoB762053c.2247T>C1.000
rpoB762056c.2250G>A0.696
rpoB762065c.2259T>G0.326
rpoB762083c.2277T>C0.976
rpoB762086c.2280G>C0.976
rpoB762101c.2295C>G0.980
rpoB762114p.Ile770Val0.979
rpoB762122c.2316C>T0.735
rpoB762131c.2325C>G0.975
rpoB762134c.2328C>A0.707
rpoB762137c.2331C>T0.974
rpoB762140c.2334G>C1.000
rpoB762143c.2337T>C1.000
rpoB762149c.2343G>T0.298
rpoB762158c.2352G>C1.000
rpoB762167c.2361T>C1.000
rpoB762176c.2370T>C1.000
rpoB762185c.2379G>C1.000
rpoB762194c.2388G>C0.679
rpoB762224c.2418C>G0.292
rpoB762233c.2427G>C1.000
rpoB762236c.2430G>C0.717
rpoB762245c.2439G>C1.000
rpoB762275c.2469C>T0.702
rpoB762284c.2478G>C0.304
rpoB762293c.2487T>C0.976
rpoB762296c.2490G>C0.690
rpoB762308c.2502G>C0.306
rpoB762314c.2508C>T0.306
rpoB762317c.2511A>G0.973
rpoB762323c.2517C>A0.632
rpoB762329c.2523G>C0.973
rpoB762338c.2532T>C1.000
rpoB762341c.2535G>C1.000
rpoB762347c.2541T>C1.000
rpoB762350c.2544C>T1.000
rpoB762362p.Glu852Asp1.000
rpoB762369c.2563T>C1.000
rpoB762374c.2568G>C1.000
rpoB762395c.2589G>C0.190
rpoB762398c.2592T>C1.000
rpoB762401c.2595G>C0.372
rpoB762404c.2598T>C1.000
rpoB762410c.2604T>G0.348
rpoB762416c.2610A>G0.979
rpoB762434c.2628T>C0.309
rpoB762443c.2637G>C0.309
rpoB762449c.2643C>A0.963
rpoB762452c.2646G>C0.964
rpoB762470c.2664G>C0.964
rpoB762488c.2682G>C0.638
rpoB762491c.2685T>C0.958
rpoB762509c.2703T>G0.882
rpoB762510p.Ala902Pro0.882
rpoB762515c.2709C>T0.935
rpoB762527c.2721G>C0.379
rpoB762533c.2727T>C0.875
rpoB762536c.2730T>C0.857
rpoB762537c.2731T>C0.857
rpoB762551c.2745C>T0.824
rpoB762557c.2751G>A0.438
rpoB762560c.2754A>T0.357
rpoB762563c.2757G>T0.833
rpoB762827c.3021G>C0.261
rpoB762830c.3024C>G0.600
rpoB762833c.3027C>T0.320
rpoB762839c.3033G>A0.320
rpoB762857c.3051C>G0.931
rpoB762860c.3054G>C0.600
rpoB762863c.3057T>C0.938
rpoB762866c.3060C>T0.625
rpoB762879p.Met1025Leu0.953
rpoB762894c.3088C>T0.694
rpoB762899c.3093G>C0.714
rpoB762917c.3111C>G1.000
rpoB762920c.3114C>T1.000
rpoB762923c.3117C>G0.712
rpoB762929c.3123G>C0.263
rpoB762959c.3153G>C1.000
rpoB762962c.3156C>T1.000
rpoB762995c.3189G>T1.000
rpoB763004c.3198G>A0.232
rpoB763007c.3201C>T0.236
rpoB763022c.3216C>G0.250
rpoB763028c.3222T>C0.200
rpoB763031c.3225T>G1.000
rpoB763034c.3228C>G0.744
rpoB763040c.3234C>G0.744
rpoB763053c.3247T>C0.292
rpoB763070c.3264T>C1.000
rpoB763082c.3276C>T0.738
rpoB763085c.3279C>G0.250
rpoB763088c.3282C>G0.744
rpoB763094c.3288G>C0.750
rpoB763103c.3297G>C0.238
rpoB763115c.3309T>C0.976
rpoB763127c.3321G>C0.973
rpoB763130c.3324G>A0.189
rpoB763133c.3327G>C0.194
rpoB763136c.3330C>T0.969
rpoB763142c.3336C>G0.219
rpoB763145c.3339G>A0.714
rpoB763157c.3351G>T0.704
rpoB763160c.3354G>T0.259
rpoB763166c.3360A>G0.963
rpoB763169c.3363A>G0.231
rpoB763172c.3366G>C0.731
rpoB763190c.3384C>T0.208
rpoB763193c.3387C>G0.727
rpoC763375c.6C>A0.818
rpoC763402c.33C>T0.214
rpoC763408c.39T>C1.000
rpoC763411c.42T>C1.000
rpoC763414c.45T>C0.214
rpoC763415p.Thr16Ser0.214
rpoC763423p.Glu18Asp0.214
rpoC763430c.61A>C1.000
rpoC763433p.Gln22Asn1.000
rpoC763443p.Tyr25Phe1.000
rpoC763450c.81G>A0.613
rpoC763456c.87A>G0.969
rpoC763468c.99G>C0.971
rpoC763486c.117T>C0.974
