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: 5d80676eb0258
Sample: 5d80676eb0258

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Summary
ID: 5d80676eb0258
Date: Tue Sep 17 05:59:33 2019
Strain: lineage2.2
Drug-resistance: Sensitive

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

Lineage2FamilyMain SpoligotypeRDS
lineage2.2East-Asian (Beijing)Beijing-RD207RD105;RD207

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA8801c.1500G>C1.000
gyrA8818p.Ser506Thr1.000
gyrA8829c.1528T>C0.955
gyrA8837c.1536C>T0.978
gyrA8852c.1551T>C0.979
gyrA8855c.1554C>G0.880
gyrA8858c.1557T>G0.100
gyrA8867c.1566A>G0.882
gyrA8870c.1569G>C0.962
gyrA8897c.1596T>C0.960
gyrA8900c.1599G>C0.820
gyrA8903c.1602T>C0.941
gyrA8913p.Lys538Arg0.783
gyrA8930c.1629C>T0.786
gyrA8939c.1638T>C0.731
gyrA8942c.1641G>A0.240
gyrA8945c.1644G>T0.762
gyrA8946c.1645T>C0.880
gyrA8967p.Ala556Lys0.769
gyrA8978c.1677C>T0.200
gyrA8981c.1680G>C0.333
gyrA8982p.Cys561Ser0.364
rpoB760088c.282C>G0.727
rpoB760101c.295T>C0.933
rpoB760106c.300G>C0.824
rpoB760112c.306T>C0.944
rpoB760120p.Arg105His0.842
rpoB760130p.Asp108Glu0.964
rpoB760139c.333A>C0.967
rpoB760140p.Pro112Ser0.879
rpoB760148p.Asp114Glu0.902
rpoB760157c.351A>G0.913
rpoB760172c.366G>C0.909
rpoB760181c.375T>G0.964
rpoB760187c.381G>C0.932
rpoB760199c.393C>G0.951
rpoB760233c.427A>T0.929
rpoB760241c.435G>C0.907
rpoB760244c.438G>C0.953
rpoB760253c.447T>C0.907
rpoB760265p.Met153Ile0.921
rpoB760274p.Glu156Asp0.944
rpoB760282p.Thr159Ser0.889
rpoB760298c.492G>C0.952
rpoB760354p.Glu183Ala0.750
rpoB760356p.Thr184Ala0.786
rpoB760361c.555T>C1.000
rpoB760368p.Ser188Ala0.857
rpoB760376p.Asp190Glu1.000
rpoB760382c.576G>C0.917
rpoB760385c.579G>C0.833
rpoB760390p.Ser195Thr0.846
rpoB760394c.588C>G0.815
rpoB760400c.594G>C0.912
rpoB760406c.600G>C0.122
rpoB760407p.Ser201Gly0.929
rpoB760412c.606C>T0.951
rpoB760424c.618C>G0.938
rpoB760430c.624T>C1.000
rpoB760457c.651C>T0.843
rpoB760475c.669A>G1.000
rpoB760478c.672C>T0.844
rpoB760481c.675G>T1.000
rpoB760484c.678A>G1.000
rpoB760502c.696C>G0.902
rpoB760508c.702G>T0.741
rpoB760511c.705G>C0.741
rpoB760514c.708C>G0.704
rpoB760522p.Ser239Asn1.000
rpoB760527p.Gln241Glu0.739
rpoB760532c.726T>C1.000
rpoB760533p.Val243Thr0.864
rpoB760541c.735G>C1.000
rpoB760553c.747C>G0.188
rpoB760889c.1083C>G0.140
rpoB760910c.1104C>T0.152
rpoB760916c.1110C>T0.957
rpoB760925c.1119T>C0.804
rpoB760928c.1122G>C0.956
rpoB760946c.1140A>G0.952
rpoB760958c.1152G>C0.905
rpoB760964c.1158C>T0.840
rpoB760965p.Met387Leu0.960
rpoB760970c.1164G>C0.115
rpoB760973c.1167G>T0.923
rpoB760982c.1176G>C0.952
rpoB760985c.1179G>C0.957
rpoB760988c.1182C>G0.913
rpoB760991c.1185G>T0.130
rpoB760997c.1191G>C0.917
rpoB761006c.1200C>G0.182
rpoB761015c.1209G>C1.000
rpoB761027c.1221A>C1.000
