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: 5ccbeb88bbe9e
Sample: 5ccbeb88bbe9e

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Summary
ID: 5ccbeb88bbe9e
Date: Fri May 3 08:22:06 2019
Strain: lineage6;lineage4.6.2;lineage4.4.1.2;lineage2.2.1.1
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
EthambutolRembB p.His312Arg (0.25)
Pyrazinamide
StreptomycinRrrs r.462c>t (1.00)
Ethionamide
FluoroquinolonesRgyrB p.Thr500Asn (0.88)
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage6West-Africa 2AFRI 1RD702
lineage4.6.2Euro-AmericanT;LAMRD726
lineage4.4.1.2Euro-AmericanT1None
lineage2.2.1.1East-Asian (Beijing)Beijing-RD150RD105;RD207;RD181;RD150

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB5410c.171G>C1.000
gyrB5803c.564A>G0.833
gyrB5806c.567C>G0.692
gyrB5812c.573C>G0.462
gyrB5815c.576C>G0.846
gyrB5818c.579G>C0.286
gyrB5824c.585A>G1.000
gyrB5848c.609G>C1.000
gyrB5858p.Asn207Asp1.000
gyrB6170p.His311Ala1.000
gyrB6181c.942C>T0.200
gyrB6187c.948C>T0.364
gyrB6649c.1410T>C1.000
gyrB6655c.1416T>C1.000
gyrB6673c.1434A>C1.000
gyrB6676c.1437T>G0.933
gyrB6700c.1461T>C1.000
gyrB6703c.1464G>C1.000
gyrB6706c.1467G>A1.000
gyrB6709c.1470A>G1.000
gyrB6715c.1476C>T0.846
gyrB6718c.1479C>T0.846
gyrB6724c.1485G>T0.857
gyrB6730c.1491A>G1.000
gyrB6742c.1503A>G0.938
gyrB6745c.1506T>C0.941
gyrB6760c.1521G>C1.000
gyrB6763c.1524G>C0.941
gyrB6775c.1536G>T1.000
gyrB6778c.1539C>T1.000
gyrB6784c.1545C>T0.278
gyrB6793c.1554T>C0.875
gyrB6798p.Gly520Ala0.938
gyrB6811c.1572C>T0.938
gyrB6841c.1602T>C1.000
gyrB6844c.1605T>C0.938
gyrB6853c.1614A>G1.000
gyrB6856c.1617T>C1.000
gyrB6859c.1620T>C1.000
gyrB6869c.1630T>C0.900
gyrB6898c.1659G>A0.600
gyrB6904c.1665C>G1.000
gyrB6905p.Ile556Val0.800
gyrB6911p.Asn558His1.000
gyrB6919c.1680T>C1.000
gyrB6925c.1686T>C0.857
gyrB6931c.1692A>G0.857
gyrB6934c.1695A>G1.000
gyrB6949c.1710A>G1.000
gyrB6982c.1743A>C1.000
gyrB6997c.1758G>A1.000
gyrB7012c.1773G>C1.000
gyrB7015c.1776G>A1.000
gyrB7018c.1779G>C1.000
gyrB7024c.1785G>A1.000
gyrB7033c.1794G>C1.000
gyrB7047p.Lys603Met1.000
gyrB7051p.Glu604Asp1.000
gyrB7078c.1839A>C1.000
gyrB7084c.1845A>G0.933
gyrB7093c.1854T>C1.000
gyrB7100c.1861T>C1.000
gyrB7168c.1929C>G0.833
gyrB7171c.1932C>G0.875
gyrB7178c.1939T>C1.000
gyrB7183c.1944C>T0.625
gyrB7186c.1947C>G1.000
gyrA7313c.12G>C1.000
gyrA7317c.16T>C1.000
gyrA7325c.24T>C1.000
gyrA7335p.Leu12Val1.000
gyrA7355c.54T>C1.000
gyrA7362p.Glu21Gln1.000
gyrA7367p.Gln22His1.000
gyrA7394c.93T>C1.000
gyrA7397c.96G>C0.875
gyrA7418c.117C>T1.000
gyrA7427c.126G>C1.000
gyrA7436c.135C>T1.000
gyrA7442c.141G>C1.000
gyrA7451c.150C>G1.000
gyrA7457c.156T>C1.000
gyrA7463c.162G>A1.000
gyrA7502c.201C>T1.000
gyrA7520c.219G>T1.000
gyrA7523c.222C>A1.000
gyrA7526c.225G>C0.833
gyrA7532c.231T>C0.364
gyrA7538c.237G>A1.000
gyrA7547c.246C>T1.000
gyrA7559c.258G>C0.364
gyrA7565c.264C>T1.000
gyrA7569p.Ala90Ser0.833
gyrA7585p.Ser95Thr1.000
gyrA7587c.286C>T0.500
gyrA7592c.291G>C1.000
gyrA7595c.294C>G1.000
gyrA7607c.306C>G0.800
gyrA7625c.324G>C0.222
gyrA7626c.325C>T0.700
gyrA7694c.393A>G0.800
gyrA7697c.396C>G0.364
gyrA7700c.399G>C0.182
gyrA7703c.402G>C0.182
gyrA7710c.409T>C1.000
gyrA7715c.414G>C0.800
gyrA7721p.Glu140Asp0.200
gyrA7728c.427A>C1.000
gyrA7742c.441G>A0.167
gyrA7745c.444G>A0.833
gyrA7758p.Ile153Val0.545
gyrA7763c.462T>G0.818
gyrA7778c.477G>A0.182
gyrA7784c.483A>G0.636
gyrA7793c.492G>C0.750
gyrA7799c.498A>G0.833
gyrA7814c.513C>G0.727
gyrA7832c.531G>T0.909
gyrA7835c.534A>T0.300
gyrA7841c.540C>T0.750
gyrA7853c.552C>T0.750
gyrA7859c.558A>G0.200
gyrA7865c.564T>C0.833
gyrA7871c.570G>A0.667
gyrA8111c.810G>C1.000
gyrA8120c.819G>A0.815
gyrA8121c.820T>C1.000
gyrA8156c.855T>G1.000
gyrA8168c.867A>G1.000
gyrA8264c.963T>C1.000
gyrA8270c.969G>T0.722
gyrA8276c.975G>A0.167
gyrA8282c.981G>A0.167
gyrA8283p.Ile328Leu1.000
gyrA8288c.987T>C1.000
gyrA8291c.990C>T0.143
gyrA8294c.993T>C1.000
gyrA8324c.1023T>C1.000
gyrA8327c.1026C>T0.273
gyrA8337p.Leu346Phe0.143
gyrA8340p.Ala347Ser1.000
gyrA8348c.1047C>G0.143
gyrA8351c.1050C>T0.810
gyrA8354c.1053G>C0.143
gyrA8366c.1065G>C0.850
gyrA8375c.1074G>C0.158
gyrA8378c.1077C>T0.526
gyrA8382p.Leu361Met1.000
gyrA8390c.1089C>G0.375
gyrA8393c.1092T>C1.000
gyrA8399c.1098T>G0.300
gyrA8459c.1158G>A0.273
gyrA8462c.1161A>G0.400
gyrA8471c.1170T>C0.733
gyrA8480c.1179C>T0.857
gyrA8486c.1185T>C0.933
gyrA8489c.1188A>G0.600
gyrA8492c.1191G>A0.333
gyrA8498c.1197C>T0.846
gyrA8501c.1200G>C0.385
gyrA8504c.1203G>C0.846
gyrA8513c.1212C>G0.917
gyrA8516c.1215T>C1.000
gyrA8519c.1218A>C1.000
gyrA8531c.1230G>A0.900
gyrA8535p.Glu412Gln0.909
gyrA8540c.1239C>T0.400
gyrA8619c.1318T>C1.000
gyrA8624c.1323G>C0.857
gyrA8627c.1326C>G1.000
gyrA8633c.1332C>T1.000
gyrA8636c.1335A>G1.000
gyrA8649p.Arg450Lys0.857
gyrA8660c.1359C>T0.857
gyrA8663p.Asp454Glu1.000
gyrA8664c.1363C>T0.857
gyrA8672c.1371A>G1.000
gyrA8777c.1476C>T1.000
gyrA8801c.1500G>C1.000
gyrA8810c.1509A>T1.000
gyrA8817p.Ser506Ala0.957
gyrA8828c.1527T>C0.917
gyrA8829c.1528T>C1.000
gyrA8834c.1533C>T0.913
gyrA8846c.1545C>T0.741
gyrA8852c.1551T>C1.000
gyrA8858c.1557T>G0.207
gyrA8867c.1566A>G0.931
gyrA8870c.1569G>C1.000
gyrA8873c.1572A>C0.929
gyrA8882c.1581G>A0.964
gyrA8888c.1587C>G0.880