rpoC763492c.123G>C0.308
rpoC763528c.159G>A0.977
rpoC763531c.162G>T0.721
rpoC763546c.177A>G0.978
rpoC763558c.189C>T0.268
rpoC763570c.201G>C0.973
rpoC763573c.204G>C0.250
rpoC763594c.225C>T0.976
rpoC763603c.234C>T0.227
rpoC763615c.246G>C0.229
rpoC763618c.249C>T0.224
rpoC763633c.264T>C1.000
rpoC763657c.288G>A0.763
rpoC763660c.291T>G1.000
rpoC763666c.297G>C0.263
rpoC763669c.300C>G0.730
rpoC763675c.306C>G1.000
rpoC763696c.327T>C0.500
rpoC763699c.330G>T0.542
rpoC763702c.333C>G1.000
rpoC763705c.336G>A0.435
rpoC763708c.339G>C0.542
rpoC763709p.Leu114Phe0.458
rpoC763714c.345G>C1.000
rpoC763717c.348T>C1.000
rpoC763723c.354G>C1.000
rpoC763732c.363C>A0.480
rpoC763741c.372C>T1.000
rpoC763744c.375G>C0.478
rpoC763747c.378G>A1.000
rpoC763765c.396T>G0.263
rpoC763774c.405G>C0.211
rpoC763792p.Glu141Asp1.000
rpoC763807c.438T>C1.000
rpoC763813c.444C>G1.000
rpoC763831c.462A>G1.000
rpoC763837c.468G>C1.000
rpoC763840c.471G>C1.000
rpoC763855c.486C>G0.929
rpoC763858c.489A>G0.923
rpoC763861c.492C>T0.929
rpoC763879c.510A>G0.900
rpoC763882c.513G>A0.667
rpoC763888c.519G>T0.231
rpoC763891c.522G>C0.917
rpoC763894c.525A>G0.923
rpoC763900c.531G>C0.971
rpoC763921c.552G>C0.188
rpoC763924c.555G>A0.161
rpoC763933c.564C>T0.966
rpoC763940p.Ala191Ser0.964
rpoC763945c.576T>C0.964
rpoC763947p.Ala193Val0.964
rpoC763951c.582G>C0.964
rpoC763960c.591T>G0.964
rpoC763969c.600C>T0.964
rpoC763987c.618C>T0.952
rpoC763991p.Ile208Leu0.950
rpoC763996c.627T>C0.947
rpoC763999c.630C>T0.889
rpoC764002c.633C>G0.889
rpoC764003p.Ala212Ser0.889
rpoC764024c.655T>C1.000
rpoC764029p.Glu220Asp1.000
rpoC764032p.Asp221Glu1.000
rpoC764040p.Ser224Thr1.000
rpoC764044c.675T>C1.000
rpoC764054c.685C>T0.900
rpoC764059c.690G>T1.000
rpoC764083c.714A>G1.000
rpoC764084p.Asn239Val1.000
rpoC764095c.726C>T0.906
rpoC764098c.729A>G1.000
rpoC764134c.765C>G0.182
rpoC764143c.774G>C0.739
rpoC764147p.Ser260Ala0.714
rpoC764150p.Ile261Val0.714
rpoC764153p.Gln262Lys0.286
rpoC764161c.792G>C0.211
rpoC764165p.Glu266Gln0.778
rpoC764266c.897T>C1.000
rpoC764272c.903G>C1.000
rpoC764278c.909A>G1.000
rpoC764293c.924G>C1.000
rpoC764297p.Met310Leu1.000
rpoC764311c.942C>G0.381
rpoC764317c.948C>G0.400
rpoC764320c.951C>G0.452
rpoC764332c.963G>A0.474
rpoC764338c.969G>A0.585
rpoC764344c.975C>T0.405
rpoC764353c.984G>T1.000
rpoC764365c.996C>T1.000
rpoC764371c.1002G>C1.000
rpoC764377c.1008C>G0.640
rpoC764380c.1011G>C1.000
rpoC764387c.1018T>C1.000
rpoC764405c.1036A>C1.000
rpoC764428c.1059G>C0.742
rpoC764431c.1062G>C1.000
rpoC764434c.1065A>G1.000
rpoC764435c.1066A>C1.000
rpoC764446c.1077T>C0.232
rpoC764449c.1080G>C0.232
rpoC764458c.1089G>C1.000
rpoC764461c.1092A>G1.000
rpoC764485c.1116G>C0.230
rpoC764491c.1122G>T0.237
rpoC764497c.1128A>G1.000
rpoC764500c.1131C>G0.197
rpoC764510c.1141C>T0.774
rpoC764521c.1152T>C0.212
rpoC764524c.1155C>G0.788
rpoC764527c.1158C>T0.219
rpoC764530c.1161C>G0.733
rpoC764534p.Arg389Ser0.724
rpoC764539c.1170C>T0.273
rpoC764542c.1173C>T0.714
rpoC764545c.1176C>A0.714
rpoC764560c.1191T>C0.742
rpoC764575c.1206T>G1.000
rpoC764605c.1236G>C0.271
rpoC764611c.1242G>T1.000
rpoC764623c.1254C>G0.253