rpoB761153c.1347G>C0.167
rpoB761165c.1359G>C0.250
rpoB761171c.1365C>T0.692
rpoB761178c.1372T>A0.636
rpoB761183c.1377T>C0.273
rpoB761186p.Glu460Asp0.364
rpoB761189c.1383T>C0.818
rpoB761192c.1386C>A0.273
rpoB761195c.1389G>C0.900
rpoB761198c.1392G>T0.571
rpoB761204c.1398C>T0.500
rpoB761207c.1401C>T0.571
rpoB761213c.1407G>C0.846
rpoB761234c.1428G>C0.897
rpoB761249c.1443A>G0.961
rpoB761255c.1449T>G0.103
rpoB761261c.1455G>T0.964
rpoB761264c.1458C>G0.949
rpoB761282c.1476C>T0.868
rpoB761288c.1482G>C0.871
rpoB761318c.1512G>C0.983
rpoB761327c.1521A>G0.982
rpoB761345c.1539G>C0.976
rpoB761346p.Val514Ile0.976
rpoB761357c.1551G>C1.000
rpoB761360c.1554T>C1.000
rpoB761362p.Ser519Thr1.000
rpoB761369p.Glu521Asp1.000
rpoB761374p.Val523Glu1.000
rpoB761396c.1590G>A0.963
rpoB761531c.1725C>G0.300
rpoB761537c.1731C>G0.909
rpoB761540c.1734C>G0.462
rpoB761549c.1743G>C0.704
rpoB761555c.1749G>C0.966
rpoB761558c.1752C>G0.967
rpoB761564c.1758G>C0.200
rpoB761570c.1764T>C0.737
rpoB761573c.1767C>G0.927
rpoB761579c.1773G>C1.000
rpoB761606c.1800C>G1.000
rpoB761612c.1806G>T1.000
rpoB761615c.1809A>C1.000
rpoB761627c.1821C>T0.816
rpoB761633c.1827G>C0.833
rpoB761636c.1830G>T0.146
rpoB761645c.1839C>G0.109
rpoB761648c.1842T>C0.109
rpoB761650p.Ser615Asn0.850
rpoB761655p.Ala617Ser0.842
rpoB761666c.1860G>C0.833
rpoB761669c.1863C>T0.139
rpoB761675c.1869G>T0.143
rpoB761687c.1881C>T0.962
rpoB761690c.1884G>A0.125
rpoB761693c.1887G>C0.125
rpoB761694p.Ile630Val0.833
rpoB761702c.1896C>G0.850
rpoB761930c.2124G>C0.700
rpoB761948c.2142G>C0.952
rpoB761954c.2148C>G0.952
rpoB761972c.2166C>T0.871
rpoB761990c.2184G>C0.969
rpoB762000c.2194T>A0.829
rpoB762003p.Asn733Gln0.806
rpoB762008c.2202C>G0.237
rpoB762011c.2205G>C0.763
rpoB762014c.2208C>G1.000
rpoB762017c.2211A>G0.786
rpoB762032c.2226C>G0.846
rpoB762038c.2232C>T0.147
rpoB762047c.2241G>A0.127
rpoB762053c.2247T>C1.000
rpoB762056c.2250G>A0.122
rpoB762065c.2259T>C0.123
rpoB762083c.2277T>C0.118
rpoB762086c.2280G>C1.000
rpoB762098c.2292C>G0.887
rpoB762114p.Ile770Val0.976
rpoB762128c.2322G>C0.876
rpoB762137c.2331C>T0.870
rpoB762140c.2334G>C0.974
rpoB762143c.2337T>C0.976
rpoB762149c.2343G>C0.914
rpoB762161c.2355C>T0.926
rpoB762170c.2364C>G0.946
rpoB762176c.2370T>C0.946
rpoB762182c.2376C>T0.902
rpoB762185c.2379G>C0.969
rpoB762218c.2412T>C0.907
rpoB762233c.2427G>C0.980
rpoB762239c.2433G>A0.958
rpoB762245c.2439G>T0.952
rpoB762266c.2460T>C0.882
rpoB762269c.2463G>A0.890
rpoB762284c.2478G>T0.985
rpoB762293c.2487T>G0.980
rpoB762299c.2493G>C0.878
rpoB762305c.2499G>T0.864
rpoB762308c.2502G>C0.857
rpoB762317c.2511A>G0.971
rpoB762318p.Ser838Thr0.886
rpoB762329c.2523G>C0.920
rpoB762827c.3021G>T0.333
rpoB762830c.3024C>T0.667
rpoB762831c.3025A>T0.667
rpoB762857c.3051C>G1.000
rpoB762858p.Thr1018Ser0.846
rpoB762863c.3057T>C1.000
