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: 5cc552ef9c04f
Sample: 5cc552ef9c04f

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Summary
ID: 5cc552ef9c04f
Date: Sun Apr 28 08:17:17 2019
Strain: lineage1.2.1
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
EthambutolRembB p.His312Arg (0.16)
Pyrazinamide
StreptomycinRrrs r.462c>t (0.48)
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage1.2.1Indo-OceanicEAI2RD239

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB5341c.102T>C1.000
gyrB5344c.105C>G0.400
gyrB5347c.108G>C1.000
gyrB5350c.111C>G0.700
gyrB5362c.123T>G0.300
gyrB5363c.124T>C0.400
gyrB6169c.930C>G0.625
gyrB6181c.942C>A0.647
gyrB6184c.945C>G0.938
gyrB6193c.954G>A0.250
gyrB6196c.957C>G0.267
gyrB6214c.975G>C0.765
gyrB6238c.999G>A1.000
gyrB6242p.Arg335Lys1.000
gyrB6248c.1009C>T0.300
gyrB6253c.1014G>C0.583
gyrB6262c.1023G>A0.417
gyrB6268c.1029C>A0.500
gyrB6274c.1035C>G0.417
gyrB6280c.1041T>C0.583
gyrB6286c.1047T>C1.000
gyrB6289c.1050C>T0.182
gyrB6292c.1053G>C0.500
gyrB6295c.1056A>G0.300
gyrB6670c.1431G>C0.300
gyrB6673c.1434A>C1.000
gyrB6676c.1437T>G1.000
gyrB6680c.1441C>T0.667
gyrB6700c.1461T>C1.000
gyrB6703c.1464G>C1.000
gyrB6706c.1467G>A0.727
gyrB6709c.1470A>G1.000
gyrB6712c.1473G>C0.231
gyrB6715c.1476C>T0.786
gyrB6730c.1491A>G1.000
gyrB6742c.1503A>G0.857
gyrB6745c.1506T>C1.000
gyrB6760c.1521G>C1.000
gyrB6766c.1527G>C0.750
gyrB6769c.1530C>T0.750
gyrB6775c.1536G>T0.750
gyrB6778c.1539C>T1.000
gyrB6793c.1554T>C1.000
gyrB6794p.Ile519Leu0.800
gyrB6797p.Gly520Thr0.200
gyrB6803c.1564C>T0.200
gyrB7093c.1854T>C1.000
gyrB7114c.1875C>G1.000
gyrB7120c.1881T>C0.917
gyrB7123c.1884C>G0.909
gyrB7129c.1890T>G1.000
gyrB7132c.1893T>G1.000
gyrB7135c.1896G>A0.818
gyrB7141c.1902T>C1.000
gyrB7150c.1911G>C0.600
gyrB7162c.1923C>G0.357
gyrB7165c.1926C>G1.000
gyrB7168c.1929C>G0.357
gyrB7177c.1938G>A0.400
gyrB7190c.1951C>T0.533
gyrB7201c.1962G>A0.429
gyrB7210p.Asp657Glu0.417
gyrB7213c.1974G>A0.364
gyrB7216c.1977G>C1.000
gyrB7225c.1986T>C0.909
gyrA7337c.36C>A0.636
gyrA7343c.42G>C0.167
gyrA7349c.48A>G1.000
gyrA7352c.51G>C0.167
gyrA7355c.54T>C0.833
gyrA7361c.60C>T0.333
gyrA7362p.Glu21Gln1.000
gyrA7382c.81C>T0.333
gyrA7394c.93T>C1.000
gyrA7406c.105G>C0.167
gyrA7412c.111C>T0.389
gyrA7415c.114C>G0.444
gyrA7421c.120G>A0.444
gyrA7427c.126G>C1.000
gyrA7436c.135C>T0.333
gyrA7442c.141G>C1.000
gyrA7451c.150C>G1.000
gyrA7457c.156T>C1.000
gyrA7460c.159C>G0.500
gyrA7463c.162G>C0.750
gyrA7469c.168C>G0.769
gyrA7472c.171T>C0.500
gyrA7475c.174A>G1.000
gyrA7480p.Phe60Tyr1.000
gyrA7484c.183T>C1.000
gyrA7487c.186C>G0.429
gyrA7490c.189C>G0.429
gyrA7496c.195C>G0.261
gyrA7499c.198G>T0.667
gyrA7502c.201C>T0.250
gyrA7514c.213C>G0.320
gyrA7523c.222C>G0.727
gyrA7526c.225G>C0.667
gyrA7532c.231T>C1.000
gyrA7541c.240C>G0.273
gyrA7547c.246C>T1.000
gyrA7565c.264C>T0.654
gyrA7571c.270G>C0.320
gyrA7574c.273G>C0.240
gyrA7585p.Ser95Thr1.000
gyrA7587c.286C>T0.950
gyrA7595c.294C>G0.300
gyrA7601c.300C>G1.000
gyrA7607c.306C>G0.294
gyrA7613c.312G>A0.625
gyrA7619c.318C>G1.000
gyrA7622c.321C>T0.364
gyrA7625c.324G>A0.583
gyrA7626c.325C>T0.273
gyrA7631c.330G>C0.364
gyrA7712p.Leu137Phe0.364
gyrA7715c.414G>C1.000
gyrA7728c.427A>C1.000
gyrA7739c.438C>T0.176
gyrA7760c.459C>T0.222
gyrA7763c.462T>G0.389
gyrA7769c.468C>T0.211
gyrA7775c.474C>A0.667
gyrA7778c.477G>C0.158
gyrA7784c.483A>G0.850
gyrA7787c.486G>A0.714
gyrA7793c.492G>C0.273
gyrA7796c.495G>C0.167
gyrA7799c.498A>G1.000
gyrA7814c.513C>G0.174
gyrA7823c.522G>C0.143
gyrA7832c.531G>C0.150
gyrA7835c.534A>C0.167
gyrA7859c.558A>G1.000
gyrA7865c.564T>C1.000
gyrA7871c.570G>C0.900
gyrA8294c.993T>C1.000
gyrA8324c.1023T>C1.000
gyrA8339c.1038A>G1.000
gyrA8342c.1041G>C1.000
gyrA8366c.1065G>C0.964
gyrA8382p.Leu361Met1.000
gyrA8391p.Tyr364His1.000
gyrA8399c.1098T>C1.000
gyrA8401p.Asp367Ala1.000
gyrA8420c.1119T>C1.000
gyrA8426c.1125G>C1.000
gyrA8453c.1152A>C1.000
gyrA8459c.1158G>A1.000
gyrA8462c.1161A>C1.000
gyrA8471c.1170T>C1.000
gyrA8486c.1185T>C1.000
gyrA8882c.1581G>A0.667
gyrA8888c.1587C>G0.643
gyrA8897c.1596T>C0.400
gyrA8900c.1599G>C0.600
gyrA8903c.1602T>C1.000
gyrA8912c.1611G>A0.200
gyrA8915c.1614A>G0.933
gyrA8924c.1623C>T0.188
gyrA8930c.1629C>T0.933
gyrA8939c.1638T>C0.917
gyrA8942c.1641G>C0.917
gyrA8945c.1644G>C0.667
gyrA8946c.1645T>C1.000
gyrA8966c.1665C>G0.308
gyrA8967p.Ala556Lys0.308
gyrA8981c.1680G>C0.846
gyrA8982p.Cys561Ser0.692
gyrA8987c.1686C>G0.286
gyrA8990c.1689C>G0.733
gyrA8996c.1695T>C0.933
gyrA8998p.Leu566Trp1.000
gyrA9017c.1716C>G0.211