rpoC764626c.1257C>T1.000
rpoC764632c.1263T>C0.988
rpoC764650c.1281G>T1.000
rpoC764668c.1299C>T0.695
rpoC764692c.1323C>T0.713
rpoC764701c.1332C>G0.295
rpoC764713c.1344G>T1.000
rpoC764716c.1347G>C1.000
rpoC764746c.1377G>T1.000
rpoC764752c.1383G>C1.000
rpoC764758c.1389C>G1.000
rpoC764764c.1395T>C0.984
rpoC764791c.1422C>G0.739
rpoC764803c.1434C>T0.984
rpoC764809c.1440C>T0.981
rpoC764810p.Pro481Ala0.736
rpoC764815c.1446A>G0.982
rpoC764824c.1455T>C0.981
rpoC764827c.1458G>C0.981
rpoC764851c.1482C>T0.218
rpoC764858c.1489T>C0.981
rpoC764869c.1500C>T0.983
rpoC764875c.1506C>A0.148
rpoC764878c.1509C>G0.145
rpoC764887c.1518G>C0.968
rpoC764888c.1519T>C0.967
rpoC764911c.1542A>G0.969
rpoC764912p.Met515Gln0.969
rpoC764932c.1563C>A0.986
rpoC764935c.1566T>C0.114
rpoC764948c.1579T>C0.986
rpoC764968c.1599T>C0.986
rpoC765004c.1635G>C0.727
rpoC765007c.1638T>G0.966
rpoC765008c.1639T>C0.966
rpoC765011c.1642A>T0.966
rpoC765016c.1647C>G0.172
rpoC765019c.1650A>G0.821
rpoC765022c.1653G>T0.111
rpoC765034c.1665T>C0.111
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
rpoC765121c.1752G>T1.000
rpoC765129p.Tyr587Phe1.000
rpoC765143p.Val592Ile0.938
rpoC765343c.1974G>A1.000
rpoC765352c.1983G>C1.000
rpoC765356p.Met663Val1.000
rpoC765370c.2001G>C0.900
rpoC765379c.2010G>C0.864
rpoC765382c.2013G>T0.864
rpoC765383p.Met672Leu1.000
rpoC765403c.2034G>C1.000
rpoC765405p.Leu679His0.968
rpoC765409c.2040T>G1.000
rpoC765421c.2052C>G0.841
rpoC765425p.Lys686Glu0.167
rpoC765445c.2076G>C0.236
rpoC765449p.Ala694Ser0.745
rpoC765452p.Ala695Arg0.236
rpoC765466c.2097C>T0.212
rpoC765469c.2100G>C0.746
rpoC765478c.2109T>G0.254
rpoC765480p.Tyr704Phe0.984
rpoC765496c.2127C>G0.262
rpoC765499c.2130C>G0.984
rpoC765517c.2148C>G0.709
rpoC765529c.2160C>T0.283
rpoC765533p.Tyr722His0.956
rpoC765544c.2175C>G0.583
rpoC765547c.2178C>T0.576
rpoC765548c.2179A>T0.933
rpoC765553c.2184C>T0.967
rpoC765556c.2187G>C0.967
rpoC765562c.2193G>T0.333
rpoC765577c.2208G>T0.259
rpoC765772c.2403C>G0.909
rpoC765778c.2409C>G0.900
rpoC765779p.Asp804Lys0.909
rpoC765793c.2424C>G0.917
rpoC765796c.2427C>T0.917
rpoC765800p.Phe811Leu0.923
rpoC765811c.2442T>G0.929
rpoC765814c.2445A>C0.929
rpoC765817c.2448G>C0.938
rpoC765823c.2454C>A0.412
rpoC765826c.2457T>C0.944
rpoC765835c.2466C>T0.977
rpoC765841c.2472G>T0.604
rpoC765861p.Phe831Tyr0.610
rpoC765871c.2502T>C0.344
rpoC765875p.Val836Ile0.984
rpoC765886c.2517C>G0.309
rpoC765904c.2535C>G0.303
rpoC765907c.2538G>T0.682
rpoC765908p.Leu847Phe0.308
rpoC765928c.2559C>G0.672
rpoC765934c.2565C>T0.333
rpoC765940c.2571A>T1.000
rpoC765946c.2577C>T0.333
rpoC765947c.2578T>C1.000
rpoC765952c.2583G>C0.333
rpoC765961c.2592G>T0.327
rpoC765962c.2593T>C1.000
rpoC765967c.2598C>T1.000
rpoC765973c.2604C>G0.556
rpoC765979c.2610C>G1.000
rpoC765982c.2613C>T1.000
rpoC765994c.2625A>T1.000
rpoC766003c.2634G>C0.500
rpoC766009c.2640G>C0.550
rpoC766012c.2643C>G1.000
rpoC766021c.2652G>C1.000
rpoC766027c.2658G>T0.364
rpoC766030c.2661C>T0.300
rpoC766321c.2952C>G0.800
rpoC766333c.2964G>T0.792
rpoC766345c.2976T>C1.000
rpoC766348c.2979A>G1.000
rpoC766351c.2982C>G0.792
rpoC766353p.Val995Ala0.792