rpoB762866c.3060C>T0.136
rpoB762879p.Met1025Leu0.146
rpoB762894c.3088C>T0.119
rpoB762899c.3093G>C0.984
rpoB762917c.3111C>T1.000
rpoB762929c.3123G>T0.127
rpoB762959c.3153G>C0.984
rpoB762971c.3165G>C0.893
rpoB762989c.3183G>C0.923
rpoB762995c.3189G>T1.000
rpoB763013c.3207C>G0.943
rpoB763022c.3216C>G0.927
rpoB763028c.3222T>C0.944
rpoB763040c.3234C>G0.109
rpoB763053c.3247T>C0.886
rpoB763058c.3252C>G0.886
rpoB763070c.3264T>C1.000
rpoB763074p.Thr1090Val0.842
rpoB763094c.3288G>C0.957
rpoB763103c.3297G>C0.907
rpoB763115c.3309T>C0.977
rpoB763127c.3321G>C0.925
rpoB763160c.3354G>C0.824
rpoB763166c.3360A>G0.964
rpoB763169c.3363A>G0.815
rpoB763178c.3372G>C0.800
rpoB763181c.3375G>C0.833
rpoB763185c.3379C>T0.833
rpoC763450c.81G>A0.192
rpoC763456c.87A>G0.964
rpoC763468c.99G>C0.939
rpoC763486c.117T>C0.976
rpoC763492c.123G>C0.978
rpoC763528c.159G>A0.967
rpoC763546c.177A>G0.963
rpoC763570c.201G>C0.984
rpoC763615c.246G>C0.904
rpoC763619p.Arg84Lys0.900
rpoC763657c.288G>A0.121
rpoC763660c.291T>G0.982
rpoC763666c.297G>C0.962
rpoC763669c.300C>G0.980
rpoC763675c.306C>G1.000
rpoC764116c.747C>G0.913
rpoC764134c.765C>G0.880
rpoC764143c.774G>C0.960
rpoC764147p.Ser260Ala0.960
rpoC764153p.Gln262Lys0.880
rpoC764161c.792G>C0.862
rpoC764162p.Ile265Leu0.862
rpoC764188c.819A>G1.000
rpoC764197c.828G>C1.000
rpoC764203c.834G>C1.000
rpoC764206p.Asp279Glu1.000
rpoC764207p.Val280Thr0.960
rpoC764215c.846A>C1.000
rpoC764217p.Asn283Ser0.964
rpoC764227c.858G>A0.975
rpoC764239c.870T>G0.953
rpoC764242c.873C>T0.957
rpoC764245c.876C>G0.936
rpoC764254c.885G>A0.938
rpoC764263c.894G>C0.941
rpoC764266c.897T>C1.000
rpoC764278c.909A>G0.985
rpoC764284c.915G>C0.925
rpoC764297p.Met310Leu0.932
rpoC764320c.951C>G0.935
rpoC764341c.972G>C0.910
rpoC764344c.975C>T0.910
rpoC764365c.996C>T0.972
rpoC764371c.1002G>C0.940
rpoC764377c.1008C>G0.937
rpoC764380c.1011G>C0.967
rpoC764387c.1018T>C0.968
rpoC764405c.1036A>C0.967
rpoC764410c.1041G>C0.806
rpoC764428c.1059G>C0.195
rpoC764431c.1062G>C1.000
rpoC764434c.1065A>G1.000
rpoC764435c.1066A>C0.949
rpoC764446c.1077T>C0.800
rpoC764449c.1080G>C0.800
rpoC764452c.1083T>C0.239
rpoC764455c.1086G>A0.745
rpoC764458c.1089G>C1.000
rpoC764461c.1092A>G1.000
rpoC764497c.1128A>G0.985
rpoC764500c.1131C>G0.800
rpoC764503c.1134G>C0.806
rpoC764509c.1140G>T0.130
rpoC764510c.1141C>T0.174
rpoC764521c.1152T>C0.145
rpoC764536c.1167G>T0.984
rpoC764539c.1170C>G0.985
rpoC764545c.1176C>G0.947
rpoC764548c.1179G>A0.877
rpoC764560c.1191T>C0.895
rpoC764575c.1206T>G0.987
rpoC764578c.1209C>G0.893
rpoC764602c.1233C>T0.871
rpoC764605c.1236G>T0.875
rpoC764611c.1242G>T0.972
rpoC764632c.1263T>C0.959
rpoC764650c.1281G>T0.976
rpoC764662c.1293G>C0.919
rpoC764668c.1299C>T0.951
rpoC764686c.1317C>T0.894
rpoC764701c.1332C>G0.917
rpoC764713c.1344G>A0.960