gyrA8903c.1602T>C1.000
gyrA8915c.1614A>G1.000
gyrA8918c.1617C>G0.793
gyrA8930c.1629C>T0.733
gyrA8939c.1638T>C1.000
gyrA8945c.1644G>C0.917
gyrA8946c.1645T>C1.000
gyrA8957c.1656C>T0.786
gyrA8981c.1680G>C0.960
gyrA8990c.1689C>G1.000
gyrA8996c.1695T>C1.000
gyrA8998p.Leu566Trp1.000
gyrA9017c.1716C>G1.000
gyrA9023c.1722A>C1.000
gyrA9029c.1728T>G1.000
gyrA9032c.1731T>C0.944
gyrA9035c.1734G>A0.944
gyrA9051c.1750T>C1.000
gyrA9056c.1755C>G1.000
gyrA9080c.1779G>C1.000
gyrA9089c.1788G>C1.000
gyrA9099c.1798T>C1.000
gyrA9116c.1815G>A1.000
gyrA9119c.1818A>G1.000
gyrA9182c.1881T>C1.000
gyrA9191c.1890G>T0.857
gyrA9197c.1896G>C0.857
gyrA9200c.1899A>G1.000
gyrA9323c.2022C>G1.000
gyrA9329c.2028C>G0.333
gyrA9335c.2034G>T0.167
gyrA9345c.2044A>C0.895
gyrA9365p.Glu688Asp0.188
gyrA9377c.2076A>G1.000
gyrA9383c.2082T>C0.176
gyrA9386c.2085T>C1.000
gyrA9395c.2094G>C1.000
gyrA9419c.2118T>C1.000
gyrA9420p.Ile707Ala1.000
gyrA9425c.2124C>T1.000
gyrA9443c.2142G>C1.000
rpoB759604c.-203A>T0.867
rpoB759606c.-201T>C1.000
rpoB759814p.Asp3Val0.947
rpoB760121c.315T>G1.000
rpoB760130p.Asp108Glu1.000
rpoB760139c.333A>C1.000
rpoB760142c.336C>G0.750
rpoB760148p.Asp114Glu0.833
rpoB760155p.Lys117Arg0.818
rpoB760172c.366G>C0.833
rpoB760181c.375T>C1.000
rpoB760184c.378A>G1.000
rpoB760196c.390C>G0.143
rpoB760199c.393C>G0.857
rpoB760223c.417T>C1.000
rpoB760235c.429T>C1.000
rpoB760283c.477G>C1.000
rpoB760298c.492G>C1.000
rpoB760310c.504G>C1.000
rpoB760317c.511A>T1.000
rpoB760331c.525G>C0.217
rpoB760340c.534G>T1.000
rpoB760354p.Glu183Ala1.000
rpoB760357p.Thr184Asn1.000
rpoB760376p.Asp190Glu1.000
rpoB760389c.583A>T0.833
rpoB760394c.588C>G0.833
rpoB760407p.Ser201Gly0.889
rpoB760412c.606C>T0.833
rpoB760418c.612G>C0.900
rpoB760424c.618C>G1.000
rpoB760430c.624T>C1.000
rpoB760442c.636G>A0.200
rpoB760449p.Thr215Leu0.647
rpoB760460c.654G>T0.647
rpoB760463c.657C>T0.625
rpoB760472c.666C>T0.222
rpoB760475c.669A>G1.000
rpoB760478c.672C>T0.867
rpoB760481c.675G>C1.000
rpoB760484c.678A>G1.000
rpoB760490c.684C>G0.222
rpoB760494p.Val230Ile0.667
rpoB760521c.715A>T0.889
rpoB760526c.720G>A0.727
rpoB760541c.735G>C0.750
rpoB760547c.741G>C1.000
rpoB760563p.Arg253Met1.000
rpoB760585p.Asn260Ser0.933
rpoB760587p.Thr261Ala0.824
rpoB760591p.Val262Ala1.000
rpoB760593p.Gly263Ser0.824
rpoB760596p.Thr264Pro0.824
rpoB760611c.805T>C1.000
rpoB760634c.828T>C0.150
rpoB760640c.834C>T0.833
rpoB760643c.837G>A0.800
rpoB760646c.840C>G0.160
rpoB760649c.843G>C0.846
rpoB760655c.849A>G1.000
rpoB760658c.852G>A0.154
rpoB760661c.855A>C1.000
rpoB760670c.864G>C1.000
rpoB760674c.868T>C1.000
rpoB760679c.873A>G1.000
rpoB760683c.877T>C1.000
rpoB760715c.909C>G0.952
rpoB760718c.912C>G0.739
rpoB760721c.915C>G0.174
rpoB760724c.918T>C0.174
rpoB760730c.924T>C1.000
rpoB760734p.Val310Ile0.864
rpoB760916c.1110C>G1.000
rpoB760919c.1113C>T1.000
rpoB760925c.1119T>C1.000
rpoB760931c.1125C>G1.000
rpoB760934c.1128C>T1.000
rpoB760946c.1140A>G1.000
rpoB760964c.1158C>T1.000
rpoB760965p.Met387Leu1.000
rpoB760970c.1164G>C0.944
rpoB760979c.1173G>A0.812
rpoB760982c.1176G>T0.200
rpoB760985c.1179G>C0.867
rpoB760988c.1182C>T0.875
rpoB760991c.1185G>C0.143
rpoB761006c.1200C>T0.850
rpoB761015c.1209G>C1.000
rpoB761021c.1215G>C1.000
rpoB761027c.1221A>G1.000
rpoB761036c.1230G>C0.933
rpoB761037c.1231T>C1.000
rpoB761051c.1245G>C0.933
rpoB761096c.1290G>C0.846
rpoB761097c.1291A>T1.000
rpoB761102c.1296A>G1.000
rpoB761132c.1326G>T0.933
rpoB761133c.1327T>C0.867
rpoB761138c.1332C>T0.667
rpoB761150c.1344A>T0.182
rpoB761165c.1359G>A0.800
rpoB761168c.1362C>G0.833
rpoB761171c.1365C>T0.333
rpoB761180c.1374A>G1.000
rpoB761189c.1383T>G1.000
rpoB761195c.1389G>C1.000
rpoB761201c.1395G>A0.900
rpoB761204c.1398C>A0.300
rpoB761207c.1401C>T1.000
rpoB761222c.1416G>C0.938
rpoB761240c.1434C>T0.944
rpoB761249c.1443A>G1.000
rpoB761255c.1449T>G1.000
rpoB761258c.1452G>A1.000
rpoB761261c.1455G>C1.000
rpoB761264c.1458C>G0.294
rpoB761282c.1476C>A0.929
rpoB761300c.1494G>A0.462
rpoB761318c.1512G>C0.929
rpoB761321c.1515C>T0.267
rpoB761327c.1521A>G1.000
rpoB761330c.1524G>C1.000
rpoB761354c.1548C>T0.700
rpoB761360c.1554T>C1.000
rpoB761362p.Ser519Thr0.182
rpoB761369p.Glu521Asp0.800
rpoB761408c.1602G>C0.900
rpoB761414c.1608A>G1.000
rpoB761423c.1617T>C1.000
rpoB761502p.Pro566Ser0.857
rpoB761508p.Ser568Ala0.200
rpoB761516c.1710G>C0.933
rpoB761528c.1722C>T0.667
rpoB761537c.1731C>G1.000
rpoB761549c.1743G>T0.211
rpoB761561c.1755C>G1.000
rpoB761564c.1758G>C1.000
rpoB761573c.1767C>G1.000
rpoB761579c.1773G>C1.000
rpoB761606c.1800C>G1.000
rpoB761612c.1806G>T1.000
rpoB761615c.1809A>C1.000
rpoB761627c.1821C>T0.900
rpoB761636c.1830G>T1.000
rpoB761645c.1839C>G1.000
rpoB761648c.1842T>C1.000
rpoB761657c.1851C>A0.211
rpoB761666c.1860G>C0.222
rpoB761669c.1863C>T0.833
rpoB761675c.1869G>T0.368
rpoB761687c.1881C>T0.789
rpoB761690c.1884G>C0.952
rpoB761711c.1905C>G0.941
rpoB761712p.Val636Ile0.941
rpoB761723p.Glu639Asp1.000
rpoB761724p.Glu640Lys1.000
rpoB761728p.Ser641Thr1.000
rpoB761732c.1926C>T1.000
rpoB761750c.1944G>C1.000
rpoB761760p.Ile652Val1.000
rpoB761765c.1959T>G1.000
rpoB761772p.His656Ala1.000
rpoB761777c.1971C>T1.000
rpoB761778p.Asn658Asp1.000
rpoB761783c.1977C>G0.643