rpoC766363c.2994G>C0.132
rpoC766369c.3000C>G0.881
rpoC766375c.3006C>G0.881
rpoC766381c.3012C>T1.000
rpoC766384c.3015A>G1.000
rpoC766390c.3021C>T1.000
rpoC766393c.3024C>T0.915
rpoC766408c.3039C>T1.000
rpoC766435p.Glu1022Asp0.980
rpoC766507c.3138C>T1.000
rpoC766513c.3144C>T1.000
rpoC766522c.3153C>A1.000
rpoC766528c.3159T>G1.000
rpoC766531c.3162G>C1.000
rpoC766534c.3165C>G1.000
rpoC766537c.3168G>A1.000
rpoC766540p.Asp1057Glu1.000
rpoC766549c.3180G>C1.000
rpoC766570c.3201T>C1.000
rpoC766573c.3204T>G1.000
rpoC766594c.3225G>T1.000
rpoC766607p.Ile1080Leu1.000
rpoC766618c.3249G>T1.000
rpoC766624c.3255G>C1.000
rpoC766630c.3261G>C1.000
rpoC766633c.3264G>C1.000
rpoC766776p.Arg1136Gln1.000
rpoC766792c.3423C>G0.586
rpoC766798c.3429C>G0.414
rpoC766799p.Ala1144Ser0.586
rpoC766804c.3435A>G1.000
rpoC766837c.3468G>C1.000
rpoC766843c.3474T>G0.292
rpoC766846c.3477C>A0.280
rpoC766858c.3489C>T1.000
rpoC766861c.3492G>C1.000
rpoC766867c.3498C>G1.000
rpoC766876c.3507C>T1.000
rpoC766921c.3552G>C0.917
rpoC766931p.Ala1188Ser0.175
rpoC766942c.3573C>T1.000
rpoC766945c.3576A>C1.000
rpoC766948c.3579G>C0.170
rpoC766963c.3594T>C1.000
rpoC766978c.3609C>T0.186
rpoC766981c.3612T>C0.183
rpoC766996c.3627C>T1.000
rpoC767002c.3633G>C1.000
rpoC767008c.3639G>A1.000
rpoC767020c.3651C>G0.274
rpoC767023c.3654C>T1.000
rpoC767044c.3675G>C0.685
rpoC767080c.3711G>C0.676
rpoC767095c.3726C>T0.639
rpoC767098c.3729T>C0.984
rpoC767104c.3735C>G0.982
rpoC767105p.Asn1246His0.316
rpoC767119c.3750A>G0.985
rpoC767125c.3756G>C0.710
rpoC767134c.3765C>T0.983
rpoC767138c.3769C>T0.983
rpoC767149c.3780C>T0.727
rpoC767158c.3789T>C0.980
rpoC767162p.Asn1265Ala0.160
rpoC767167c.3798C>T0.163
rpoC767174p.Asn1269Asp0.163
rpoC767179c.3810C>T0.809
rpoC7671801271A>1271*0.170
rpoC767191c.3822C>G0.981
rpoC767197c.3828G>A0.980
rpoC767203c.3834C>G0.791
rpoC767206c.3837C>G0.791
rpoC767209c.3840T>C0.791
rpoC767212c.3843G>C0.800
rpoC767221c.3852C>G1.000
rpoC767230c.3861G>C1.000
rpoC767233c.3864T>C1.000
rpoC767254c.3885G>C0.857
rpoC767264p.Ala1299Ser1.000
rpoC767267p.Ala1300Asn0.926
rpoC767281c.3912C>G1.000
rpoC767284c.3915C>G1.000
rpsL781559c.-1G>C1.000
rpsL781572p.Gln5Asn1.000
rpsL781586c.27C>T0.778
rpsL781595c.36T>C1.000
rpsL781598c.39G>C0.205
rpsL781605p.Ile16Val0.205
rpsL781608p.Ser17Ala0.974
rpsL781616c.57C>G0.739
rpsL781628c.69T>C1.000
rpsL781631c.72G>C0.273
rpsL781649c.90T>C1.000
rpsL781655c.96T>C1.000
rpsL781658c.99A>C0.333
rpsL781670c.111G>C0.655
rpsL781682c.123T>C0.358
rpsL781706c.147T>C0.585
rpsL781709c.150G>C0.410
rpsL781715c.156T>G0.400
rpsL781721c.162C>T0.222
rpsL781728c.169T>C0.909
rpsL781742c.183C>T1.000
rpsL781751c.192G>C1.000
rpsL781754c.195G>T0.211
rpsL781760c.201T>C1.000
rpsL781763c.204C>G0.238
rpsL781766c.207C>T0.190
rpsL781772c.213C>T1.000
rpsL781802c.243G>C0.744
rpsL781808c.249C>T0.250
rpsL781814c.255C>T1.000
rpsL781817c.258G>T1.000
rpsL781829c.270G>C1.000
rpsL781832c.273T>C1.000
rpsL781838c.279G>C0.241
rpsL781841c.282C>T0.226
rpsL781859c.300T>C0.229
rpsL781865c.306G>C0.196
rpsL781868c.309T>C1.000
rpsL781871c.312G>C1.000
rpsL781877c.318T>A0.696
rpsL781892c.333A>G1.000