rpoC764716c.1347G>C0.962
rpoC764746c.1377G>T0.949
rpoC764749c.1380G>C0.873
rpoC764752c.1383G>C0.987
rpoC764758c.1389C>G0.949
rpoC764764p.His465Gln0.101
rpoC764767c.1398G>A0.887
rpoC764797c.1428G>C0.921
rpoC764803c.1434C>G0.972
rpoC764824c.1455T>C0.959
rpoC764858c.1489T>C1.000
rpoC764863c.1494G>C0.857
rpoC764869c.1500C>T0.966
rpoC764872c.1503A>G0.915
rpoC764887c.1518G>T0.960
rpoC764888c.1519T>C1.000
rpoC764893c.1524T>C0.880
rpoC764902c.1533C>G0.878
rpoC764911c.1542A>G1.000
rpoC764912p.Met515Gln0.923
rpoC764917c.1548G>C0.778
rpoC764920c.1551G>C0.786
rpoC764923c.1554A>G0.857
rpoC764932c.1563C>A0.113
rpoC764935c.1566T>C0.887
rpoC764939c.1570C>T0.893
rpoC764948c.1579T>C1.000
rpoC764968c.1599T>C1.000
rpoC765004c.1635G>C1.000
rpoC765007c.1638T>G1.000
rpoC765008c.1639T>C1.000
rpoC765019c.1650A>G1.000
rpoC765028c.1659C>G0.979
rpoC765034c.1665T>A1.000
rpoC765040c.1671T>C1.000
rpoC765041c.1672T>C1.000
rpoC765047c.1678T>C1.000
rpoC765052c.1683C>G0.964
rpoC765053c.1684T>A0.964
rpoC765073c.1704G>C1.000
rpoC765076c.1707A>G1.000
rpoC765079c.1710T>G1.000
rpoC765082c.1713G>T1.000
rpoC765089c.1720T>C1.000
rpoC765103c.1734G>T1.000
rpoC765466c.2097C>T0.907
rpoC765469c.2100G>C0.977
rpoC765478c.2109T>C1.000
rpoC765493c.2124G>C0.942
rpoC765499c.2130C>G1.000
rpoC765525p.Ala719Val0.932
rpoC765544c.2175C>G0.951
rpoC765547c.2178C>T0.950
rpoC765548c.2179A>T0.950
rpoC765553c.2184C>T1.000
rpoC765559c.2190G>C0.950
rpoC765835c.2466C>G0.977
rpoC765844c.2475C>G0.895
rpoC765875p.Val836Ile0.952
rpoC765886c.2517C>G0.906
rpoC765898c.2529C>T0.875
rpoC765907c.2538G>C0.933
rpoC765908p.Leu847Ala0.840
rpoC765928c.2559C>G0.913
rpoC765940c.2571A>T0.892
rpoC765946c.2577C>T0.812
rpoC765947c.2578T>C1.000
rpoC766315c.2946C>G0.750
rpoC766333c.2964G>C0.880
rpoC766345c.2976T>C0.929
rpoC766348c.2979A>G0.929
rpoC766357c.2988C>T0.844
rpoC766361p.Val998Ile0.781
rpoC766366c.2997C>G0.875
rpoC766369c.3000C>G0.875
rpoC766375c.3006C>G0.911
rpoC766381c.3012C>T0.111
rpoC766384c.3015A>G0.935
rpoC766390c.3021C>T0.915
rpoC766402c.3033C>G0.792
rpoC766408c.3039C>T0.933
rpoC766411c.3042C>G0.851
rpoC766426c.3057C>T0.851
rpoC766435p.Glu1022Asp0.894
rpoC766456c.3087C>G0.861
rpoC766459c.3090G>T0.882
rpoC766462c.3093G>C0.971
rpoC766471c.3102G>C0.839
rpoC766799p.Ala1144Ser0.864
rpoC766804c.3435A>G1.000
rpoC766835p.Val1156Thr0.905
rpoC766843c.3474T>G0.905
rpoC766846c.3477C>T0.905
rpoC766858c.3489C>T0.905
rpoC766861c.3492G>C1.000
rpoC766867c.3498C>G0.905
rpoC766882c.3513C>T0.864
rpoC766894c.3525T>C0.700
rpoC766895c.3526T>C0.600
rpoC766931p.Ala1188Ser0.364
rpoC766948c.3579G>C0.417
rpoC766952p.Ala1195Ser0.462
rpoC766963c.3594T>C1.000
rpoC766972c.3603G>T0.821
rpoC766975c.3606C>T0.171
rpoC766978c.3609C>A0.837
rpoC766996c.3627C>T1.000
rpoC767002c.3633G>C1.000