rpoB761791p.Arg662Gln1.000
rpoB761885c.2079T>C1.000
rpoB761897c.2091C>G1.000
rpoB761906c.2100C>G0.938
rpoB761909c.2103T>C0.188
rpoB761912c.2106T>C1.000
rpoB761915c.2109C>T0.812
rpoB761916p.Asp704Asn1.000
rpoB761930c.2124G>C1.000
rpoB761948c.2142G>C1.000
rpoB761954c.2148C>G1.000
rpoB761969c.2163G>A0.875
rpoB761972c.2166C>G1.000
rpoB762006c.2200C>A1.000
rpoB762017c.2211A>G0.263
rpoB762024p.Val740Thr1.000
rpoB762029c.2223C>G1.000
rpoB762038c.2232C>T0.294
rpoB762053c.2247T>C0.800
rpoB762062c.2256T>C1.000
rpoB762065c.2259T>C1.000
rpoB762083c.2277T>C1.000
rpoB762086c.2280G>C1.000
rpoB762101c.2295C>G1.000
rpoB762104c.2298C>T0.200
rpoB762114p.Ile770Val1.000
rpoB762131c.2325C>G1.000
rpoB762134c.2328C>T1.000
rpoB762140c.2334G>C1.000
rpoB762143c.2337T>C1.000
rpoB762149c.2343G>C1.000
rpoB762158c.2352G>C1.000
rpoB762167c.2361T>C1.000
rpoB762176c.2370T>C1.000
rpoB762185c.2379G>C1.000
rpoB762212c.2406G>C0.960
rpoB762236c.2430G>C0.957
rpoB762254c.2448T>C0.947
rpoB762257c.2451C>G1.000
rpoB762266c.2460T>C1.000
rpoB762281c.2475G>A1.000
rpoB762284c.2478G>C1.000
rpoB762293c.2487T>C1.000
rpoB762314c.2508C>T1.000
rpoB762317c.2511A>G1.000
rpoB762329c.2523G>C1.000
rpoB762338c.2532T>C1.000
rpoB762347c.2541T>C1.000
rpoB762362p.Glu852Asp1.000
rpoB762369c.2563T>C1.000
rpoB762374c.2568G>C1.000
rpoB762380c.2574T>G0.968
rpoB762398c.2592T>C1.000
rpoB762401c.2595G>C1.000
rpoB762404c.2598T>C1.000
rpoB762407c.2601G>C0.963
rpoB762410c.2604T>G1.000
rpoB762416c.2610A>G1.000
rpoB762449c.2643C>T1.000
rpoB762452c.2646G>T0.147
rpoB762470c.2664G>C1.000
rpoB762490p.Val895Ala1.000
rpoB762509c.2703T>G0.958
rpoB762510p.Ala902Pro0.958
rpoB762521c.2715C>G0.130
rpoB762527c.2721G>C0.857
rpoB762533c.2727T>C1.000
rpoB762536c.2730T>C1.000
rpoB762537c.2731T>C0.737
rpoB762551c.2745C>T1.000
rpoB762563c.2757G>T0.824
rpoB762575c.2769C>T0.917
rpoB762581c.2775T>C1.000
rpoB762582c.2776T>C1.000
rpoB762812c.3006C>G1.000
rpoB762818c.3012C>G1.000
rpoB762827c.3021G>T0.150
rpoB762831c.3025A>T1.000
rpoB762836c.3030C>T1.000
rpoB762857c.3051C>G1.000
rpoB762860c.3054G>C1.000
rpoB762863c.3057T>C0.171
rpoB762894c.3088C>T0.842
rpoB762911c.3105C>T0.865
rpoB762917c.3111C>G1.000
rpoB762920c.3114C>T1.000
rpoB762929c.3123G>C1.000
rpoB762957c.3151C>T0.857
rpoB762962c.3156C>T0.806
rpoB762995c.3189G>T1.000
rpoB762998c.3192G>A0.222
rpoB763031c.3225T>G1.000
rpoB763034c.3228C>G1.000
rpoB763040c.3234C>G1.000
rpoB763050c.3244C>T0.842
rpoB763053c.3247T>C0.947
rpoB763058c.3252C>G0.944
rpoB763070c.3264T>C1.000
rpoB763076c.3270C>G0.722
rpoB763085c.3279C>T0.812
rpoB763094c.3288G>C1.000
rpoB763100c.3294G>A0.176
rpoB763115c.3309T>C1.000
rpoB763127c.3321G>C0.824
rpoB763136c.3330C>T0.625
rpoB763139c.3333C>T0.188
rpoB763142c.3336C>G0.812
rpoB763148c.3342G>C0.857
rpoB763169c.3363A>G0.885
rpoB763193c.3387C>T0.885
rpoB763200c.3394C>T0.808
rpoB763203p.Ser1133Ala0.958
rpoB763207p.Ser1134Lys1.000
rpoB763226c.3420A>G0.147
rpoB763227c.3421C>T0.853
rpoB763238c.3432T>C1.000
rpoB763262c.3456C>A0.938
rpoB763265c.3459G>C0.938
rpoB763283c.3477T>C1.000
rpoC763351c.-19T>C1.000
rpoC763352c.-18T>A1.000
rpoC763396c.27A>G0.806
rpoC763408c.39T>C0.885
rpoC763411c.42T>G1.000
rpoC763414c.45T>G1.000
rpoC763430c.61A>C0.935
rpoC763444c.75T>C1.000
rpoC763447c.78C>T0.933
rpoC763456c.87A>G1.000
rpoC763465c.96G>A0.829
rpoC763468c.99G>C0.171
rpoC763483c.114G>C0.156
rpoC763486c.117T>C1.000
rpoC763492c.123G>C0.818
rpoC763528c.159G>A1.000
rpoC763546c.177A>G1.000
rpoC763570c.201G>C0.788
rpoC763573c.204G>C0.226
rpoC763594c.225C>T0.731
rpoC763603c.234C>T0.833
rpoC763609c.240C>T0.261
rpoC763618c.249C>T1.000
rpoC763657c.288G>A0.909
rpoC763660c.291T>G1.000
rpoC763666c.297G>C0.857
rpoC763669c.300C>G0.857
rpoC763675c.306C>T0.500
rpoC763696c.327T>C0.842
rpoC763702c.333C>G1.000
rpoC763705c.336G>C0.214
rpoC763708c.339G>C0.286
rpoC763709c.340C>T0.667
rpoC763714c.345G>A0.417
rpoC763717c.348T>C1.000
rpoC763723c.354G>C0.357
rpoC763732c.363C>G0.882
rpoC763735c.366G>C0.882
rpoC763741c.372C>T0.389
rpoC763744c.375G>C1.000
rpoC763747c.378G>A0.467
rpoC763765c.396T>G1.000
rpoC763771c.402C>T0.308
rpoC763774c.405G>C0.231
rpoC763801c.432C>G0.625
rpoC763807c.438T>C1.000
rpoC763813c.444C>G1.000
rpoC763816c.447C>G0.500
rpoC763888c.519G>C0.944
rpoC763891c.522G>C0.222
rpoC763894c.525A>G1.000
rpoC763900c.531G>C0.750
rpoC763933c.564C>T1.000
rpoC763936c.567C>G1.000
rpoC763939c.570G>A1.000
rpoC763947p.Ala193Val1.000
rpoC763951c.582G>C1.000
rpoC763987c.618C>T1.000
rpoC763991p.Ile208Leu1.000
rpoC764002c.633C>T1.000
rpoC764005c.636G>C1.000
rpoC764059c.690G>T1.000
rpoC764083c.714A>G1.000
rpoC764085p.Asn239Thr0.947
rpoC764087p.Leu240Val1.000
rpoC764095c.726C>G0.737
rpoC764098c.729A>G1.000
rpoC764101c.732C>G1.000
rpoC764104c.735C>G1.000
rpoC764110c.741C>T0.762
rpoC764134c.765C>G0.238
rpoC764140c.771C>T0.227
rpoC764143c.774G>C1.000
rpoC764161c.792G>C0.778
rpoC764169p.Asn267Thr0.938
rpoC764188c.819A>G1.000
rpoC764242c.873C>T0.867
rpoC764245c.876C>T1.000
rpoC764254c.885G>C0.875
rpoC764257c.888G>C0.882
rpoC764266c.897T>G0.235
rpoC764269c.900G>C1.000
rpoC764272c.903G>C1.000
rpoC764278c.909A>G1.000
rpoC764287c.918C>T0.867
rpoC764293c.924G>C0.875
rpoC764302c.933C>T0.765
rpoC764317c.948C>G0.933