rpsL781898c.339A>T0.308
rpsL781901c.342C>T0.333
rpsL781907c.348T>C1.000
rpsL781916c.357T>C1.000
rpsL781929p.Gly124Ser1.000
rpsL781933c.374G>A0.500
rplC800796c.-13ATTGG>A1.000
rrs1471922r.77gt>g0.938
rrs1471925r.80t>c0.917
rrs1471931r.86ga>g0.917
rrs1471934r.89a>g0.917
rrs1471985r.140t>c0.450
rrs1471986r.141c>t0.950
rrs1472019r.174g>a0.444
rrs1472023r.178g>t0.444
rrs1472030r.185g>a0.333
rrs1472031r.186g>c0.917
rrs1472032r.187g>a0.333
rrs1472033r.188a>c0.917
rrs1472035r.190g>t0.917
rrs1472040r.195t>g0.917
rrs1472041r.196c>t0.917
rrs1472042r.197t>g0.917
rrs1472043r.198t>a0.333
rrs1472050r.205g>c0.308
rrs1472061r.216a>t0.933
rrs1472075r.230a>g0.524
rrs1472106r.261g>a0.957
rrs1472108r.263c>t0.960
rrs1472113r.268t>c0.538
rrs1472150r.305t>a0.963
rrs1472251r.406g>a0.952
rrs1472337r.492c>g0.933
rrs1472380r.535g>c0.920
rrs1472446r.601t>a0.880
rrs1472452r.607g>a0.885
rrs1472464r.619a>g0.880
rrs1472612r.767g>t0.316
rrs1472734r.889c>t0.526
rrs1472741r.896g>a0.500
rrs1472846r.1001c>a0.400
rrs1472847r.1002g>c0.400
rrs1472848r.1003t>c0.400
rrs1472849r.1004c>g0.333
rrs1472850r.1005t>c0.333
rrs1472857r.1012a>g0.286
rrs1472858r.1013g>t0.286
rrs1472860r.1015c>g0.308
rrs1472861r.1016g>t0.308
rrs1472956r.1111t>c0.857
rrs1472957r.1112c>t0.857
rrs1472969r.1124a>g0.923
rrs1472970r.1125c>g0.923
rrs1472977r.1132g>c0.923
rrs1472978r.1133t>c0.923
rrs1472989r.1144g>a0.933
rrs1472990r.1145a>g0.933
rrs1473082r.1237g>a0.643
rrs1473088r.1243a>g0.615
rrs1473099r.1254t>a0.538
rrs1473104r.1259c>t0.833
rrs1473105r.1260g>a0.500
rrs1473110r.1265t>g0.833
rrs1473111r.1266a>g0.833
rrs1473121r.1276t>c0.643
rrs1473123r.1278a>t0.833
rrs1473129r.1284c>t0.667
rrs1473145r.1300c>t0.692
rrs1473166r.1321g>a0.692
rrs1473276r.1431a>g0.312
rrs1473288r.1443c>t0.467
rrs1473290r.1445c>t0.867
rrs1473291r.1446g>t0.467
rrs1473301r.1456t>c0.400
rrl1473731r.74t>a0.300
rrl1473756r.99g>t0.400
rrl1473758r.101g>t0.800
rrl1473788r.131a>g0.400
rrl1473806r.149c>t0.800
rrl1473807r.150t>c0.400
rrl1473839r.182g>a0.462
rrl1473876r.219g>a0.909
rrl1473887r.230t>a0.300
rrl1473888r.231t>c0.600
rrl1473898r.241c>t0.800
rrl1473899r.242a>g0.900
rrl1474074r.417c>t0.900
rrl1474089r.432c>t0.846
rrl1474093r.436g>a0.923
rrl1474100r.443c>t0.846
rrl1474103r.446a>c0.917
rrl1474130r.473c>t0.619
rrl1474135r.478g>a0.333
rrl1474140r.483c>t0.957
rrl1474151r.494c>t0.957
rrl1474174r.517a>g0.318
rrl1474181r.524c>t0.389
rrl1474183r.526t>c0.438
rrl1474184r.527c>a0.562
rrl1474185r.528g>a0.438
rrl1474185r.528ga>g1.000
rrl1474249r.592g>t1.000
rrl1474263r.606g>a0.571
rrl1474266r.609t>c0.385
rrl1474269r.612c>t0.385
rrl1474282r.625g>a0.667
rrl1474356r.699t>c0.667
rrl1474362r.705a>g1.000
rrl1474387r.730c>t0.667
rrl1474413r.756a>c0.800
rrl1474446r.789c>t0.200
rrl1474496r.839c>g0.571
rrl1474497r.840g>c0.545
rrl1474506r.849c>g0.522
rrl1474507r.850g>c0.522
rrl1474673r.1016t>c0.333
rrl1474676r.1019t>a0.333
rrl1474677r.1020a>g0.333
rrl1474710r.1053t>a0.308
rrl1474717r.1060a>g1.000
rrl1474720r.1063c>t0.308
rrl1474722r.1065t>c0.600
rrl1474743r.1086t>g0.579
rrl1474753r.1096a>g0.350
rrl1474760r.1103a>g0.955
rrl1474794r.1137c>t1.000