gyrA9023c.1722A>C1.000
gyrA9035c.1734G>C0.929
gyrA9044c.1743C>G1.000
gyrA9050p.Asp583Glu1.000
gyrA9051c.1750T>C1.000
gyrA9062c.1761C>G1.000
gyrA9065c.1764C>G1.000
gyrA9068c.1767G>C1.000
gyrA9099c.1798T>C0.952
gyrA9119c.1818A>G0.955
gyrA9125c.1824C>T0.850
gyrA9143c.1842T>C1.000
gyrA9147p.Gly616Ser0.727
gyrA9153p.Thr618Glu0.909
gyrA9161c.1860C>G0.286
gyrA9164c.1863G>C0.600
gyrA9167c.1866C>T0.800
gyrA9168c.1867C>T0.600
gyrA9182c.1881T>C0.947
gyrA9191c.1890G>C0.789
gyrA9192c.1891C>T0.150
gyrA9200c.1899A>G0.950
gyrA9204p.Ser635Thr0.810
gyrA9230c.1929T>C0.947
gyrA9233c.1932C>G0.833
gyrA9236c.1935G>C1.000
gyrA9242c.1941A>G0.150
gyrA9248c.1947G>C0.850
gyrA9252p.Val651Ile0.850
gyrA9267p.Asn656Gly0.158
gyrA9276c.1975C>T0.895
gyrA9284c.1983T>C0.833
gyrA9296c.1995T>C1.000
gyrA9300p.Ala667Ser0.909
gyrA9304p.Gly668Glu1.000
gyrA9308p.Asp669Glu0.769
gyrA9323c.2022C>G1.000
gyrA9329c.2028C>G0.211
gyrA9335c.2034G>C0.211
gyrA9338c.2037G>A0.211
gyrA9345c.2044A>C1.000
gyrA9356c.2055G>C0.714
gyrA9368c.2067G>A0.714
gyrA9374c.2073G>C0.667
gyrA9377c.2076A>G0.667
gyrA9383c.2082T>G0.364
gyrA9386c.2085T>C0.636
gyrA9389c.2088C>T0.636
gyrA9395c.2094G>C1.000
gyrA9398c.2097T>C1.000
gyrA9401c.2100G>C0.364
rpoB759577c.-230G>A0.600
rpoB759606c.-201T>C0.720
rpoB759629c.-178T>C0.176
rpoB759636c.-171C>T0.625
rpoB759644c.-163T>A0.667
rpoB759647c.-160T>C1.000
rpoB760067c.261G>C0.900
rpoB760070c.264T>G1.000
rpoB760091c.285G>C1.000
rpoB760101c.295T>C1.000
rpoB760112c.306T>C1.000
rpoB760118c.312T>G1.000
rpoB760121c.315T>C1.000
rpoB760130p.Asp108Glu1.000
rpoB760139c.333A>G1.000
rpoB760142c.336C>G1.000
rpoB760148p.Asp114Glu0.882
rpoB760181c.375T>C1.000
rpoB760184c.378A>G1.000
rpoB760196c.390C>G0.800
rpoB760223c.417T>C1.000
rpoB760235c.429T>C1.000
rpoB760241c.435G>C0.273
rpoB760271c.465C>G0.950
rpoB760283c.477G>C1.000
rpoB760298c.492G>C1.000
rpoB760307c.501T>G0.808
rpoB760313c.507G>C0.731
rpoB760331c.525G>C1.000
rpoB760337c.531C>G0.955
rpoB760340c.534G>C0.286
rpoB760361c.555T>C1.000
rpoB760376p.Asp190Glu1.000
rpoB760380p.Thr192Leu1.000
rpoB760406c.600G>C0.810
rpoB760409c.603C>T0.143
rpoB760412c.606C>A0.143
rpoB760415c.609C>T1.000
rpoB760424c.618C>G1.000
rpoB760430c.624T>C1.000
rpoB760475c.669A>G1.000
rpoB760481c.675G>C1.000
rpoB760484c.678A>G1.000
rpoB760508c.702G>C0.182
rpoB760511c.705G>C0.190
rpoB760520c.714C>G0.824
rpoB760522p.Ser239Asn1.000
rpoB760532c.726T>C1.000
rpoB760533p.Val243His1.000
rpoB760547c.741G>C0.833
rpoB760567p.Ser254Trp0.917
rpoB760574c.768G>C0.188
rpoB760591p.Val262Ala1.000
rpoB760598c.792C>T0.188
rpoB760611c.805T>C1.000
rpoB760634c.828T>C0.750
rpoB760646c.840C>G1.000
rpoB760655c.849A>G1.000
rpoB760661c.855A>C1.000
rpoB760674c.868T>C1.000
rpoB760679c.873A>G1.000
rpoB760683c.877T>C1.000
rpoB760724c.918T>C1.000
rpoB760730c.924T>C1.000
rpoB760748c.942C>G0.900
rpoB760751c.945G>C1.000
rpoB760757c.951T>C1.000
rpoB760759p.Val318Ala1.000
rpoB760769c.963C>G1.000
rpoB760775c.969G>C1.000
rpoB760862c.1056G>C1.000
rpoB760869p.Val355Thr1.000
rpoB760883c.1077G>C0.250
rpoB760886c.1080A>G1.000
rpoB760913c.1107C>T0.562
rpoB760916c.1110C>A0.250
rpoB760919c.1113C>G0.812
rpoB760920c.1114C>T0.812
rpoB760925c.1119T>C1.000
rpoB760928c.1122G>C0.562
rpoB760931c.1125C>G0.333
rpoB760934c.1128C>T1.000
rpoB760938c.1132C>T0.632
rpoB760946c.1140A>G1.000
rpoB760970c.1164G>C0.867
rpoB760982c.1176G>C1.000
rpoB760985c.1179G>C0.962
rpoB760991c.1185G>C1.000
rpoB761015c.1209G>C1.000
rpoB761027c.1221A>G1.000
rpoB761036c.1230G>C1.000
rpoB761037c.1231T>C1.000
rpoB761051c.1245G>C0.667
rpoB761054c.1248G>A0.292
rpoB761057c.1251G>C1.000
rpoB761060c.1254C>G0.333
rpoB761063c.1257C>G0.625
rpoB761096c.1290G>C0.318
rpoB761097c.1291A>T0.950
rpoB761102c.1296A>G1.000
rpoB761132c.1326G>T0.273
rpoB761133c.1327T>C1.000
rpoB761150c.1344A>C1.000
rpoB761165c.1359G>C0.962
rpoB761168c.1362C>G0.667
rpoB761171c.1365C>T0.250
rpoB761180c.1374A>C1.000
rpoB761183c.1377T>C0.727
rpoB761189c.1383T>C0.762
rpoB761195c.1389G>C1.000
rpoB761201c.1395G>A0.182
rpoB761204c.1398C>G0.952
rpoB761219c.1413G>C0.208
rpoB761234c.1428G>T0.200
rpoB761249c.1443A>G1.000
rpoB761252c.1446C>G0.708
rpoB761255c.1449T>G1.000
rpoB761258c.1452G>A0.208
rpoB761261c.1455G>C0.227
rpoB761264c.1458C>G0.917
rpoB761282c.1476C>G0.208
rpoB761300c.1494G>C0.696
rpoB761303c.1497G>A0.217
rpoB761309c.1503C>T0.905
rpoB761318c.1512G>C0.211
rpoB761327c.1521A>G0.238
rpoB761333c.1527G>C0.762
rpoB761354c.1548C>T1.000
rpoB761360c.1554T>C1.000
rpoB761362p.Ser519Thr1.000
rpoB761408c.1602G>C0.812