rpoC767008c.3639G>C0.153
rpoC767017c.3648C>G0.846
rpoC767023p.Asp1218Glu0.121
rpoC767026c.3657G>C0.862
rpoC767059c.3690T>G0.869
rpoC767062c.3693C>T0.850
rpoC767065c.3696G>C0.823
rpoC767080c.3711G>C0.962
rpoC767087p.Cys1240Ser0.816
rpoC767098c.3729T>C0.978
rpoC767104c.3735C>G0.933
rpoC767106p.Asn1246Ile0.822
rpoC767119c.3750A>G0.975
rpoC767125c.3756G>C0.118
rpoC767134c.3765C>T0.960
rpoC767138c.3769C>T0.893
rpoC767149c.3780C>T0.273
rpoC767155c.3786C>G0.526
rpoC767158c.3789T>C0.471
rpoC767167c.3798C>G0.333
rrs1471922r.77gt>g0.957
rrs1471923r.78t>c1.000
rrs1471925r.80t>g1.000
rrs1471929r.84c>g0.969
rrs1471930r.85g>c0.969
rrs1471931r.86g>t0.969
rrs1471932r.87a>g1.000
rrs1471934r.89a>g1.000
rrs1471979r.134t>c0.949
rrs1471980r.135g>t0.961
rrs1471981r.136c>g0.961
rrs1471985r.140t>c0.987
rrs1471986r.141c>t0.987
rrs1472068r.223t>g0.600
rrs1472075r.230a>g0.965
rrs1472106r.261g>a0.987
rrs1472108r.263c>t1.000
rrs1472137r.292g>a0.981
rrs1472150r.305t>a0.991
rrs1472151r.306c>t0.972
rrs1472172r.327t>c0.969
rrs1472251r.406g>a0.985
rrs1472286r.441c>g0.963
rrs1472288r.443a>t0.961
rrs1472289r.444t>c0.960
rrs1472313r.468g>a0.959
rrs1472315r.470t>g0.980
rrs1472326r.481t>a1.000
rrs1472328r.483g>c1.000
rrs1472382r.537g>a0.963
rrs1472422r.577t>c0.938
rrs1472435r.590t>c0.889
rrs1472438r.593t>c0.889
rrs1472439r.594c>t0.889
rrs1472446r.601t>a0.127
rrs1472463r.618g>a0.925
rrs1472464r.619a>g1.000
rrs1472471r.626g>a0.919
rrs1472489r.644a>t0.924
rrs1472497r.652g>a0.907
rrs1472530r.685g>a0.906
rrs1472580r.735c>t0.915
rrs1472612r.767g>t0.980
rrs1472677r.832c>a0.909
rrs1472680r.835c>t0.906
rrs1472682r.837t>a0.906
rrs1472683r.838t>c0.906
rrs1472686r.841g>a0.915
rrs1472836r.991g>a0.900
rrs1472840r.995a>c0.894
rrs1472841r.996g>a0.894
rrs1472846r.1001c>t0.106
rrs1472847r.1002g>a0.106
rrs1472857r.1012a>g0.894
rrs1472859r.1014g>c0.894
rrs1472860r.1015c>t1.000
rrs1472861r.1016g>a0.104
rrs1472873r.1028c>t0.917
rrs1472874r.1029c>t0.917
rrs1472875r.1030t>g0.917
rrs1472880r.1035g>a0.920
rrs1472956r.1111t>c1.000
rrs1472957r.1112c>t1.000
rrs1472958r.1113a>g0.902
rrs1472960r.1115g>a0.902
rrs1472969r.1124a>g1.000
rrs1472970r.1125c>g1.000
rrs1472973r.1128a>t0.949
rrs1472977r.1132g>c0.974
rrs1472978r.1133t>c1.000
rrs1472986r.1141c>t0.902
rrs1472988r.1143t>c0.902
rrs1472989r.1144g>a1.000
rrs1472990r.1145a>g1.000
rrs1473081r.1236c>t0.979
rrs1473088r.1243a>g1.000
rrs1473099r.1254t>g1.000
rrs1473100r.1255g>a1.000
rrs1473104r.1259c>t1.000
rrs1473110r.1265t>g1.000
rrs1473111r.1266a>g1.000
rrs1473121r.1276t>c0.960
rrs1473123r.1278a>t0.990
rrs1473130r.1285g>a0.990
rrs1473145r.1300c>t1.000
rrs1473166r.1321g>a1.000
rrs1473276r.1431a>g0.926
rrs1473290r.1445c>t1.000
rrs1473291r.1446g>gt0.920
rrl1473696r.39t>c1.000
rrl1473698r.41g>a0.969
rrl1473699r.42a>g0.969