rrl1474803r.1146g>a0.947
rrl1474812r.1155g>a0.947
rrl1474830r.1173a>g0.938
rrl1474913r.1256t>c0.500
rrl1474932r.1275c>t0.941
rrl1475061r.1404c>a0.462
rrl1475061r.1404ca>c0.538
rrl1475076r.1419c>a0.389
rrl1475090r.1433a>t0.450
rrl1475114r.1457c>t0.389
rrl1475120r.1463g>t1.000
rrl1475129r.1472g>a0.353
rrl1475505r.1848g>a1.000
rrl1475526r.1869c>a1.000
rrl1475531r.1874c>t1.000
rrl1475545r.1888t>g0.200
rrl1475573r.1916g>a0.455
rrl1475647r.1990g>c0.400
rrl1475649r.1992a>g0.455
rrl1475659r.2002g>a0.917
rrl1475765r.2108a>g0.400
rrl1475775r.2118g>a0.400
rrl1475975r.2318c>t0.455
rrl1475977r.2320a>g0.455
rrl1476214r.2557g>t1.000
rrl1476215r.2558c>t1.000
rrl1476221r.2564t>c0.833
rrl1476224r.2567a>g1.000
rrl1476251r.2594t>g0.154
rrl1476281r.2624t>c1.000
rrl1476297r.2640c>t1.000
rrl1476299r.2642c>t1.000
rrl1476529r.2872a>g0.231
rrl1476540r.2883c>t0.294
rrl1476583r.2926g>a0.400
rrl1476584r.2927c>t1.000
rrl1476594r.2937c>t1.000
rrl1476597r.2940g>a1.000
rrl1476603r.2946g>a1.000
rrl1476608r.2951c>g0.609
rrl1476619r.2962c>t0.609
rrl1476628r.2971t>a1.000
rrl1476664r.3007t>c0.471
rrl1476665r.3008t>c0.471
rrl1476666r.3009c>t0.467
rrl1476674r.3017t>c1.000
rrl1476679r.3022t>c0.533
fabG11673916c.477A>C0.800
fabG11673917p.Val160Leu0.800
fabG11673922c.483T>C0.818
fabG11673931c.492C>G0.846
fabG11673941p.Ala168Ser0.846
fabG11673955c.516G>C0.917
fabG11673961c.522A>C0.917
fabG11673962p.Asn175Gly0.917
fabG11673967c.528G>C0.917
fabG11673973c.534G>C0.917
fabG11673976c.537T>C0.923
fabG11674006p.Asp189Glu0.950
fabG11674024c.585T>C0.938
fabG11674037p.Gln200Ala0.917
fabG11674042c.603G>C1.000
fabG11674045c.606G>C1.000
fabG11674049p.Gln204Asp1.000
fabG11674054c.615T>C1.000
fabG11674060c.621A>C0.909
inhA1674651c.450C>T1.000
inhA1674656p.Ser152Thr1.000
inhA1674660c.459G>C1.000
inhA1674663c.462G>C1.000
inhA1674672c.471C>A1.000
inhA1674690c.489C>G1.000
inhA1674702c.501G>T1.000
inhA1674703c.502T>C1.000
inhA1674718c.517A>C1.000
inhA1674729c.528G>T1.000
inhA1674858c.657G>A0.909
inhA1674876c.675C>T0.957
inhA1674879c.678T>G0.375
inhA1674892p.Asn231Asp0.375
inhA1674903c.702T>C0.375
inhA1674904p.Ala235Pro0.958
inhA1674909c.708G>A0.375
inhA1674912c.711G>C0.375
inhA1674915c.714C>G0.375
inhA1674924c.723G>T0.565
inhA1674930c.729C>T0.545
inhA1674934c.733C>T0.545
inhA1674942c.741T>C0.955
inhA1674949c.748C>T0.474
inhA1674954c.753G>C0.947
inhA1674957c.756G>C0.947
inhA1674963c.762G>C0.474
inhA1674966c.765T>C0.944
inhA1674967p.Asp256Thr0.444
inhA1674975c.774C>T0.500
inhA1674977p.Tyr259Phe0.500
rpsA1833536c.-6A>C0.938
rpsA1833538c.-4CA>C1.000
rpsA1833541c.-1T>C0.944
rpsA1833547c.6G>A1.000
rpsA1833554p.Thr5Ser0.179
rpsA1833589c.48A>C1.000
rpsA1833595c.54T>G1.000
rpsA1833596p.Ser19Ala1.000
rpsA1833604c.63C>T0.824
rpsA1833616c.75A>T0.173
rpsA1833619c.78A>C1.000
rpsA1833625c.84A>G0.833
rpsA1833628c.87G>C0.167
rpsA1833634c.93G>A0.164
rpsA1833661c.120A>G0.182
rpsA1833664c.123C>G0.192
rpsA1833676c.135A>G1.000
rpsA1833679c.138G>T1.000
rpsA1833685c.144G>C0.286
rpsA1833691c.150G>A0.700
rpsA1833694c.153G>T0.308
rpsA1833697c.156C>T0.289
rpsA1833700c.159C>T0.725
rpsA1833703c.162C>T0.238