rpoB761414c.1608A>G1.000
rpoB761423c.1617T>C1.000
rpoB761435c.1629T>C1.000
rpoB761436p.Ala544Ser0.273
rpoB761444c.1638T>C1.000
rpoB761447c.1641C>G1.000
rpoB761450c.1644C>T0.250
rpoB761457p.Pro551Ala0.667
rpoB761462c.1656C>T0.235
rpoB761465c.1659G>C0.375
rpoB761471c.1665C>G0.733
rpoB761477c.1671C>T0.286
rpoB761480c.1674G>A0.250
rpoB761492c.1686G>C1.000
rpoB761504c.1698C>G0.688
rpoB761510c.1704T>G0.294
rpoB761531c.1725C>G0.188
rpoB761534c.1728G>C0.176
rpoB761537c.1731C>G1.000
rpoB761549c.1743G>T0.150
rpoB761570c.1764T>C0.826
rpoB761573c.1767C>G1.000
rpoB761579c.1773G>C1.000
rpoB761600c.1794T>G0.818
rpoB761606c.1800C>G1.000
rpoB761612c.1806G>C1.000
rpoB761615c.1809A>C1.000
rpoB761636c.1830G>T1.000
rpoB761645c.1839C>G1.000
rpoB761648c.1842T>C1.000
rpoB761657c.1851C>G0.889
rpoB761675c.1869G>C0.176
rpoB761948c.2142G>C0.800
rpoB761954c.2148C>G1.000
rpoB761955p.Ile717Val0.235
rpoB761969c.2163G>A0.261
rpoB761972c.2166C>T0.682
rpoB761990c.2184G>C0.269
rpoB761999c.2193G>C0.714
rpoB762008c.2202C>G0.630
rpoB762011c.2205G>C0.333
rpoB762029c.2223C>G0.250
rpoB762053c.2247T>C1.000
rpoB762062c.2256T>C0.292
rpoB762065c.2259T>C1.000
rpoB762083c.2277T>C1.000
rpoB762086c.2280G>C1.000
rpoB762101c.2295C>G1.000
rpoB762114p.Ile770Val1.000
rpoB762131c.2325C>G1.000
rpoB762140c.2334G>C0.875
rpoB762143c.2337T>C1.000
rpoB762149c.2343G>C1.000
rpoB762158c.2352G>C0.800
rpoB762167c.2361T>C1.000
rpoB762176c.2370T>C0.238
rpoB762185c.2379G>C1.000
rpoB762212c.2406G>C0.267
rpoB762221c.2415G>A0.286
rpoB762233c.2427G>C1.000
rpoB762239c.2433G>A0.241
rpoB762246c.2440C>T0.407
rpoB762254c.2448T>C0.185
rpoB762257c.2451C>G0.720
rpoB762266c.2460T>C0.720
rpoB762284c.2478G>C1.000
rpoB762287c.2481C>T0.286
rpoB762293c.2487T>C1.000
rpoB762296c.2490G>C0.316
rpoB762299c.2493G>C0.474
rpoB762314c.2508C>T0.556
rpoB762317c.2511A>G0.667
rpoB762323c.2517C>G0.353
rpoB762329c.2523G>C0.500
rpoB762338c.2532T>C0.714
rpoB762347c.2541T>C1.000
rpoB762353c.2547C>G0.714
rpoB762362p.Glu852Asp1.000
rpoB762369c.2563T>C1.000
rpoB762374c.2568G>C0.273
rpoB762377c.2571C>G0.667
rpoB762380c.2574T>C1.000
rpoB762395c.2589G>C1.000
rpoB762398c.2592T>C1.000
rpoB762404c.2598T>C1.000
rpoB762410c.2604T>C1.000
rpoB762416c.2610A>G1.000
rpoB762434c.2628T>C1.000
rpoB762443c.2637G>C0.688
rpoB762449c.2643C>A0.294
rpoB762458c.2652C>G0.684
rpoB762467c.2661C>T0.750
rpoB762470c.2664G>C0.250
rpoB762491c.2685T>C0.300
rpoB762507c.2702 2702del1.000
rpoC763351c.-19T>C1.000
rpoC763352c.-18T>A1.000
rpoC763375c.6C>A0.333
rpoC763402c.33C>T0.600
rpoC763408c.39T>C0.880
rpoC763411c.42T>G1.000
rpoC763414c.45T>C0.680
rpoC763430c.61A>C0.231
rpoC763435c.66A>G0.240
rpoC763441c.72C>T0.769
rpoC763444c.75T>C1.000
rpoC763456c.87A>G1.000
rpoC763468c.99G>C0.238
rpoC763486c.117T>G1.000
rpoC763501c.132C>T0.211
rpoC763528c.159G>A1.000
rpoC763546c.177A>G1.000
rpoC763570c.201G>C1.000
rpoC763573c.204G>C1.000
rpoC763594c.225C>T1.000
rpoC763603c.234C>T0.296
rpoC763633c.264T>C0.741
rpoC763636c.267T>C0.852
rpoC763660c.291T>C0.258
rpoC763666c.297G>T0.226
rpoC763669c.300C>G0.233
rpoC763675c.306C>G0.793
rpoC763696c.327T>C0.231
rpoC763702c.333C>T0.192
rpoC763705c.336G>A0.192
rpoC763708c.339G>C0.192
rpoC763709c.340C>T1.000
rpoC763714c.345G>C1.000
rpoC763717c.348T>C1.000
rpoC763723c.354G>C0.708
rpoC763732c.363C>G1.000
rpoC763735c.366G>C0.231
rpoC763741c.372C>T0.739
rpoC763744c.375G>C1.000
rpoC763765c.396T>G0.478
rpoC763768c.399C>G0.542
rpoC763780c.411C>G0.556
rpoC763781p.Ser138Ala0.370
rpoC763792p.Glu141Asp0.560
rpoC763807c.438T>C1.000
rpoC763813c.444C>G0.926
rpoC763822c.453C>G0.280
rpoC763825c.456G>A0.280
rpoC763831c.462A>G0.292
rpoC763835p.Ala156Met0.696
rpoC763855c.486C>T0.625
rpoC763858c.489A>G1.000
rpoC763867c.498C>T0.261
rpoC763872p.Gly168Ala1.000
rpoC763876p.Glu169Asp1.000
rpoC763879c.510A>G1.000
rpoC763882c.513G>A0.273
rpoC763888c.519G>C1.000
rpoC763894c.525A>G1.000
rpoC763900c.531G>C0.318
rpoC763933c.564C>T0.333
rpoC763945c.576T>C1.000
rpoC763948c.579G>C1.000
rpoC763949p.Arg194Asn0.176
rpoC763960c.591T>G1.000
rpoC763978c.609C>G1.000
rpoC763981c.612G>A0.167
rpoC764059c.690G>C0.182
rpoC764077c.708C>G0.250
rpoC764083c.714A>G1.000
rpoC764098c.729A>G1.000
rpoC764101c.732C>G1.000
rpoC764102p.Val245Gln0.214
rpoC764131c.762T>C1.000
rpoC764140c.771C>T0.227
rpoC764161c.792G>C0.842
rpoC764188c.819A>G1.000
rpoC764194p.Glu275Asp0.895
rpoC764203c.834G>C1.000
rpoC764206c.837T>C1.000
rpoC764254c.885G>C0.167
rpoC764255c.886C>T0.833
rpoC764266c.897T>C1.000
rpoC764269c.900G>C0.200
rpoC764272c.903G>C1.000