rpoC764320c.951C>G0.933
rpoC764344c.975C>T0.941
rpoC764365c.996C>T1.000
rpoC764368c.999C>T0.875
rpoC764371c.1002G>C0.938
rpoC764377c.1008C>G0.941
rpoC764380c.1011G>C1.000
rpoC764387c.1018T>C1.000
rpoC764405c.1036A>C1.000
rpoC764410c.1041G>C1.000
rpoC764428c.1059G>C1.000
rpoC764431c.1062G>C1.000
rpoC764434c.1065A>G1.000
rpoC764435c.1066A>C1.000
rpoC764446c.1077T>C1.000
rpoC764449c.1080G>C1.000
rpoC764452c.1083T>C1.000
rpoC764455c.1086G>T0.750
rpoC764458c.1089G>C1.000
rpoC764461c.1092A>G1.000
rpoC764497c.1128A>G1.000
rpoC764503c.1134G>C1.000
rpoC764521c.1152T>C1.000
rpoC764524c.1155C>T0.167
rpoC764527c.1158C>T1.000
rpoC764539c.1170C>G0.852
rpoC764548c.1179G>A0.857
rpoC764551c.1182G>C0.138
rpoC764566c.1197C>G1.000
rpoC764573c.1204C>T0.815
rpoC764576c.1207T>A0.808
rpoC764581c.1212T>C1.000
rpoC764611c.1242G>T0.222
rpoC764626c.1257C>T0.833
rpoC764650c.1281G>T1.000
rpoC764656c.1287C>G0.885
rpoC764668c.1299C>T0.880
rpoC764677c.1308C>G0.130
rpoC764692c.1323C>T0.208
rpoC764714c.1345C>T0.172
rpoC764719c.1350G>A0.655
rpoC764746c.1377G>A0.154
rpoC764752c.1383G>T1.000
rpoC764764c.1395T>C1.000
rpoC764791c.1422C>G1.000
rpoC764803c.1434C>G0.844
rpoC764815c.1446A>G1.000
rpoC764824c.1455T>C1.000
rpoC764827c.1458G>C1.000
rpoC764858c.1489T>C0.952
rpoC764863c.1494G>C0.895
rpoC764869c.1500C>T0.889
rpoC764878c.1509C>G0.938
rpoC764887c.1518G>C0.765
rpoC764888c.1519T>C0.765
rpoC764893c.1524T>C0.471
rpoC764896c.1527C>T0.632
rpoC764911c.1542A>G0.812
rpoC764912p.Met515Gln0.750
rpoC764923c.1554A>G0.375
rpoC764932c.1563C>G0.167
rpoC764948c.1579T>C0.933
rpoC765007c.1638T>C1.000
rpoC765008c.1639T>C1.000
rpoC765019c.1650A>G1.000
rpoC765034c.1665T>C1.000
rpoC765040c.1671T>C1.000
rpoC765041c.1672T>C1.000
rpoC765047c.1678T>C1.000
rpoC765055c.1686C>G1.000
rpoC765076c.1707A>C1.000
rpoC765079c.1710T>G1.000
rpoC765082c.1713G>T1.000
rpoC765089c.1720T>C1.000
rpoC765100c.1731G>C1.000
rpoC765103c.1734G>A1.000
rpoC765115c.1746G>T1.000
rpoC765121c.1752G>C1.000
rpoC765277c.1908G>T0.923
rpoC765281p.Thr638Asp0.923
rpoC765300p.Val644Ala0.714
rpoC765305p.Ile646Val0.714
rpoC765311p.Ala648Thr0.714
rpoC765358p.Met663Ile1.000
rpoC765379c.2010G>A0.882
rpoC765383p.Met672Leu1.000
rpoC765404p.Leu679Thr1.000
rpoC765409c.2040T>C1.000
rpoC765412c.2043T>C0.923
rpoC765421c.2052C>G0.895
rpoC765445c.2076G>T0.857
rpoC765451c.2082C>G0.150
rpoC765452p.Ala695Phe0.143
rpoC765478c.2109T>C1.000
rpoC765526c.2157C>T0.200
rpoC765533p.Tyr722His0.944
rpoC765541c.2172C>G0.150
rpoC765547c.2178C>T0.188
rpoC765548c.2179A>T0.812
rpoC765553c.2184C>A0.214
rpoC765556c.2187G>C1.000
rpoC765562c.2193G>C0.150
rpoC765578c.2209C>T0.136
rpoC765589c.2220G>C0.158
rpoC765592c.2223C>T0.143
rpoC765611p.His748Ser0.864
rpoC765625c.2256C>T1.000
rpoC765628c.2259G>C1.000
rpoC765635p.Val756Leu0.773
rpoC765640c.2271A>G0.783
rpoC765662c.2293T>C0.929
rpoC765669p.His767Arg0.875
rpoC765673p.Asp768Glu0.812
rpoC765700c.2331T>C1.000
rpoC765718p.Asp783Glu0.895
rpoC765721c.2352G>A0.895
rpoC765724c.2355C>G0.947
rpoC765734c.2365T>C1.000
rpoC765739c.2370G>T1.000
rpoC765742p.Glu791Asp0.917
rpoC765751c.2382C>G1.000
rpoC765753p.Asp795Ala1.000
rpoC765772c.2403C>G1.000
rpoC765787c.2418C>T0.955
rpoC765790c.2421C>T0.947
rpoC765793c.2424C>G1.000
rpoC765796c.2427C>T1.000
rpoC765811c.2442T>C1.000
rpoC765814c.2445A>G1.000
rpoC765826c.2457T>C1.000
rpoC765835c.2466C>T0.905
rpoC765871c.2502T>C0.900
rpoC765875p.Val836Ile1.000
rpoC765904c.2535C>G1.000
rpoC765908c.2539C>T0.833
rpoC765934c.2565C>T0.885
rpoC765937c.2568T>C0.923
rpoC765962c.2593T>C0.840
rpoC765967c.2598C>T1.000
rpoC765979c.2610C>G1.000
rpoC765982c.2613C>T1.000
rpoC765991c.2622C>G0.875
rpoC765994c.2625A>T1.000
rpoC766003c.2634G>C0.833
rpoC766009c.2640G>T0.880
rpoC766012c.2643C>T0.870
rpoC766043p.Gln892Gly0.941
rpoC766061p.Val898Ile1.000
rpoC766270c.2901G>C1.000
rpoC766273c.2904T>C1.000
rpoC766280p.Ser971Gly1.000
rpoC766288c.2919C>G1.000
rpoC766294c.2925C>T1.000
rpoC766297c.2928G>C1.000
rpoC766309c.2940G>C1.000
rpoC766312c.2943T>A1.000
rpoC766315c.2946C>G1.000
rpoC766327c.2958C>G1.000
rpoC766348c.2979A>G1.000
rpoC766351c.2982C>G1.000
rpoC766357c.2988C>T1.000
rpoC766363c.2994G>T1.000
rpoC766366c.2997C>T1.000
rpoC766381c.3012C>T1.000
rpoC766390c.3021C>T1.000
rpoC766393c.3024C>T1.000
rpoC766426c.3057C>T1.000
rpoC766435p.Glu1022Asp1.000
rpoC766456c.3087C>G1.000
rpoC766459c.3090G>T1.000
rpoC766484p.Val1039Ile1.000
rpoC766492c.3123T>C1.000
rpoC766517p.Thr1050Ala0.500
rpoC766522c.3153C>A0.500
rpoC766528c.3159T>G1.000
rpoC766530p.Arg1054Gln1.000
rpoC766537c.3168G>A1.000
rpoC766540p.Asp1057Glu1.000
rpoC766547p.Arg1060Lys1.000
rpoC766564c.3195C>G1.000
rpoC766570c.3201T>G1.000
rpoC766573c.3204T>G1.000
rpoC766576c.3207C>T1.000
rpoC766582c.3213C>T1.000
rpoC766585c.3216T>C1.000
rpoC766607p.Ile1080Leu1.000
rpoC766610p.Ser1081Pro1.000
rpoC766618c.3249G>T1.000
rpoC766630c.3261G>C1.000
rpoC766645c.3276A>G1.000
rpoC766672c.3303T>C0.818
rpoC766750c.3381C>G1.000
rpoC766753c.3384C>T0.200
rpoC766786c.3417G>A0.500
rpoC766787p.Glu1140Gln0.900
rpoC766798c.3429C>G1.000
rpoC766804c.3435A>G0.900
rpoC766843c.3474T>C0.929
rpoC766846c.3477C>G0.929
rpoC766911p.Ile1181Thr0.600
rpoC766915p.Asp1182Glu0.600