rpsA1833709c.168C>T0.750
rpsA1833724c.183C>T1.000
rpsA1833727c.186G>C1.000
rpsA1833730c.189C>T0.241
rpsA1833733c.192C>G0.250
rpsA1833734p.Ala65Ser0.964
rpsA1833742c.201A>G0.647
rpsA1833745c.204G>C1.000
rpsA1833748c.207C>G0.647
rpsA1833760c.219C>T1.000
rpsA1833787c.246C>G1.000
rpsA1833790c.249T>C1.000
rpsA1833793c.252C>T0.268
rpsA1833802c.261A>G1.000
rpsA1833811c.270G>T1.000
rpsA1833823c.282G>A0.681
rpsA1833829c.288A>G0.298
rpsA1833832c.291G>A0.957
rpsA1833838c.297G>C0.941
rpsA1833841c.300C>G0.941
rpsA1833847c.306C>G0.943
rpsA1833856c.315A>G0.945
rpsA1833862c.321G>T0.946
rpsA1833874c.333T>G0.724
rpsA1833886c.345C>G0.709
rpsA1833894p.Ala118Glu0.948
rpsA1833904c.363G>A0.295
rpsA1833928c.387G>C0.951
rpsA1833949c.408T>C0.948
rpsA1833961c.420C>G0.724
rpsA1833970c.429G>T0.945
rpsA1833976c.435C>T0.196
rpsA1833979c.438T>C0.945
rpsA1833991c.450C>G0.220
rpsA1834000c.459G>C1.000
rpsA1834009c.468C>T1.000
rpsA1834012c.471G>C0.167
rpsA1834015c.474G>C1.000
rpsA1834021c.480C>T1.000
rpsA1834030c.489C>G1.000
rpsA1834033c.492C>T0.766
rpsA1834073p.Lys178Arg0.697
rpsA1834096c.555G>C0.656
rpsA1834097p.Ser186Arg0.290
rpsA1834102c.561T>C0.290
rpsA1834108c.567C>G0.633
rpsA1834114c.573G>C0.621
rpsA1834177c.636A>C0.972
rpsA1834189c.648G>C0.200
rpsA1834213c.672G>C0.192
rpsA1834228c.687C>A0.729
rpsA1834231c.690T>G0.745
rpsA1834234c.693G>T0.255
rpsA1834240c.699T>C1.000
rpsA1834246c.705G>T0.306
rpsA1834249c.708T>C1.000
rpsA1834252c.711C>G1.000
rpsA1834261c.720A>G1.000
rpsA1834264c.723G>C1.000
rpsA1834279c.738C>T1.000
rpsA1834294c.753G>T0.737
rpsA1834297c.756C>T0.982
rpsA1834303c.762T>G0.980
rpsA1834306c.765T>C0.982
rpsA1834327c.786G>T0.746
rpsA1834345c.804C>T0.226
rpsA1834348c.807T>C0.231
rpsA1834357c.816T>C0.723
rpsA1834361c.820T>C0.227
rpsA1834366c.825A>G0.985
rpsA1834375c.834G>C0.789
rpsA1834396c.855G>C0.985
rpsA1834411c.870T>G0.193
rpsA1834414c.873C>T0.782
rpsA1834417c.876G>C0.786
rpsA1834420c.879C>T0.746
rpsA1834423c.882G>C0.220
rpsA1834429c.888C>T0.766
rpsA1834438c.897C>T0.773
rpsA1834451c.910T>C1.000
rpsA1834456c.915T>G1.000
rpsA1834468c.927A>G1.000
rpsA1834477c.936C>T0.794
rpsA1834489c.948T>C1.000
rpsA1834513c.972C>G0.206
rpsA1834519c.978G>C0.667
rpsA1834520p.Ala327Ser1.000
rpsA1834528c.987T>C1.000
rpsA1834534c.993C>T0.659
rpsA1834540c.999G>C0.286
rpsA1834543c.1002C>G1.000
rpsA1834546c.1005T>C1.000
rpsA1834552c.1011G>T0.732
rpsA1834555c.1014T>G1.000
rpsA1834557p.Ala339Gly0.725
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>T0.660
rpsA1834666c.1125G>C1.000
rpsA1834667p.Ala376Ser1.000
rpsA1834690c.1149T>C1.000
rpsA1834700p.Gln387Ala0.621
rpsA1834705c.1164C>G0.617
rpsA1834720c.1179C>G0.676
rpsA1834732c.1191T>C1.000
rpsA1834738c.1197A>G1.000
rpsA1834753c.1212T>C1.000
rpsA1834756c.1215G>A0.344
rpsA1834759c.1218A>C1.000
rpsA1834765p.Glu408Asp0.983
rpsA1834774c.1233C>T0.286
rpsA1834776p.Ala412Glu0.980
rpsA1834780c.1239A>G0.980
rpsA1834786c.1245A>G0.286
rpsA1834789c.1248T>C0.980
rpsA1834792c.1251G>C0.286
rpsA1834813c.1272G>T0.658
rpsA1834829p.Ala430Ile0.267
rpsA1834840c.1299G>A0.333
kasA2518732c.618C>G0.227
kasA2518738c.624G>C0.731