rpoC764278c.909A>G1.000
rpoC764284c.915G>A0.231
rpoC764293c.924G>C0.308
rpoC764344c.975C>T0.364
rpoC764365c.996C>T1.000
rpoC764377c.1008C>G0.550
rpoC764380c.1011G>C1.000
rpoC764381p.Ser338Arg0.667
rpoC764387c.1018T>C1.000
rpoC764405c.1036A>C1.000
rpoC764410c.1041G>C0.636
rpoC764419c.1050C>G0.174
rpoC764428c.1059G>C0.800
rpoC764431c.1062G>C1.000
rpoC764434c.1065A>G1.000
rpoC764446c.1077T>C1.000
rpoC764449c.1080G>C1.000
rpoC764452c.1083T>C1.000
rpoC764458c.1089G>C1.000
rpoC764461c.1092A>G1.000
rpoC764497c.1128A>G1.000
rpoC764521c.1152T>C1.000
rpoC764527c.1158C>T0.920
rpoC764536c.1167G>C1.000
rpoC764539c.1170C>G1.000
rpoC764554c.1185C>T0.233
rpoC764560c.1191T>C0.966
rpoC764566c.1197C>G0.214
rpoC764575c.1206T>G1.000
rpoC764578c.1209C>G0.731
rpoC764585c.1216C>T0.741
rpoC764611c.1242G>C1.000
rpoC764626c.1257C>T0.882
rpoC764632c.1263T>C0.594
rpoC764650c.1281G>T1.000
rpoC764651c.1282T>A0.133
rpoC764656c.1287C>G0.267
rpoC764692c.1323C>T0.353
rpoC764695c.1326T>C0.571
rpoC764698c.1329G>A0.613
rpoC764713c.1344G>T0.226
rpoC764716c.1347G>C0.625
rpoC764731c.1362G>C0.600
rpoC764749c.1380G>C0.613
rpoC764752c.1383G>C1.000
rpoC764758c.1389C>G0.273
rpoC764764c.1395T>C1.000
rpoC764791c.1422C>G0.321
rpoC764803c.1434C>G0.633
rpoC764809c.1440C>T0.370
rpoC764812c.1443C>G0.357
rpoC764815c.1446A>G1.000
rpoC764824c.1455T>C0.960
rpoC764827c.1458G>C0.731
rpoC764843p.Ala492Ser0.292
rpoC764858c.1489T>C1.000
rpoC764888c.1519T>C0.760
rpoC764893c.1524T>C1.000
rpoC764911c.1542A>G1.000
rpoC764923c.1554A>G0.730
rpoC764932c.1563C>G0.278
rpoC764948c.1579T>C0.737
rpoC764968c.1599T>C1.000
rpoC765006c.1638 1642del0.552
rpsL781568c.9C>G0.714
rpsL781571c.12C>T1.000
rpsL781595c.36T>C1.000
rpsL781598c.39G>C0.789
rpsL781605p.Ile16Val0.211
rpsL781608p.Ser17Ala1.000
rpsL781628c.69T>C0.286
rpsL781649c.90T>C1.000
rpsL781655c.96T>C1.000
rpsL781658c.99A>G0.273
rpsL781682c.123T>C0.605
rpsL781703c.144G>C0.588
rpsL781715c.156T>C1.000
rpsL781718c.159C>G0.576
rpsL781721c.162C>T0.324
rpsL781728c.169T>C1.000
rpsL781733c.174G>C0.281
rpsL781736c.177T>C1.000
rpsL781742c.183C>T0.344
rpsL781751c.192G>C0.645
rpsL781754c.195G>C1.000
rpsL781760c.201T>C1.000
rpsL781763c.204C>G0.844
rpsL781787c.228G>A0.595
rpsL781808c.249C>T0.424
rpsL781811c.252C>T1.000
rpsL781817c.258G>A0.588
rpsL781820c.261G>C0.588
rpsL781832c.273T>C1.000
rpsL781841c.282C>T0.303
rpsL781865c.306G>C1.000
rpsL781868c.309T>C1.000
rpsL781871c.312G>C1.000
rpsL781877c.318T>G0.318
rpsL781880c.321C>G0.227
rpsL781892c.333A>G1.000
rpsL781898c.339A>T1.000
rpsL781916c.357T>C1.000
rpsL781929p.Gly124Ser1.000
rpsL781933c.374G>A0.429
rplC801162c.354C>G0.727
rplC801171c.363A>G1.000
rplC801174c.366T>C1.000
rplC801204c.396C>T0.650
rplC801210c.402T>C0.238
rplC801228c.420T>C0.238
rplC801231c.423C>G0.667
rplC801249c.441T>G0.450
rplC801255c.447C>T0.474
rplC801258c.450C>G0.389
rplC801264c.456C>T0.562
rplC801267c.459A>C0.462
rplC801270c.462T>C0.500
rplC801276c.468G>T0.500
rplC801279c.471G>C0.538
rplC801282c.474G>C0.462
rplC801288c.480G>C0.500
rplC801307p.Ala167Ser0.389
rplC801312c.504G>C1.000
rplC801324c.516T>C1.000
rplC801333c.525G>C0.429
rplC801336c.528C>G0.500
rplC801357c.549T>C1.000
rplC801366c.558T>C0.267
rplC801367p.Ala187Thr0.733
rplC801402c.594T>C1.000
rplC801405c.597T>C1.000
rplC801423c.615G>C1.000
rplC801426c.618C>G1.000
rplC801427p.Met207Val1.000
rplC801438c.630T>C0.900
rrs1471923r.78t>c1.000
rrs1471925r.80t>c1.000
rrs1471932r.87a>g1.000
rrs1471934r.89a>g1.000
rrs1471969r.124t>c0.667
rrs1471970r.125g>a0.667
rrs1472030r.185g>t0.719
rrs1472031r.186g>t0.719
rrs1472033r.188a>g0.697
rrs1472034r.189t>c0.676
rrs1472040r.195t>c0.711
rrs1472042r.197t>c0.282
rrs1472053r.208agc>a1.000
rrs1472061r.216a>t1.000
rrs1472075r.230a>g1.000
rrs1472108r.263c>t0.776
rrs1472489r.644a>g0.270
rrs1472969r.1124a>g1.000
rrs1472970r.1125c>g1.000
rrs1472977r.1132g>c1.000
rrs1472978r.1133t>c1.000
rrs1473104r.1259c>t0.744
rrs1473105r.1260g>a0.791
rrs1473120r.1275c>ct0.950
rrs1473123r.1278a>t1.000
rrs1473290r.1445c>t1.000
rrl1473399c.-259A>AG0.577
rrl1473401c.-257G>A1.000
rrl1473408c.-250C>T1.000
rrl1473417c.-241C>T1.000
rrl1473419c.-239T>C1.000
rrl1473420c.-238A>G1.000
rrl1473421c.-237G>A1.000
rrl1473437c.-221T>C1.000
rrl1473439c.-219T>C1.000
rrl1473756r.99g>a0.862
rrl1473758r.101g>t1.000
rrl1473806r.149c>t1.000
rrl1473815r.158t>c0.939
rrl1473839r.182g>t0.756
rrl1473876r.219g>a0.143
rrl1473877r.220g>a0.857
rrl1473898r.241c>t0.829
rrl1473899r.242a>t0.953
rrl1473923r.266c>a0.186