rrl1473719r.62g>t0.952
rrl1473724r.67t>c0.930
rrl1473731r.74t>g0.955
rrl1473732r.75g>t0.933
rrl1473743r.86c>t0.926
rrl1473750r.93c>a0.926
rrl1473756r.99g>t1.000
rrl1473757r.100t>g0.926
rrl1473758r.101g>t1.000
rrl1473768r.111a>g0.944
rrl1473770r.113t>g0.957
rrl1473806r.149c>t0.983
rrl1473811r.154c>a0.911
rrl1473812r.155g>c0.927
rrl1473815r.158t>g0.912
rrl1473822r.165a>g0.879
rrl1473832r.175c>t0.909
rrl1473836r.179a>g0.533
rrl1473844r.187c>t0.930
rrl1473870r.213g>a0.938
rrl1473876r.219g>a0.972
rrl1473898r.241c>t1.000
rrl1473899r.242a>g0.989
rrl1473916r.259c>a0.988
rrl1473922r.265a>g0.948
rrl1473923r.266c>g0.987
rrl1473934r.277g>a0.918
rrl1473935r.278c>t0.918
rrl1473936r.279a>g0.918
rrl1473943r.286g>t1.000
rrl1473945r.288t>a1.000
rrl1473946r.289a>t1.000
rrl1473968r.311c>t0.946
rrl1473971r.314g>t0.943
rrl1474130r.473c>t0.979
rrl1474140r.483c>t0.980
rrl1474151r.494c>t0.983
rrl1474174r.517a>g0.958
rrl1474181r.524c>t0.971
rrl1474183r.526t>c0.971
rrl1474184r.527c>t0.986
rrl1474186r.529a>g0.986
rrl1474201r.544t>c0.990
rrl1474218r.561t>a0.978
rrl1474249r.592g>t0.985
rrl1474264r.607t>g0.961
rrl1474265r.608g>a0.959
rrl1474266r.609t>c0.959
rrl1474269r.612c>t0.959
rrl1474348r.691c>t0.964
rrl1474351r.694g>t0.964
rrl1474353r.696a>c0.964
rrl1474354r.697c>t0.964
rrl1474355r.698a>c0.964
rrl1474356r.699t>g0.981
rrl1474359r.702c>g0.964
rrl1474362r.705a>g0.982
rrl1474387r.730c>t1.000
rrl1474496r.839c>t0.978
rrl1474497r.840g>c0.978
rrl1474506r.849c>g0.978
rrl1474507r.850g>t0.978
rrl1474529r.872a>c0.947
rrl1474530r.873g>a0.947
rrl1474537r.880g>a0.946
rrl1474539r.882c>t0.934
rrl1474540r.883t>g0.946
rrl1474627r.970g>c0.943
rrl1474628r.971c>t0.942
rrl1474632r.975g>t0.988
rrl1474709r.1052gtggt>g0.989
rrl1474721r.1064g>a0.976
rrl1474722r.1065t>g0.976
rrl1474734r.1077g>t0.970
rrl1474740r.1083g>c0.970
rrl1474747r.1090c>g0.970
rrl1474749r.1092c>t0.970
rrl1474760r.1103a>g1.000
rrl1474794r.1137c>t1.000
rrl1474803r.1146g>a1.000
rrl1474812r.1155g>a1.000
rrl1474823r.1166c>g0.988
rrl1474824r.1167a>g0.988
rrl1474830r.1173a>g1.000
rrl1474903r.1246t>c0.947
rrl1474904r.1247g>c0.967
rrl1474913r.1256t>c0.957
rrl1474932r.1275c>t0.949
rrl1475031r.1374g>t0.952
rrl1475061r.1404ca>c0.974
rrl1475064r.1407g>a0.842
rrl1475076r.1419c>a0.951
rrl1475079r.1422t>c0.780
rrl1475080r.1423g>t0.780
rrl1475081r.1424c>g0.780
rrl1475090r.1433a>t0.968
rrl1475114r.1457c>t0.976
rrl1475116r.1459g>a0.855
rrl1475120r.1463g>t0.119
rrl1475129r.1472g>a0.110
rrl1475199r.1542g>a0.273
rrl1475202r.1545g>c0.700
rrl1475206r.1549c>t0.200
rrl1475209r.1552g>c0.200
rrl1475505r.1848g>a0.964
rrl1475526r.1869c>a0.984
rrl1475531r.1874c>t0.968
rrl1475538r.1881t>a0.921
rrl1475539r.1882a>t0.921
rrl1475545r.1888t>g0.943
rrl1475550r.1893a>g0.945
rrl1475649r.1992a>g0.968