rpoC766918c.3549C>G0.600
rpoC766921c.3552G>C0.600
rpoC766931p.Ala1188Thr0.600
rpoC766935p.Glu1189Ala0.600
rpoC766942c.3573C>T0.600
rpoC766945c.3576A>T0.400
rpoC766961p.Gly1198Leu0.857
rpoC766972c.3603G>C0.211
rpoC766978c.3609C>A0.267
rpoC766981c.3612T>C0.267
rpoC766996c.3627C>T1.000
rpoC767002c.3633G>C0.750
rpoC767011c.3642G>A0.250
rpoC767033c.3664T>A0.250
rpoC767041c.3672G>T0.750
rpoC767044c.3675G>C0.750
rpoC767059c.3690T>C0.167
rpoC767062c.3693C>A0.167
rpoC767086c.3717C>T0.176
rpoC767098c.3729T>C1.000
rpoC767104c.3735C>G0.800
rpoC767105p.Asn1246Gln0.800
rpoC767110c.3741T>C0.800
rpoC767119c.3750A>G1.000
rpoC767158c.3789T>G0.421
rpoC767163p.Asn1265Ser0.368
rpoC767167c.3798C>G0.389
rpoC767180p.Ala1271His0.467
rpoC767185c.3816G>T0.353
rpoC767191c.3822C>G0.412
rpoC767194c.3825C>G0.278
rpoC767197c.3828G>A0.588
rpoC767203c.3834C>G0.263
rpoC767206c.3837C>G0.684
rpoC767209c.3840T>C0.263
rpoC767212c.3843G>T0.368
rpoC767218c.3849C>T0.263
rpoC767221c.3852C>G1.000
rpoC767230c.3861G>C0.688
rpoC767233c.3864T>C1.000
rpoC767239c.3870T>C0.250
rpoC767263c.3894T>C1.000
rpoC767264p.Ala1299His0.235
rpoC767278c.3909T>C0.176
rpoC767281c.3912C>G0.812
rpoC767284c.3915C>T0.786
rpoC767302c.3933C>G0.846
rpsL781571c.12C>T1.000
rpsL781586c.27C>T1.000
rpsL781592c.33T>C0.867
rpsL781595c.36T>C1.000
rpsL781598c.39G>C1.000
rpsL781605p.Ile16Val0.857
rpsL781608p.Ser17Ala1.000
rpsL781616c.57C>G0.867
rpsL781628c.69T>C1.000
rpsL781631c.72G>C0.867
rpsL781649c.90T>A0.800
rpsL781652c.93T>G0.800
rpsL781682c.123T>C1.000
rpsL781709c.150G>C1.000
rpsL781763c.204C>G0.900
rpsL781766c.207C>T0.900
rpsL781772c.213C>T0.824
rpsL781808c.249C>T1.000
rpsL781811c.252C>T1.000
rpsL781814c.255C>T1.000
rpsL781817c.258G>T1.000
rpsL781832c.273T>G1.000
rpsL781859c.300T>C0.905
rpsL781868c.309T>C1.000
rpsL781871c.312G>C1.000
rpsL781877c.318T>A1.000
rpsL781892c.333A>G1.000
rpsL781898c.339A>C1.000
rpsL781907c.348T>C0.952
rpsL781916c.357T>G1.000
rpsL781929p.Gly124Ser1.000
rplC801147c.339T>C1.000
rplC801150c.342G>C1.000
rplC801153c.345G>C1.000
rplC801156c.348T>A1.000
rplC801168c.360C>T0.722
rplC801171c.363A>G1.000
rplC801174c.366T>C1.000
rplC801176p.Phe123Tyr0.833
rplC801210c.402T>C0.857
rplC801220p.Ser138Gly0.714
rplC801228c.420T>C1.000
rplC801231c.423C>T0.667
rplC801285c.477G>T0.200
rplC801288c.480G>C0.250
rplC801307p.Ala167Ser0.684
rplC801312c.504G>C1.000
rplC801324c.516T>C1.000
rplC801330c.522G>T0.500
rplC801333c.525G>C0.800
rplC801336c.528C>G0.200
rplC801337p.Val177Thr0.800
rplC801341p.Leu178Gln1.000
rplC801345c.537C>T0.200
rplC801348c.540T>G1.000
rplC801349p.Leu181Val0.800
rplC801357c.549T>C0.909
rplC801366c.558T>C0.750
rplC801378c.570C>T0.750
rplC801385c.577C>T0.818
rrs1471862r.17t>c0.739
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inhA1674471c.270G>C1.000
inhA1674486c.285T>C1.000
inhA1674489c.288G>C1.000
inhA1674507c.306G>C0.913
inhA1674513c.312C>G0.174
inhA1674534c.333G>C0.917
inhA1674542p.Ala114Glu1.000
inhA1674546c.345T>C1.000
inhA1674549c.348G>C1.000
inhA1674550p.Ser117Ala1.000
inhA1674573c.372G>C0.920
inhA1674576c.375T>C1.000
inhA1674579c.378G>C1.000
inhA1674585c.384T>C1.000
inhA1674589p.Met130Leu1.000
inhA1674597c.396G>A1.000
inhA1674601p.Leu134Val1.000
inhA1674624c.423A>C1.000
inhA1674627c.426T>C0.867
inhA1674628p.Ser143Gly1.000
inhA1674656p.Ser152Thr1.000
inhA1674690c.489C>G0.929
inhA1674702c.501G>C0.867
inhA1674703c.502T>C1.000
inhA1674714c.513C>G0.846
inhA1674718c.517A>C1.000
inhA1674732c.531C>T0.769
inhA1674741c.540C>T0.923
inhA1674745p.Tyr182Val0.923
inhA1674750c.549T>A1.000
inhA1674756c.555T>G1.000
inhA1674765c.564C>G1.000
inhA1674771c.570C>G1.000
inhA1674774c.573A>C1.000
inhA1674777c.576C>G1.000
inhA1674780c.579T>G1.000
inhA1674801c.600T>C0.923
inhA1674804c.603G>C0.923
inhA1674810c.609C>G0.923
inhA1674819c.618G>C1.000
inhA1674825c.624C>T0.900
inhA1674828c.627G>A1.000
inhA1674830p.Glu210Gly0.900
inhA1674839p.Ala213Glu1.000
inhA1674848p.Gln216Arg1.000
inhA1674855c.654C>G0.929
inhA1674858c.657G>A0.929
inhA1674870c.669T>C0.929
inhA1674876c.675C>G1.000
inhA1674882c.681G>C0.929
inhA1674892p.Asn231Asp1.000
inhA1674904p.Ala235Pro1.000
inhA1674915c.714C>G0.818
inhA1674924c.723G>C1.000
inhA1674927c.726G>C0.917
inhA1674942c.741T>C1.000
inhA1675002c.801A>G1.000
inhA1675011r.810gaacgc>g1.000
rpsA1833538c.-4CA>C0.875
rpsA1833541c.-1T>C1.000
rpsA1833547c.6G>A0.900
rpsA1833589c.48A>C1.000
rpsA1833595c.54T>G1.000
rpsA1833596p.Ser19Ala0.875
rpsA1833616c.75A>C0.875
rpsA1833619c.78A>C0.885
rpsA1833661c.120A>G1.000
rpsA1833664c.123C>G1.000
rpsA1833667c.126C>G1.000
rpsA1833670c.129C>T0.667
rpsA1833676c.135A>G0.800
rpsA1833679c.138G>T0.800
rpsA1833694c.153G>C0.793
rpsA1833697c.156C>G0.786
rpsA1833709c.168C>T0.739
rpsA1833718c.177C>T0.182
rpsA1833721c.180A>G0.182
rpsA1833724c.183C>G0.826
rpsA1833727c.186G>C1.000
rpsA1833734p.Ala65Ser0.840
rpsA1833742c.201A>G0.182
rpsA1833745c.204G>C0.182
rpsA1833748c.207C>G0.182
rpsA1833770p.Asn77His0.818
rpsA1833778c.237C>G0.818
rpsA1833781c.240T>G0.750
rpsA1833787c.246C>G0.160
rpsA1833790c.249T>C0.143
rpsA1833793c.252C>T0.857
rpsA1833802c.261A>G0.920
rpsA1833805c.264C>T0.500
rpsA1833811c.270G>C1.000
rpsA1833814c.273C>G0.893