rrl1473937r.280c>t0.949
rrl1473944r.287g>a0.914
rrl1473981r.324g>t0.952
rrl1473995r.338g>t0.969
rrl1474001r.344c>t1.000
rrl1474009r.352a>g1.000
rrl1474012r.355c>t0.960
rrl1474018r.361g>t0.880
rrl1474051r.394t>c0.743
rrl1474054r.397t>c0.743
rrl1474056r.399t>c0.743
rrl1474060r.403g>a0.763
rrl1474061r.404t>c0.132
rrl1474071r.414g>a0.811
rrl1474099r.442g>a0.889
rrl1474103r.446a>t1.000
rrl1474111r.454t>c0.900
rrl1474112r.455t>a0.833
rrl1474140r.483c>t1.000
rrl1474151r.494c>t1.000
rrl1474181r.524c>t1.000
rrl1474290r.633ttttcctctccggagg>t0.811
rrl1474291r.634tttcctctccggagga>t1.000
rrl1474308r.651g>t1.000
rrl1474310r.653t>g1.000
rrl1474356r.699t>c0.889
rrl1474362r.705a>g1.000
rrl1474376r.719t>c0.811
rrl1474427r.770a>c1.000
rrl1474429r.772g>c1.000
rrl1474432r.775c>g1.000
rrl1474434r.777t>g0.267
rrl1474447r.790g>a0.244
rrl1474627r.970g>a0.854
rrl1474632r.975g>t0.829
rrl1474639r.982g>a1.000
rrl1474717r.1060a>t0.797
rrl1474760r.1103a>g0.660
rrl1474794r.1137c>a0.235
rrl1474812r.1155g>a1.000
rrl1474831r.1174a>g1.000
rrl1474956r.1299c>t0.222
rrl1474957r.1300c>t0.636
rrl1474960r.1303c>g0.400
rrl1474961r.1304t>g0.600
rrl1474963r.1306g>a0.500
rrl1474964r.1307t>a0.625
rrl1474965r.1308g>t0.500
rrl1474968r.1311g>a0.600
rrl1474970r.1313g>a0.364
rrl1474991r.1334t>c0.500
rrl1474995r.1338t>g0.522
rrl1475006r.1349a>g0.286
rrl1475007r.1350c>t0.808
rrl1475013r.1356g>a0.840
rrl1475018r.1361g>c0.192
rrl1475019r.1362t>c0.192
rrl1475027r.1370g>t0.654
rrl1475028r.1371g>t0.679
rrl1475061r.1404c>a0.194
rrl1475062r.1405a>t0.194
rrl1475088r.1431a>t0.806
rrl1475202r.1545g>c0.143
rrl1475206r.1549c>t0.871
rrl1475209r.1552g>c0.867
rrl1475213r.1556c>t1.000
rrl1475249r.1592t>c1.000
rrl1475252r.1595c>t1.000
rrl1475266r.1609t>c1.000
rrl1475267r.1610g>a1.000
rrl1475275r.1618c>t1.000
rrl1475276r.1619t>c1.000
rrl1475291r.1634a>c1.000
rrl1475313r.1656g>a0.667
rrl1475315r.1658a>t0.634
rrl1475355r.1698c>t1.000
rrl1475369r.1712g>c1.000
rrl1475380r.1723c>t0.667
rrl1475387r.1730c>t0.692
rrl1475402r.1745c>t1.000
rrl1475419r.1762c>t0.727
rrl1475429r.1772g>a0.982
rrl1475479r.1822c>t0.229
rrl1475480r.1823a>t0.234
rrl1475505r.1848g>a1.000
rrl1475526r.1869c>a0.244
rrl1475573r.1916g>a0.200
rrl1475599r.1942a>g1.000
rrl1475604r.1947a>c0.186
rrl1475607r.1950a>g0.178
rrl1475608r.1951t>c0.804
rrl1475635r.1978g>a0.250
rrl1475637r.1980t>g0.250
rrl1475638r.1981c>t0.614
rrl1475642r.1985t>c0.750
rrl1475657r.2000a>g0.727
rrl1475659r.2002g>a0.262
rrl1475758r.2101ac>a0.700
rrl1475760r.2103c>t0.333
rrl1475763r.2106c>t1.000
rrl1475765r.2108ag>a0.583
rrl1475881r.2224t>c0.690
rrl1475975r.2318c>t0.333
rrl1475977r.2320a>g0.340
rrl1475988r.2331a>t0.326
rrl1476025r.2368g>t0.143
rrl1476032r.2375c>t0.154
rrl1476033r.2376t>c1.000
rrl1476035r.2378g>a0.778
rrl1476045r.2388g>c0.200
rrl1476047r.2390g>a0.200
rrl1476049r.2392c>t0.269
rrl1476086r.2429g>a1.000
rrl1476089r.2432t>c1.000
rrl1476095r.2438c>g1.000
rrl1476104r.2447tg>t1.000
rrl1476106r.2449a>t1.000
rrl1476115r.2458t>c1.000
rrl1476117r.2460g>c1.000
rrl1476131r.2474c>t0.216
rrl1476214r.2557g>t0.972
rrl1476215r.2558c>t0.971
rrl1476224r.2567a>g0.750
rrl1476251r.2594t>c0.220
rrl1476281r.2624t>c0.791
rrl1476529r.2872a>g0.196
rrl1476583r.2926g>c0.167
rrl1476584r.2927c>t0.837
rrl1476594r.2937c>t0.256
rrl1476597r.2940g>a1.000
rrl1476603r.2946g>a0.283
rrl1476628r.2971t>c0.227
rrl1476629r.2972c>a0.233
rrl1476675r.3018c>t0.231
rrl1476679r.3022t>c0.243
rrl1476689r.3032a>t1.000
rrl1476690r.3033c>t0.708
rrl1476692r.3035t>a0.292
rrl1476693r.3036g>a0.708
rrl1476695r.3038t>a1.000
rrl1476710r.3053c>t0.269
rrl1476716r.3059a>c0.750
rrl1476720r.3063g>a0.190
rrl1476723r.3066t>a0.190
rrl1476725r.3068c>t0.250
rrl1476726r.3069a>g1.000
rrl1476732r.3075t>c1.000
rrl1476750r.3093t>c0.455
rrl1476755r.3098g>a1.000
inhA1674303c.102C>T0.636
inhA1674315c.114C>G1.000
inhA1674318c.117C>G0.417
inhA1674321c.120G>C0.417
inhA1674331c.130C>T0.583
inhA1674342c.141T>C0.500
inhA1674465c.264C>G0.917
inhA1674480c.279T>C1.000
inhA1674486c.285T>C1.000
inhA1674489c.288G>C0.792
inhA1674507c.306G>C0.179
inhA1674537c.336C>G0.720
inhA1674540c.339C>T0.720
inhA1674542p.Ala114Glu1.000
inhA1674546c.345T>C0.250
inhA1674549c.348G>C0.160
inhA1674570c.369G>C1.000
inhA1674576c.375T>C0.909
inhA1674579c.378G>C0.727
inhA1674585c.384T>G0.300
inhA1674589p.Met130Leu1.000
inhA1674618c.417C>T0.769
inhA1674624c.423A>C1.000
inhA1674636c.435C>G0.385
inhA1674656p.Ser152Thr0.385
inhA1674660c.459G>C0.545
inhA1674690c.489C>G0.538
inhA1674703c.502T>C1.000