kasA2518747c.633C>G0.188
kasA2518756c.642G>C1.000
kasA2518768c.654C>G0.784
kasA2518771c.657C>G0.771
kasA2518774c.660C>T0.784
kasA2518780p.Glu222Asp0.216
kasA2518783c.669T>G0.216
kasA2518785p.Glu224Ala0.216
kasA2518787p.Arg225Asn0.216
kasA2518792c.678C>T0.216
kasA2518795c.681C>T1.000
kasA2518798c.684G>C0.714
kasA2518813c.699C>T0.211
kasA2518816c.702C>T0.237
kasA2518822c.708C>A0.750
kasA2518825c.711T>C1.000
kasA2518843c.729T>C0.250
kasA2518846c.732G>T0.750
kasA2518847p.Leu245Ile0.240
kasA2518853p.Leu247Val0.245
kasA2518864c.750G>C1.000
kasA2518877p.Lys255Leu0.238
kasA2518882c.768C>T0.231
thyX3067346c.600G>C1.000
thyX3067349c.597C>G1.000
thyX3067355c.591T>C1.000
thyX3067376c.570C>G1.000
thyX3067403c.543G>C1.000
thyX3067406c.540T>C1.000
thyX3067415c.531G>A1.000
thyX3067423c.523G>A1.000
thyX3067424c.522C>T1.000
thyX3067427c.519C>G1.000
thyX3067430c.516G>C1.000
thyX3067436c.510G>C1.000
thyX3067442c.504G>C1.000
panD4044219c.63G>A0.455
panD4044233p.Cys17His0.818
panD4044234c.48G>C0.818
panD4044249c.33G>A0.818
embC4240699c.837C>G0.231
embC4240717c.855T>C0.245
embC4240729c.867C>G0.719
embC4240735c.873C>G0.712
embC4240741c.879C>T0.705
embC4240756c.894G>C0.708
embC4240768c.906G>A0.222
embC4240771c.909G>C0.685
embC4240772p.Ser304Ala0.685
embC4240777c.915G>A0.231
embC4240778p.His306Gly0.712
embC4240781p.Ala307Ser0.712
embC4240786c.924C>T0.159
embC4240789c.927T>C0.954
embC4240819c.957A>C0.951
embC4240826p.Ala322Ser0.793
embC4240831c.969T>G0.947
embC4240856p.Ala332Thr0.737
embC4240859p.Leu333Ile0.737
embC4240876c.1014C>T1.000
embC4240879c.1017G>T1.000
embC4240885c.1023T>C1.000
embC4240886p.Ile342Val1.000
embC4240897c.1035C>G1.000
embC4240900c.1038A>G1.000
embC4241560c.1698C>G1.000
embC4241584c.1722T>C1.000
embC4241587c.1725C>G1.000
embC4241593c.1731C>G1.000
embC4241611c.1749G>C1.000
embC4241614c.1752A>C1.000
embC4241626c.1764T>C1.000
embC4241635c.1773G>C1.000
embC4241644c.1782G>C1.000
embC4241750p.Leu630Met1.000
embC4241756c.1894C>T1.000
embC4241767c.1905C>G1.000
embC4241769p.Ser636Thr1.000
embC4241809c.1947A>C1.000
embA4245431c.2199T>C1.000
embA4245454p.Ala741Val1.000
embA4245459p.Pro743Ala1.000
embA4245465p.Pro745Thr1.000
embB4247449c.936C>T0.933
embB4247464c.951C>G1.000
embB4247470c.957T>C1.000
embB4247491c.978G>C1.000
embB4247497c.984T>C1.000
embB4247511p.Tyr333Phe1.000
embB4247527c.1014G>C0.944
embB4247536c.1023C>G0.944
embB4247554c.1041T>C0.833
embB4247555p.Leu348Ile0.833
embB4248190c.1677G>C0.214
embB4248199c.1686A>G0.267
embB4248200p.Ile563Val0.933
embB4248206p.Ser565Gly0.933
embB4248220c.1707A>G0.939
embB4248225p.Ala571Val0.382
embB4248232c.1719G>T0.528
embB4248233p.Leu574Val0.417
embB4248236p.Met575Leu0.526
embB4248242p.Val577Ile0.340
embB4248245p.Ile578Val0.617
embB4248250c.1737C>T0.633
embB4248252p.Gly580Ala0.314
embB4248259p.Met582Ile0.623
embB4248264p.Phe584Cys0.340
embB4248275p.Thr588Ala0.611
embB4248292c.1779G>A0.635
embB4248304c.1791G>C0.286
embB4248319c.1806A>G0.923
embB4248322c.1809G>T0.923

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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