rpsA1833820c.279G>A0.893
rpsA1833835c.294C>T1.000
rpsA1833838c.297G>T0.917
rpsA1833841c.300C>G0.909
rpsA1833847c.306C>G0.917
rpsA1833856c.315A>G1.000
rpsA1833862c.321G>C1.000
rpsA1833871c.330G>A0.148
rpsA1833874c.333T>C0.846
rpsA1833886c.345C>G1.000
rpsA1833892c.351G>A0.833
rpsA1833894p.Ala118Glu0.833
rpsA1833928c.387G>C0.815
rpsA1833949c.408T>C1.000
rpsA1833970c.429G>C0.737
rpsA1833979c.438T>C1.000
rpsA1833988c.447C>G0.778
rpsA1833991c.450C>G0.222
rpsA1834000c.459G>T0.211
rpsA1834015c.474G>C1.000
rpsA1834024c.483G>C0.200
rpsA1834030c.489C>G0.238
rpsA1834042c.501G>A0.947
rpsA1834051c.510G>A0.944
rpsA1834105c.564C>T0.588
rpsA1834150c.609G>C1.000
rpsA1834153c.612T>C1.000
rpsA1834154p.Asn205Gln0.786
rpsA1834157c.616T>C1.000
rpsA1834162c.621A>G1.000
rpsA1834165c.624A>G1.000
rpsA1834169p.Thr210Ala0.786
rpsA1834172p.Ile211Val0.643
rpsA1834177c.636A>C1.000
rpsA1834186c.645C>G0.267
rpsA1834189c.648G>C0.867
rpsA1834213c.672G>C0.533
rpsA1834222c.681T>C1.000
rpsA1834225c.684C>G0.857
rpsA1834231c.690T>C0.750
rpsA1834240c.699T>C0.933
rpsA1834249c.708T>C1.000
rpsA1834261c.720A>G1.000
rpsA1834264c.723G>C1.000
rpsA1834294c.753G>C1.000
rpsA1834297c.756C>T1.000
rpsA1834303c.762T>G1.000
rpsA1834306c.765T>C1.000
rpsA1834348c.807T>C1.000
rpsA1834361c.820T>C1.000
rpsA1834366c.825A>G1.000
rpsA1834375c.834G>C1.000
rpsA1834396c.855G>C1.000
rpsA1834411c.870T>C1.000
rpsA1834423c.882G>T1.000
rpsA1834432c.891G>C1.000
rpsA1834451c.910T>C1.000
rpsA1834456c.915T>G0.941
rpsA1834468c.927A>G1.000
rpsA1834489c.948T>C1.000
rpsA1834498c.957C>T0.200
rpsA1834522c.981C>T0.933
rpsA1834527p.Arg329His1.000
rpsA1834540c.999G>C1.000
rpsA1834573c.1032G>C0.947
rpsA1834603p.Glu354Asp0.941
rpsA1834609c.1068T>C1.000
rpsA1834619c.1078T>C1.000
rpsA1834622c.1081T>A1.000
rpsA1834633c.1092A>G1.000
rpsA1834639c.1098T>C1.000
rpsA1834666c.1125G>C0.647
rpsA1834667p.Ala376Ser0.588
rpsA1834690c.1149T>C1.000
rpsA1834732c.1191T>C1.000
rpsA1834738c.1197A>G1.000
rpsA1834765p.Glu408Asp1.000
rpsA1834775p.Ala412Thr1.000
rpsA1834780c.1239A>G1.000
rpsA1834786c.1245A>G1.000
rpsA1834789c.1248T>C1.000
rpsA1834792c.1251G>C1.000
rpsA1834810c.1269C>T0.393
rpsA1834813c.1272G>T0.370
rpsA1834852c.1311C>T0.647
kasA2518204c.90G>A0.222
kasA2518219c.105T>C1.000
kasA2518223c.109T>C1.000
kasA2518228c.114C>A0.750
kasA2518231c.117C>T0.750
kasA2518246c.132C>T1.000
kasA2518248p.Ala45Val1.000
kasA2518488p.Ser125Thr0.818
kasA2518492c.378C>T0.818
kasA2518495p.Asp127Glu0.182
kasA2518504c.390T>C1.000
kasA2518506p.Ala131Glu1.000
kasA2518519c.405G>C1.000
kasA2518528c.414C>G1.000
kasA2518561c.447T>C0.312
kasA2518564c.450C>G0.545
kasA2518567c.453G>C0.846
kasA2518570c.456G>A0.462
kasA2518574p.Ile154Val1.000
kasA2518579c.465T>C0.786
kasA2518583p.Gln157Glu0.214
kasA2518586p.Leu158Val0.357
kasA2518591c.477G>C0.786
kasA2518594c.480C>T0.429
kasA2518597c.483C>T0.357
kasA2518606c.492G>C0.786
kasA2518609p.Met165Ile1.000
kasA2518627c.513T>C0.917
kasA2518630c.516G>C0.500
kasA2518636c.522C>A0.455
kasA2518642c.528A>G0.462
kasA2518645c.531G>C0.538
kasA2518651c.537C>G1.000
kasA2518657c.543G>A0.583
kasA2518672c.558G>C1.000
kasA2518684c.570C>G0.600
kasA2518690c.576C>G0.300
kasA2518692p.Ala193Val0.333
kasA2518702c.588C>T0.800
kasA2518705c.591T>C0.273
kasA2518898c.784T>C1.000
kasA2518906c.792A>G1.000
kasA2518910p.Leu266Met1.000
eis2714952c.381G>C1.000
ahpC2726600c.408T>C1.000
ahpC2726638p.Ala149Val1.000
ahpC2726645c.453C>G0.941
ahpC2726657c.465A>C1.000
ahpC2726669c.477T>C1.000
ahpC2726675c.483A>G1.000
ahpC2726681c.489A>G1.000
ahpC2726684c.492G>A1.000
ahpC2726687c.495C>G1.000
ahpC2726693c.501C>A1.000
ahpC2726696c.504C>G1.000
ahpC2726717c.525A>C1.000
folC2746948c.651C>G0.857
folC2746958p.Gly214Ala0.857
folC2746975c.624A>G1.000
folC2746979p.Ala207Asp0.929
folC2746981c.618A>G0.857
folC2746999c.600A>G0.750
folC2747002c.597A>G1.000
folC2747007p.Ser198Gly1.000
folC2747014c.585G>C0.250
folC2747020c.579G>C0.267
folC2747023c.576G>C0.267
folC2747026c.573G>C0.267
folC2747032c.567T>A0.308
folC2747037p.Asn188Asp0.636
folC2747040p.Ile187Val0.636
folC2747041c.558C>G0.636
folC2747129p.Ala157Gly0.882
folC2747155c.444C>G1.000
thyX3067355c.591T>C1.000
thyX3067364c.582G>A0.875
thyX3067373c.573G>C1.000
thyX3067382c.564G>A0.867
thyX3067388c.558G>C0.867
thyX3067406c.540T>C1.000
thyX3067427c.519C>G1.000
thyX3067433c.513G>A1.000
thyX3067445c.501G>A1.000
thyX3067457c.489G>C1.000
thyX3067814c.132A>G1.000
thyX3067844c.102C>T0.867
thyX3067849p.Pro33Ser1.000
thyX3067850c.96T>C1.000
thyX3067869p.Thr26Ser1.000
thyX3067874c.72G>C1.000
thyX3067883c.63G>C1.000
thyX3067886c.60T>C1.000
thyX3067891p.Ala19Pro0.909
thyX3067894p.Leu18Ser1.000
thyX3067898p.Asp16Glu1.000
thyX3067910c.36G>A1.000
thyX3067915c.31G>A0.706
thyX3067934c.12G>C0.889
thyX3067949c.-4C>T1.000
thyA3073863c.609A>G1.000
thyA3073889p.Ser195Gly1.000
thyA3073892c.580A>G1.000
thyA3073893c.579G>C0.920
thyA3073902c.570G>C0.931
thyA3073905c.567G>C0.133
thyA3073920c.552G>C0.871
thyA3073925c.547A>G1.000
thyA3073929c.543A>G0.129
thyA3073953c.519A>C0.231
thyA3073956c.516C>G0.923
thyA3073959c.513A>G1.000
thyA3073964p.Leu170Met0.680
thyA3073971c.501G>A0.760
thyA3073977c.495T>C1.000