inhA1674708c.507G>A1.000
inhA1674864c.663C>T0.545
inhA1674870c.669T>C1.000
inhA1674879c.678T>G0.500
inhA1674892p.Asn231Asp0.500
inhA1674903c.702T>C1.000
inhA1674904p.Ala235Pro1.000
inhA1674909c.708G>C0.545
inhA1674930c.729C>T0.600
inhA1674933c.732G>C0.400
inhA1674963c.762G>C0.273
inhA1674966c.765T>C1.000
inhA1674967p.Asp256Thr0.273
inhA1674977p.Tyr259Phe0.250
inhA1674993c.792G>C1.000
rpsA1833517c.-25AC>A1.000
rpsA1833539c.-3A>C0.542
rpsA1833541c.-1T>C0.542
rpsA1833554p.Thr5Ala0.379
rpsA1833568c.27G>C0.686
rpsA1833589c.48A>C0.389
rpsA1833595c.54T>C1.000
rpsA1833596p.Ser19Ala0.343
rpsA1833604c.63C>T0.971
rpsA1833610c.69C>T0.618
rpsA1833613c.72C>A0.375
rpsA1833619c.78A>C0.594
rpsA1833658c.117C>G0.633
rpsA1833667c.126C>G0.750
rpsA1833679c.138G>T0.261
rpsA1833721c.180A>G0.737
rpsA1833724c.183C>G0.294
rpsA1833727c.186G>C1.000
rpsA1833742c.201A>G1.000
rpsA1833745c.204G>C1.000
rpsA1833769c.228C>G0.824
rpsA1833771p.Asn77Ser0.706
rpsA1833790c.249T>C0.941
rpsA1833793c.252C>T0.882
rpsA1833802c.261A>G0.412
rpsA1833805c.264C>G0.562
rpsA1833808c.267G>C0.562
rpsA1833811c.270G>C0.353
rpsA1833832c.291G>A0.188
rpsA1833835c.294C>T0.625
rpsA1833838c.297G>C0.200
rpsA1833841c.300C>G1.000
rpsA1833847c.306C>G1.000
rpsA1833856c.315A>G1.000
rpsA1833862c.321G>T0.188
rpsA1833874c.333T>C1.000
rpsA1833892c.351G>A0.292
rpsA1833894p.Ala118Glu0.292
rpsA1833928c.387G>C1.000
rpsA1833949c.408T>C0.952
rpsA1833970c.429G>C0.700
rpsA1833971c.430C>T0.316
rpsA1833976c.435C>T0.700
rpsA1833979c.438T>C1.000
rpsA1833991c.450C>G0.684
rpsA1834000c.459G>C1.000
rpsA1834012c.471G>C0.850
rpsA1834015c.474G>C0.684
rpsA1834021c.480C>T1.000
rpsA1834030c.489C>G1.000
rpsA1834096c.555G>C0.722
rpsA1834099c.558C>G0.941
rpsA1834102c.561T>C0.824
rpsA1834105c.564C>G0.176
rpsA1834177c.636A>C1.000
rpsA1834189c.648G>C0.818
rpsA1834195c.654G>C1.000
rpsA1834201c.660C>G0.667
rpsA1834210c.669C>T0.750
rpsA1834222c.681T>C1.000
rpsA1834225c.684C>G0.250
rpsA1834231c.690T>G0.267
rpsA1834240c.699T>C0.933
rpsA1834249c.708T>C1.000
rpsA1834252c.711C>G0.667
rpsA1834261c.720A>G1.000
rpsA1834264c.723G>C1.000
rpsA1834288c.747C>G0.750
rpsA1834294c.753G>C0.750
rpsA1834297c.756C>G0.208
rpsA1834303c.762T>C0.231
rpsA1834306c.765T>C1.000
rpsA1834336c.795C>G0.680
rpsA1834348c.807T>C1.000
rpsA1834366c.825A>G1.000
rpsA1834381c.840G>A0.250
rpsA1834396c.855G>C0.364
rpsA1834411c.870T>G1.000
rpsA1834417c.876G>C1.000
rpsA1834423c.882G>C0.684
rpsA1834435c.894G>C0.667
rpsA1834451c.910T>C1.000
rpsA1834456c.915T>G0.250
rpsA1834465c.924T>C0.733
rpsA1834468c.927A>G1.000
rpsA1834489c.948T>C1.000
rpsA1834498c.957C>T0.278
rpsA1834513c.972C>G0.667
rpsA1834528c.987T>C1.000
rpsA1834546c.1005T>C1.000
rpsA1834555c.1014T>C1.000
rpsA1834607p.Arg356Ser0.158
rpsA1834633c.1092A>G1.000
rpsA1834639c.1098T>C1.000
rpsA1834654p.Glu371Asp0.217
rpsA1834690c.1149T>C1.000
rpsA1834732c.1191T>C1.000
rpsA1834738c.1197A>G0.708
rpsA1834747c.1206A>G0.158
rpsA1834751p.Leu404Ile0.158
rpsA1834756c.1215G>A0.941
rpsA1834759c.1218A>C0.176
rpsA1834765c.1224A>G0.250
rpsA1834766p.Lys409Ala0.188
rpsA1834775p.Ala412Asn0.250
rpsA1834780c.1239A>G1.000
rpsA1834786c.1245A>G1.000
rpsA1834789c.1248T>C1.000
rpsA1834792c.1251G>T0.188
rpsA1834804c.1263C>G0.250
rpsA1834852c.1311C>G1.000
katG2155616p.Val166Ile0.900
katG2155617c.495A>G1.000
katG2155632c.480T>G1.000
katG2155637p.Leu159Ile0.917
katG2155641p.Lys157Asn1.000
katG2155668c.444C>T0.882
katG2155680c.432C>G0.938
katG2155691c.421A>G1.000
katG2155696p.Ala139Val0.857
katG2155716c.396A>G1.000
kasA2518146p.Phe11Tyr1.000
kasA2518162c.48G>A1.000
kasA2518172p.Thr20Ala0.158
kasA2518183c.69G>A0.875
kasA2518190p.Ser26Ala1.000
kasA2518219c.105T>C0.208
kasA2518220c.106C>T1.000
kasA2518223c.109T>C0.208
kasA2518231c.117C>A0.208
kasA2518234c.120G>A1.000
kasA2518248p.Ala45Val1.000
kasA2518255c.141A>G0.636
kasA2518279c.165T>C1.000
kasA2518282c.168A>G0.500
kasA2518606c.492G>T0.200
kasA2518609p.Met165Ile1.000
kasA2518627c.513T>C0.900
kasA2518651c.537C>G0.909
kasA2518663c.549T>C0.917
kasA2518671p.Val186Ala1.000
kasA2518678c.564C>T1.000
kasA2518688p.Val192Phe1.000
kasA2518711c.597A>G1.000
kasA2518714c.600A>T1.000
kasA2518732c.618C>G1.000
kasA2518765c.651G>C1.000
kasA2518768c.654C>G1.000
kasA2518783c.669T>C1.000
kasA2518789c.675G>C1.000
kasA2518792c.678C>G1.000
kasA2518795c.681C>G1.000
kasA2518825c.711T>C1.000
kasA2518843c.729T>G1.000
kasA2518846c.732G>C1.000
kasA2518853p.Leu247Ile1.000
kasA2518864c.750G>C1.000
kasA2518879c.765A>G1.000
kasA2518885c.771T>C1.000
ahpC2726642c.450C>G0.364