rrl1475655r.1998t>a0.939
rrl1475659r.2002g>a1.000
rrl1475699r.2042c>t0.957
rrl1475753r.2096c>g0.896
rrl1475758r.2101a>t0.878
rrl1475769r.2112t>c0.867
rrl1475775r.2118g>t0.935
rrl1475883r.2226a>t0.935
rrl1475884r.2227a>g0.935
rrl1475897r.2240t>c0.940
rrl1475916r.2259c>g0.935
rrl1475975r.2318c>t1.000
rrl1475977r.2320a>g1.000
rrl1475988r.2331a>g1.000
rrl1475997r.2340a>t1.000
rrl1476029r.2372aacctc>a0.735
rrl1476056r.2399g>a0.970
rrl1476086r.2429g>a0.987
rrl1476088r.2431a>t0.975
rrl1476099r.2442a>g0.979
rrl1476105r.2448ga>g0.979
rrl1476115r.2458t>c0.990
rrl1476131r.2474c>t0.973
rrl1476194r.2537a>g0.972
rrl1476200r.2543a>t0.970
rrl1476201r.2544c>t0.969
rrl1476214r.2557g>t1.000
rrl1476215r.2558c>t0.990
rrl1476224r.2567a>g1.000
rrl1476245r.2588c>t0.972
rrl1476251r.2594t>g0.990
rrl1476256r.2599a>t0.962
rrl1476260r.2603a>g0.960
rrl1476281r.2624t>c1.000
rrl1476297r.2640c>a0.957
rrl1476298r.2641c>a0.946
rrl1476301r.2644a>t0.947
rrl1476309r.2652g>t0.944
rrl1476428r.2771c>t0.948
rrl1476524r.2867c>t0.960
rrl1476584r.2927c>t1.000
rrl1476585r.2928a>g0.975
rrl1476594r.2937c>t1.000
rrl1476603r.2946g>a1.000
rrl1476608r.2951c>t1.000
rrl1476614r.2957a>t0.947
rrl1476619r.2962c>t1.000
rrl1476628r.2971t>a1.000
rrl1476629r.2972c>a0.935
rrl1476630r.2973a>g0.935
rrl1476661r.3004a>g0.903
rrl1476665r.3008t>g0.963
rrl1476666r.3009c>t0.966
rrl1476675r.3018c>g0.870
rrl1476689r.3032a>t1.000
rrl1476694r.3037g>a0.909
rrl1476695r.3038t>a1.000
rrl1476699r.3042a>t0.900
rpsA1833568c.27G>C0.167
rpsA1833583c.42C>T0.462
rpsA1833589c.48A>C0.308
rpsA1833595c.54T>G0.308
rpsA1833596p.Ser19Ala0.692
rpsA1833604c.63C>T0.231
rpsA1833607c.66T>C0.462
rpsA1833613c.72C>A0.429
rpsA1833616c.75A>C0.600
rpsA1833619c.78A>C0.714
rpsA1833623p.Lys28Ser0.429
rpsA1833664c.123C>G0.973
rpsA1833676c.135A>G0.976
rpsA1833679c.138G>C0.975
rpsA1833682c.141C>T0.951
rpsA1833694c.153G>T0.977
rpsA1833697c.156C>G0.977
rpsA1833709c.168C>T0.977
rpsA1833734p.Ala65Ser1.000
rpsA1833748c.207C>G1.000
rpsA1833770p.Asn77Ser0.895
rpsA1833781c.240T>C0.895
rpsA1833782p.Ser81Asn0.895
rpsA1833802c.261A>G1.000
rpsA1833805c.264C>T0.851
rpsA1833808c.267G>T0.848
rpsA1833811c.270G>T1.000
rpsA1833832c.291G>A0.964
rpsA1833838c.297G>C1.000
rpsA1833841c.300C>G0.105
rpsA1833847c.306C>G1.000
rpsA1833856c.315A>G0.914
rpsA1833862c.321G>T0.951
rpsA1833894p.Ala118Glu0.949
rpsA1833904c.363G>A0.889
rpsA1833928c.387G>C0.956
rpsA1833949c.408T>C0.937
rpsA1833961c.420C>G0.939
rpsA1833970c.429G>C0.950
rpsA1833979c.438T>C0.952
rpsA1833985c.444G>C0.828
rpsA1833988c.447C>G0.828
rpsA1833991c.450C>A0.136
rpsA1833997c.456G>C0.831
rpsA1834000c.459G>C0.136
rpsA1834009c.468C>T0.951
rpsA1834012c.471G>C0.952
rpsA1834015c.474G>C0.156
rpsA1834021c.480C>T0.970
rpsA1834030c.489C>G0.970
rpsA1834051c.510G>A0.773