thyA3073980c.492G>A0.909
thyA3073989c.483A>G1.000
thyA3073994c.478C>G0.875
thyA3074000p.Arg158Lys0.875
thyA3074001c.471G>C0.235
thyA3074004c.468A>G1.000
thyA3074027p.Phe149Leu0.818
thyA3074070c.402G>A1.000
thyA3074076c.396G>T1.000
thyA3074082c.390C>A1.000
thyA3074229c.243G>A0.800
thyA3074235c.237G>A0.200
thyA3074244c.228T>A0.200
thyA3074252p.Glu74Arg0.200
thyA3074255p.His73Asn0.800
thyA3074256c.216C>T0.800
thyA3074263p.Gly70Ala0.200
thyA3074267p.Ile69Val0.200
thyA3074268c.204A>G1.000
thyA3074274c.198A>G1.000
thyA3074277c.195G>A0.818
thyA3074285c.187A>G0.867
thyA3074466c.6C>G1.000
thyA3074470p.Val1Ala1.000
fbiA3640319c.-224A>T1.000
fbiA3640350c.-193C>T0.846
fbiA3640355c.-188C>T0.833
fbiA3640365c.-178C>G1.000
fbiA3640692c.150C>T0.941
fbiA3640701p.Ile53Met1.000
fbiA3640708p.Leu56Val1.000
fbiA3640713c.171T>C1.000
fbiA3640714p.Val58Ile1.000
fbiA3640722c.180G>C1.000
fbiA3640743c.201T>C1.000
fbiA3640758c.216G>C1.000
fbiA3640764c.222C>T1.000
fbiA3640765p.Pro75Ala1.000
fbiA3640768p.Gln76Glu1.000
fbiA3640773c.231C>G0.818
fbiA3640782c.240C>A0.889
fbiA3640785p.Gln81His1.000
fbiA3640788c.246T>G1.000
fbiA3640791c.249C>T0.800
fbiA3640797c.255T>C1.000
fbiA3641046c.504T>C1.000
fbiA3641049c.507T>C1.000
panD4044188c.94A>G1.000
panD4044189c.93G>A0.818
panD4044195c.87A>G1.000
panD4044216c.66G>A0.833
panD4044240c.42C>G0.200
panD4044246c.36G>A0.200
panD4044252c.30G>A0.800
panD4044264c.18C>G0.800
panD4044273c.9C>T0.200
panD4044276p.Leu2Phe0.800
embC4240435c.573C>T1.000
embC4240456c.594C>G0.588
embC4240459c.597G>C0.588
embC4240462c.600G>C0.176
embC4240464p.Phe201Tyr0.765
embC4240475p.Ala205Ser0.929
embC4240480c.618G>C1.000
embC4240708c.846G>C0.875
embC4240717c.855T>C0.824
embC4240726c.864G>C1.000
embC4240736c.874T>A0.609
embC4240765c.903C>G0.789
embC4240769p.Val303Ile0.895
embC4240783c.921G>C1.000
embC4240789c.927T>C1.000
embC4240800p.Tyr313Phe0.889
embC4240819c.957A>C0.211
embC4240822c.960C>G0.316
embC4240831c.969T>G1.000
embC4240855c.993G>C0.600
embC4240859p.Leu333Val0.200
embC4240912c.1050G>C0.900
embC4240921c.1059C>G1.000
embC4240922p.Thr354Ala0.900
embC4240934p.Val358Leu0.900
embC4241135p.Val425Leu1.000
embC4241173c.1311C>T0.300
embC4241179c.1317G>C0.300
embC4241185c.1323G>C0.700
embC4241188c.1326C>G0.700
embC4241194c.1332C>G0.727
embC4241197c.1335G>C0.250
embC4241203c.1341T>C0.250
embC4241210c.1348C>T0.250
embC4241215c.1353C>G0.750
embC4241224c.1362G>T0.273
embC4241227c.1365G>A0.273
embC4241230c.1368A>G1.000
embC4241233c.1371G>C0.700
embC4241240c.1378C>T0.700
embC4241245c.1383C>T0.700
embC4241404p.Asp514Glu0.643
embC4241407c.1545A>G0.643
embC4241411p.Ile517Val0.750
embC4241432p.Met524Leu0.786
embC4241439p.Ser526Thr0.846
embC4241443c.1581C>T0.909
embC4242388p.Asn842Lys0.900
embC4242907c.3045G>T0.800
embA4244195c.963C>G0.800
embA4244198c.966C>G1.000
embA4244207c.975C>G0.400
embA4244219c.987C>G1.000
embA4244220c.988C>T0.200
embA4244228c.996A>C1.000
embA4244229p.Ile333Val0.200
embA4244234c.1002C>G0.200
embA4244603c.1371G>C0.182
embA4244609c.1377G>C0.143
embA4244612c.1380C>G0.143
embA4244664p.Thr478Ala0.636
embA4244669c.1437G>C0.636
embA4244676p.Ser482Ala0.545
embA4244681c.1449A>C0.333
embA4244684c.1452C>G0.917
embA4244694p.Lys488Val0.733
embA4244702c.1470C>T1.000
embA4244708c.1476C>G0.267
embA4244726p.Asp498Glu0.692
embA4244729c.1497C>T0.286
embA4244735c.1503C>G0.750
embA4244738c.1506C>T0.750
embA4244747c.1515T>G0.200
embA4244750c.1518C>G0.200
embA4244751p.Val507Leu0.200
embA4244792c.1560G>C1.000
embA4244802c.1570T>C0.889
embA4244814p.Leu528Met0.933
embA4244821p.Gly530Ala1.000
embA4244823p.Val531Met1.000
embA4244829p.Phe533Val1.000
embA4244837c.1605G>C0.917
embA4244853p.Val541Ile1.000
embA4244856p.Ala542Asn1.000
embA4244862p.Leu544Val1.000
embA4244885c.1653A>G1.000
embA4244894c.1662C>A1.000
embA4244895p.Thr555Ser1.000
embA4244900c.1668G>C0.789
embA4244906c.1674C>G0.818
embA4244913c.1681C>T0.682
embA4244919c.1687C>T1.000
embA4244930c.1698G>C1.000
embA4244933c.1701A>C0.167
embA4244945c.1713C>G1.000
embA4244959p.Ala576Gly1.000
embA4245050c.1818C>T0.583
embA4245053c.1821G>C0.417
embA4245060c.1828T>C1.000
embB4247425c.912G>C0.667
embB4247428c.915C>G0.750
embB4247437c.924A>G0.727
embB4247440c.927C>G0.727
embB4247446c.933C>T0.182
embB4247462c.949T>A0.750
embB4247491c.978G>C0.176
embB4247494c.981G>A0.250
embB4247497c.984T>C1.000
embB4247500c.987C>G1.000
embB4247512c.999T>C1.000
embB4247536c.1023C>G0.857
embB4247539c.1026T>C0.929
embB4247543c.1030A>T0.846
embB4247554c.1041T>C1.000
embB4247555p.Leu348Ile0.800
embB4247563p.Met350Ile0.800
embB4247566c.1053C>G0.294
embB4247572c.1059A>C1.000
embB4247579p.Ala356Ile0.278
embB4247590c.1077A>G1.000
embB4247722c.1209G>C0.667
embB4247725c.1212G>C0.818
embB4247731c.1218C>G0.750
embB4247861p.Ile450Val0.364
embB4247875c.1362G>A0.462
embB4247879p.Val456Leu0.538
embB4248085c.1572T>C0.818
embB4248097c.1584C>G1.000
embB4248106c.1593C>G0.733
embB4248118c.1605T>C1.000
embB4248121c.1608G>A0.733
embB4248133c.1620C>A0.267
embB4248139c.1626C>A0.733
embB4248142c.1629T>C1.000
embB4248143c.1630T>C1.000
embB4248149p.Thr546Cys0.867
embB4248157c.1644A>G1.000
embB4248173p.Val554Met0.909
embB4248199c.1686A>T0.875