ahpC2726648c.456T>A0.545
ahpC2726651c.459G>C0.538
ahpC2726657c.465A>G0.308
ahpC2726660c.468C>T0.250
ahpC2726666c.474C>G0.625
ahpC2726669p.Asp159Glu0.800
ahpC2726672c.480G>A0.800
ahpC2726675c.483A>G1.000
ahpC2726681c.489A>G1.000
ahpC2726687c.495C>G0.235
ahpC2726693c.501C>G0.882
ahpC2726696c.504C>G1.000
ahpC2726717c.525A>C1.000
folC2747314c.285T>G0.200
folC2747317c.282G>C1.000
folC2747331p.His90Gly0.833
folC2747335c.264C>G0.167
folC2747343p.Val86Met0.214
folC2747355p.Val82Ile0.200
folC2747362c.237C>G1.000
folC2747371c.228G>A0.857
folC2747389c.210C>G0.933
folC2747395c.204A>G1.000
thyX3067305p.Glu214Ala0.273
thyX3067307c.639G>A0.273
thyX3067316c.630T>C0.400
thyX3067322c.624G>T0.300
thyX3067325c.621T>C0.727
thyX3067330p.Val206Met0.250
thyX3067337c.609G>A0.273
thyX3067349c.597C>G0.692
thyX3067355c.591T>G1.000
thyX3067379c.567G>A0.692
thyX3067382c.564G>A0.231
thyX3067388c.558G>C0.667
thyX3067394c.552C>G1.000
thyX3067406c.540T>C0.909
thyX3067412c.534G>C0.700
thyX3067415c.531G>A0.700
thyX3067418c.528G>C0.900
thyX3067427c.519C>G0.800
thyX3067433c.513G>T0.200
thyX3067439c.507T>C1.000
thyX3067442c.504G>C1.000
thyX3067465p.Ile161Val0.182
thyX3067466c.480C>G0.818
thyX3067577c.369C>T0.923
thyX3067612p.Lys112Gly0.650
thyX3067619c.327T>C1.000
thyX3067631c.315G>C0.333
thyX3067640c.306C>G0.286
thyX3067652c.294A>G0.650
thyX3067661c.285G>C1.000
thyX3067676c.270G>C0.550
thyX3067681p.Cys89Leu0.550
thyX3067682c.264C>G0.400
thyX3067685c.261T>C1.000
thyX3067688c.258C>G0.950
thyX3067694c.252C>G0.381
thyX3067709c.237C>G0.615
thyX3067715c.231G>A0.292
thyX3067721c.225A>G1.000
thyX3067724c.222C>T0.565
thyX3067727c.219T>G1.000
thyX3067739c.207A>G0.920
thyX3067742c.204T>C0.960
thyX3067745c.201G>C0.280
thyX3067748c.198G>A0.192
thyX3067762p.Arg62Lys1.000
thyX3067765p.Leu61Ile1.000
thyX3067781c.165G>C1.000
thyX3067802c.144G>C1.000
thyX3067826c.120G>C0.941
thyX3067838c.108G>C0.938
thyX3067874c.72G>C1.000
thyA3073857c.615G>A0.182
thyA3073863c.609A>G1.000
thyA3073866c.606G>C0.818
thyA3073874p.Ile200Val1.000
thyA3073878c.594C>T0.615
thyA3073881c.591G>C0.308
thyA3073889p.Ser195Ala0.923
thyA3073892c.580C>G1.000
thyA3073903p.Ala190Asp0.235
thyA3073905c.567G>C0.235
thyA3073917c.555G>C0.278
thyA3073925c.547A>G0.778
thyA3073929c.543A>G1.000
thyA3073932c.540G>A0.200
thyA3073953c.519A>G0.238
thyA3073956c.516C>G1.000
thyA3073959c.513A>G0.300
thyA3073977c.495T>C1.000
thyA3073980c.492G>A0.571
thyA3073983c.489G>C0.571
thyA3073989c.483A>G1.000
thyA3073998c.474C>G0.263
thyA3074004c.468A>G1.000
thyA3074010c.462G>C0.688
thyA3074013c.459G>A0.267
thyA3074031c.441A>G1.000
thyA3074034c.438A>G0.765
thyA3074037c.435G>C0.765
thyA3074057p.Glu139Pro1.000
thyA3074058c.414G>T0.188
thyA3074061c.411T>C1.000
thyA3074064c.408G>C0.765
thyA3074076c.396G>C0.750
thyA3074079c.393C>T0.267
thyA3074100c.372A>G1.000
thyA3074103c.369G>C1.000
thyA3074121p.Asp117Glu0.923
thyA3074127c.345C>G0.769
thyA3074130c.342C>G0.364
thyA3074334c.138A>G1.000
thyA3074360c.112A>G1.000
thyA3074361c.111A>G1.000
thyA3074364c.108A>G1.000
thyA3074372p.Met34Leu1.000
ald3087704c.885T>C1.000
ald3087707c.888C>T0.818
ald3087726p.Ala303Ser1.000
ald3087729p.Ser304Ala1.000
ald3087734c.915G>A0.167
ald3087737c.918G>C1.000
ald3087750p.Tyr311Val0.833
ald3087770c.951G>C1.000
ald3087779c.960T>C0.909
ald3087791c.972T>G1.000
ald3087799p.His327Arg0.909
fbiA3640303c.-240TA>T1.000
fbiA3640347c.-196A>G1.000
fbiA3640365c.-178C>G1.000
fbiA3640378c.-165A>T0.750
panD4044180p.Asp34Glu0.200
panD4044188c.94A>G1.000
panD4044195c.87A>G1.000
panD4044210c.72G>C0.167
embC4240693c.831T>C0.273
embC4240699c.837C>G0.846
embC4240717p.His285Gln0.750
embC4240726c.864G>C0.400
embC4240735c.873C>T0.200
embC4240759c.897C>T0.211
embC4240771c.909G>C0.222
embC4240777c.915G>A0.235
embC4240780c.918T>C1.000
embC4240783c.921G>C1.000
embC4240786c.924C>T0.200
embC4240789c.927T>C1.000
embC4240795c.933C>G0.533
embC4240819c.957A>C1.000
embC4240822c.960C>G0.357
embC4240831c.969T>C0.467
embC4240859p.Leu333Val0.583
embC4240867c.1005T>G0.417
embC4240870c.1008T>C1.000
embC4240879c.1017G>C1.000
embC4240885c.1023T>C1.000
embC4241026c.1164C>G0.700
embC4241038c.1176G>C0.800
embC4241039p.Asp393Asn0.700
embC4241050c.1188T>G1.000
embC4241053c.1191G>C1.000
embC4241071c.1209C>G0.882
embC4241077c.1215C>A0.167
embC4241089c.1227C>G0.143
embC4241104c.1242G>A0.667
embC4241107c.1245G>C0.920
embC4241116c.1254C>G0.214
embC4241140c.1278A>C1.000
embC4241141p.Ile427Ala0.692
embC4241158c.1296T>C1.000
embC4241161c.1299C>G1.000