rpsA1834066c.525G>A0.790
rpsA1834069c.528G>C0.803
rpsA1834073p.Lys178Arg0.177
rpsA1834093c.552G>C0.830
rpsA1834096c.555G>C0.143
rpsA1834099c.558C>G1.000
rpsA1834105c.564C>T0.829
rpsA1834108c.567C>G1.000
rpsA1834114c.573G>C0.976
rpsA1834135c.594G>C0.968
rpsA1834183c.642T>C0.852
rpsA1834210c.669C>T0.838
rpsA1834231c.690T>C0.951
rpsA1834234c.693G>C0.953
rpsA1834246c.705G>C0.956
rpsA1834249c.708T>C0.958
rpsA1834261c.720A>C0.962
rpsA1834264c.723G>C0.966
rpsA1834279c.738C>T0.962
rpsA1834294c.753G>T0.957
rpsA1834298p.Gln253Thr0.889
rpsA1834303c.762T>C0.978
rpsA1834327c.786G>C0.979
rpsA1834339c.798C>T0.886
rpsA1834340p.Met267Leu0.886
rpsA1834348c.807T>C0.980
rpsA1834354c.813G>T0.923
rpsA1834357c.816T>G1.000
rpsA1834366c.825A>G1.000
rpsA1834375c.834G>A1.000
rpsA1834396c.855G>T1.000
rpsA1834399p.His286Gln0.967
rpsA1834411c.870T>C1.000
rpsA1834423c.882G>T0.984
rpsA1834451c.910T>C0.986
rpsA1834468c.927A>G0.985
rpsA1834483p.Glu314Asp0.921
rpsA1834486p.Glu315Asp0.918
rpsA1834489c.948T>C0.984
rpsA1834498c.957C>T0.903
rpsA1834528c.987T>C0.108
rpsA1834540c.999G>T0.906
rpsA1834543c.1002C>G0.937
rpsA1834546c.1005T>C0.985
rpsA1834552c.1011G>T0.953
rpsA1834555c.1014T>C0.951
rpsA1834600c.1059G>C0.846
rpsA1834606c.1065C>T0.949
rpsA1834609c.1068T>C0.158
rpsA1834612c.1071G>T0.818
rpsA1834619c.1078T>C0.935
rpsA1834622c.1081T>A0.936
rpsA1834633c.1092A>G0.984
rpsA1834639c.1098T>C0.984
rpsA1834645c.1104C>T0.121
rpsA1834666c.1125G>C0.106
rpsA1834667p.Ala376Ser0.985
rpsA1834690c.1149T>C1.000
rpsA1834732c.1191T>C1.000
rpsA1834738c.1197A>G0.980
kasA2518822c.708C>A0.500
kasA2518825c.711T>C0.600
kasA2518846c.732G>T0.500
kasA2518849c.735G>C0.500
kasA2518853p.Leu247Val0.500
kasA2518864c.750G>C0.600
ahpC2726600c.408T>C0.900
ahpC2726638p.Ala149Val0.941
ahpC2726648c.456T>C0.941
ahpC2726651c.459G>C0.941
ahpC2726654c.462G>C0.941
ahpC2726657c.465A>C0.941
ahpC2726669c.477T>C0.941
ahpC2726678c.486G>C0.941
ahpC2726681c.489A>C0.941
ahpC2726684c.492G>T0.941
ahpC2726693c.501C>A0.941
ahpC2726696c.504C>G0.941
ahpC2726702c.510C>T0.941
ahpC2726708c.516G>A0.941
ahpC2726717c.525A>C0.933
ahpC2726727p.Arg179Lys0.900
thyX3067367c.579C>G0.700
thyX3067373c.573G>C0.700
thyX3067391c.555C>G0.700
thyX3067394c.552C>G0.700
embC4240710283W>283*0.154
embC4240726c.864G>C0.385
embC4240729c.867C>G0.500
embC4240735c.873C>G0.538
embC4240741c.879C>T0.571
embC4240756c.894G>C0.500
embC4240771c.909G>C0.471
embC4240772p.Ser304Ala0.471
embC4240778p.His306Gly0.471
embC4240781p.Ala307Ser0.444
embC4240789c.927T>C0.895
embC4240819c.957A>C0.450
embC4240826p.Ala322Ser0.333
embC4240831c.969T>G0.857
embA4245764c.2532G>C0.727
embA4245772p.Asn847Thr0.727
embA4245785c.2553G>C0.700

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.
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