embB4248200p.Ile563Val0.824
embB4248206p.Ser565Gly1.000
embB4248211c.1698G>C0.944
embB4248215p.Arg568Ser0.944
embB4248220c.1707A>C0.167
embB4248225p.Ala571Val0.895
embB4248248p.Phe579Leu0.769
embB4248252p.Gly580Ala0.714
embB4248264p.Phe584Ser0.769
embB4248275p.Thr588Ala0.519
embB4248280c.1767C>T0.500
embB4249483c.2970C>G0.917
embB4249486c.2973T>C1.000
embB4249487c.2974T>C1.000
embB4249507p.Gln998His1.000
ethA4326587p.Val296Ala1.000
ethA4326598c.876T>C1.000
ethA4326603p.Gln291Glu1.000
ethA4326610c.864G>C1.000
ethA4326620p.His285Arg1.000
ethA4326625c.849G>C1.000
ethA4327043p.Asp144Ala0.733
ethA4327388p.Thr29Asn1.000
ethA4327396c.78A>G1.000
ethA4327401p.Asp25Asn0.926
ethA4327425p.Val17Ile1.000
ethA4327435c.39T>G1.000
ethA4327438c.36A>G1.000
ethA4327444c.30C>G1.000
ethA4327450c.24G>C1.000
ethA4327456c.18G>A1.000
ethA4327465c.9C>T1.000
ethA4327468c.6G>A1.000

Analysis pipeline specifications

TBProfiler Version: 2.1.1

AnalysisProgram
Mappingbwa
Variant CallingBCFtools


Log

Drug Details
The estimated accuracy of drug resistance predictions is:

Drug1Sensitivity (%)Specificity (%)
Isoniazid 92.8 (89.9-95.7)100 (100-100)
Rifampicin 96.2 (93.9-98.5)98.1 (96.8-99.4)
Ethambutal 88.7 (83.6-93.8)81.7 (77.6-85.8)
Pyrazinamide70.9 (62.4-79.4)93.9 (90.6-97.2)
Streptomycin87.1 (82.7-91.5)89.7 (86.0-93.4)
Ethionamide 73.6 (66.7-80.5)93.3 (89.6-97.0)
Moxifloxacin60.0 (29.6-90.4)68.7 (52.6-84.8)
Ofloxacin 85.5 (79.1-91.9)94.9 (91.8-98.0)
Amikacin 82.9 (74.4-91.4)98.3 (96.0-100)
Capreomycin 60.7 (50.6-70.8)90.7 (87.2-94.2)
Kanamycin 87.3 (81.3-93.3)93.4 (89.9-96.9)
Para-aminosalisylic acidNot determinedNot determined
Linezolid Not determinedNot determined
Clofazimine Not determinedNot determined
Bedaquiline Not determinedNot determined
Multi drug resistance91.2 (87.8-94.6)98.4 (97.2-99.6)
Extremely drug resistance75.9 (64.5-87.3)98.4 (97.3-99.5)

Lineages
Lineage2LocationStrainRD type
lineage1Indo-OceanicEAIRD239
lineage1.1Indo-OceanicEAI3;EAI4;EAI5;EAI6RD239
lineage1.1.1Indo-OceanicEAI4;EAI5RD239
lineage1.1.1.1Indo-OceanicEAI4;ZERORD239
lineage1.1.2Indo-OceanicEAI3;EAI5RD239
lineage1.1.3Indo-OceanicEAI6RD239
lineage1.2Indo-OceanicEAI1;EAI2RD239
lineage1.2.1Indo-OceanicEAI2RD239
lineage1.2.2Indo-OceanicEAI1RD239
lineage2East-AsianBeijingRD105
lineage2.1East-Asian (non-Beijing)NoneNone
lineage2.2East-Asian (Beijing)Beijing-RD207RD105;RD207
lineage2.2.2East-Asian (Beijing)Beijing-RD105/RD207RD105;RD207
lineage2.2.1East-Asian (Beijing)Beijing-RD181RD105;RD207;RD181
lineage2.2.1.2East-Asian (Beijing)Beijing-RD142RD105;RD207;RD181;RD142
lineage2.2.1.1East-Asian (Beijing)Beijing-RD150RD105;RD207;RD181;RD150
lineage3East-African-IndianCASRD750
lineage3.1East-African-IndianNon-CAS1-DelhiRD750
lineage3.1.1East-African-IndianCAS1-KiliRD750
lineage3.1.2East-African-IndianCAS;CAS2RD750
lineage3.1.2.1East-African-IndianCAS2RD750
lineage3.1.2.2East-African-IndianCASRD750
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.1Euro-AmericanT;X;HNone
lineage4.1.2Euro-American (X-type)T;HNone
lineage4.1.2.1Euro-American (X-type)T1;H1RD182
lineage4.1.1Euro-American (X-type)X1;X2;X3None
lineage4.1.1.2Euro-American (X-type)X1None
lineage4.1.1.1Euro-American (X-type)X2RD183
lineage4.1.1.3Euro-American (Haarlem)X1;X3RD193
lineage4.2Euro-AmericanH;T;LAMNone
lineage4.2.2Euro-American (Ural)T;LAM7-TURNone
lineage4.2.2.1Euro-AmericanLAM7-TURNone
lineage4.2.1Euro-American (TUR)H3;H4None
lineage4.3Euro-American (LAM)mainly-LAMNone
lineage4.3.1Euro-American (LAM)LAM9None
lineage4.3.3Euro-American (LAM)LAM;TRD115
lineage4.3.4Euro-American (LAM)LAMRD174
lineage4.3.4.1Euro-American (LAM)LAM1;LAM2RD174
lineage4.3.4.2Euro-American (LAM)LAM1;LAM4;LAM11RD174
lineage4.3.4.2.1Euro-American (LAM)LAM11RD174
lineage4.3.2Euro-American (LAM)LAM3None
lineage4.3.2.1Euro-American (LAM)LAM3RD761
lineage4.4Euro-AmericanS;TNone
lineage4.4.2Euro-AmericanT1;T2None
lineage4.4.1Euro-American (S-type)S;TNone
lineage4.4.1.2Euro-AmericanT1None
lineage4.4.1.1Euro-AmericanS;OrphansNone
lineage4.5Euro-AmericanH;TRD122
lineage4.6Euro-AmericanT;LAMNone
lineage4.6.1Euro-American (Uganda)T2RD724
lineage4.6.1.1Euro-American T2-UgandaRD724
lineage4.6.1.2Euro-AmericanT2RD724
lineage4.6.2Euro-AmericanT;LAMRD726
lineage4.6.2.1Euro-AmericanT3RD726
lineage4.6.2.2Euro-American (Cameroon)LAM10-CAMRD726
lineage4.7Euro-American (mainly T)T1;T5None
lineage4.8Euro-American (mainly T)T1;T2;T3;T5RD219
lineage4.9Euro-American (H37Rv-like)T1None
lineage5West-Africa 1AFRI_2;AFRI_3RD711
lineage6West-Africa 2AFRI_1RD702
lineage7Lineage 7NoneNone
lineageBOVM. bovisBOV_1;BOV_2None

Citations
1. Coll F, et al. Rapid determination of anti-tuberculosis drug resistance from whole genome sequences. Genome Medicine (in press)
2. Coll F, et al. A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nature Communications 2014.

Disclaimer
This tool is for Research Use Only and is offered free for use. The London School of Hygiene and Tropical Medicine shall have no liability for any loss or damages of any kind, however sustained relating to the use of this tool.
© 2019 London School of Hygiene and Tropical Medicine;