embC4241162c.1300T>C1.000
embC4241167c.1305C>G0.905
embC4241168c.1306C>T0.714
embC4241179c.1317G>T0.182
embC4241182c.1320G>A0.167
embC4241188c.1326C>G0.750
embC4241206c.1344G>C0.850
embC4241218c.1356G>C0.263
embC4241230c.1368A>G1.000
embC4241233c.1371G>C0.800
embC4241236c.1374C>G0.231
embC4241374c.1512T>C1.000
embC4241380c.1518A>C1.000
embC4241394p.Lys511Ser0.812
embC4241407c.1545A>G0.158
embC4241416c.1554C>T0.810
embC4241449c.1587C>T0.944
embC4241453p.Ile531Val1.000
embC4241458c.1596C>G0.158
embC4242844c.2982A>G1.000
embC4242847c.2985C>A1.000
embC4242859c.2997C>T0.909
embC4242862c.3000A>G1.000
embC4242863p.Tyr1001Asn1.000
embC4242880c.3018A>G0.846
embC4242883c.3021C>G0.786
embC4242886c.3024G>A0.786
embC4242892c.3030G>C0.786
embC4242901c.3039G>C0.214
embC4242919c.3057A>G0.231
embC4242922c.3060C>G0.231
embC4242928c.3066A>G0.727
embC4242931c.3069G>C0.273
embA4245060c.1828T>C1.000
embA4245077c.1845G>C1.000
embA4245083c.1851A>C1.000
embA4245089c.1857G>C0.867
embA4245101c.1869G>C1.000
embA4245110c.1878C>T0.778
embA4245128c.1896G>C0.143
embA4245137c.1905T>C1.000
embA4245143c.1911C>A0.667
embA4245145p.Gln638Pro0.667
embA4245149c.1917C>G1.000
embA4245152c.1920C>G0.786
embA4245153p.Ile641Val0.214
embA4245158c.1926C>G0.786
embA4245164c.1932C>T0.714
embA4245182c.1950T>C1.000
embA4245183c.1951C>T0.615
embA4245189p.Leu653Phe0.750
embA4245194c.1962G>C0.636
embA4245620c.2388T>C0.200
embA4245623c.2391G>C1.000
embA4245626c.2394G>A1.000
embA4245647c.2415C>G0.857
embA4245650p.Ile806Met0.857
embA4245652p.Thr807Ser0.857
embA4245668c.2436C>G0.867
embA4245674c.2442A>C1.000
embA4245688p.Val819Ala1.000
embA4245692c.2460G>C1.000
embA4245693p.Ile821Val1.000
embA4245701c.2469G>C1.000
embA4245737c.2505A>C1.000
embA4245740c.2508T>C1.000
embA4245764c.2532G>C1.000
embB4246603c.90C>G1.000
embB4246621c.108T>C1.000
embB4246624c.111C>G1.000
embB4246627c.114T>C1.000
embB4246630c.117G>C1.000
embB4246642c.129G>C1.000
embB4246645c.132G>C1.000
embB4247365c.852A>C1.000
embB4247370p.Gly286Ala0.231
embB4247375p.Leu288Val0.786
embB4247386c.873T>C0.800
embB4247389c.876C>G0.750
embB4247395c.882C>G0.833
embB4247398c.885G>C0.167
embB4247401c.888T>C1.000
embB4247407c.894G>C0.810
embB4247437c.924A>G1.000
embB4247446c.933C>T0.160
embB4247452c.939C>G0.840
embB4247464c.951C>G0.913
embB4247470c.957T>C1.000
embB4247476c.963C>T0.167
embB4247491c.978G>C0.870
embB4247494c.981G>A0.917
embB4247497c.984T>C0.208
embB4247512c.999T>C1.000
embB4247539c.1026T>C1.000
embB4247965c.1452C>G0.786
embB4247977c.1464C>G0.842
embB4248007c.1494C>G1.000
embB4248008c.1495C>T0.792
embB4248011p.Ser500Ala0.905
embB4248035p.Val508Ile0.923
embB4248040c.1527C>G0.200
embB4248041p.Ala510Thr0.917
embB4248044p.Lys511Ser0.905
embB4248052c.1539G>A0.792
embB4248055c.1542G>C0.792
embB4248070c.1557T>C1.000
embB4248085c.1572T>C1.000
embB4248088c.1575C>T0.765
embB4248097c.1584C>G1.000
embB4248100c.1587C>T0.767
embB4248124c.1611G>C0.750
embB4248130c.1617G>C0.273
embB4248133c.1620C>A0.182
embB4248139c.1626C>G0.190
embB4248142c.1629T>C1.000
embB4248143p.Leu544Met0.300
embB4248157c.1644A>G0.259
embB4248163c.1650G>C0.621
embB4248169c.1656C>G0.250
embB4248172c.1659G>C0.741
embB4248173p.Val554Met0.593
embB4248199c.1686A>G1.000
embB4248200p.Ile563Val0.682
embB4248205c.1692C>G0.182
embB4248206p.Ser565Gly1.000
embB4248211c.1698G>C0.500
embB4248220c.1707A>T0.360
embB4248226c.1713G>A0.552
embB4248232c.1719G>T0.571
embB4248242p.Val577Ile0.320
embB4248265c.1752C>T0.308
embB4248266c.1753C>T0.320
embB4248277c.1764G>C0.857
embB4248280c.1767C>G0.840
embB4248304c.1791G>C0.273
embB4248313c.1800C>G0.611
embB4248316c.1803C>G0.889
embB4248319c.1806A>G1.000
embB4248322c.1809G>C0.316
embB4248325c.1812G>C0.550
embB4248350c.1837T>C1.000
embB4248355c.1842A>G1.000
embB4248358c.1845C>G0.348
embB4248361c.1848A>G1.000
embB4248362p.Ser617Lys0.609
embB4248394c.1881G>C0.280
embB4248407p.Leu632Val1.000
embB4248410p.Phe633Leu0.583
embB4248416p.Leu635Ile0.917
embB4248421c.1908G>T0.417
embB4248424c.1911G>C0.500
embB4248425c.1912T>C1.000
embB4248430c.1917T>C1.000
embB4248432p.Trp640Phe1.000
embB4248448c.1935C>A0.174
embB4248457c.1944T>C1.000
embB4248469c.1956C>T0.810
embB4248472c.1959T>C0.190
embB4248488p.Ala659Ser1.000
embB4248508c.1995G>A1.000
embB4248514c.2001A>C1.000
embB4248515p.Val668Ile0.923
embB4248526c.2013C>A0.923
embB4248535c.2022C>G1.000
embB4248541c.2028T>C1.000

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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