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: 5d77174a9d79d
Sample: 5d77174a9d79d

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Summary
ID: 5d77174a9d79d
Date: Tue Sep 10 04:24:57 2019
Strain: lineage2;lineage4.3.2.1
Drug-resistance: Sensitive

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

Lineage2FamilyMain SpoligotypeRDS
lineage2East-AsianBeijingRD105
lineage4.3.2.1Euro-American (LAM)LAM3RD761

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7415c.114C>T1.000
gyrA7421c.120G>A1.000
gyrA7424c.123G>A1.000
gyrA7427c.126G>C1.000
gyrA7436c.135C>T1.000
gyrA7454c.153G>C1.000
gyrA7457c.156T>C1.000
gyrA7464p.Val55Leu1.000
gyrA8873c.1572A>G1.000
gyrA8897c.1596T>C1.000
rpoB760143p.Val113Ile0.200
rpoB760148p.Asp114Glu1.000
rpoB760157c.351A>G1.000
rpoB760166c.360C>T0.692
rpoB760172c.366G>C1.000
rpoB760181c.375T>G1.000
rpoB760184c.378A>C0.267
rpoB760185p.Leu127Phe0.733
rpoB760193c.387C>G0.250
rpoB760199c.393C>G1.000
rpoB760223c.417T>C0.200
rpoB760233c.427A>T1.000
rpoB760241c.435G>C1.000
rpoB760244c.438G>C1.000
rpoB760253c.447T>C1.000
rpoB760265p.Met153Ile1.000
rpoB760274p.Glu156Asp1.000
rpoB760400c.594G>C0.600
rpoB760407p.Ser201Gly1.000
rpoB760412c.606C>T1.000
rpoB760415c.609C>T0.400
rpoB760418c.612G>C1.000
rpoB760430c.624T>C1.000
rpoB760454c.648C>G0.500
rpoB760457c.651C>T1.000
rpoB760460c.654G>C0.545
rpoB760469c.663C>T0.545
rpoB760475c.669A>G1.000
rpoB760478c.672C>T1.000
rpoB760481c.675G>C1.000
rpoB760484c.678A>G1.000
rpoB761213c.1407G>C0.727
rpoB761231c.1425C>T0.750
rpoB761234c.1428G>C1.000
rpoB761249c.1443A>G1.000
rpoB761255c.1449T>C0.250
rpoB761261c.1455G>T1.000
rpoB761264c.1458C>G0.750
rpoB761282c.1476C>T0.917
rpoB761288c.1482G>C0.917
rpoB761318c.1512G>C1.000
rpoB761321c.1515C>T0.818
rpoB761327c.1521A>G1.000
rpoB761330c.1524G>C0.818
rpoB761333c.1527G>T0.182
rpoB761930c.2124G>C1.000
rpoB761948c.2142G>C1.000
rpoB761954c.2148C>G1.000
rpoB761972c.2166C>T0.944
rpoB762017c.2211A>G1.000
rpoB762032c.2226C>G0.929
rpoB762053c.2247T>C1.000
rpoB762065c.2259T>C1.000
rpoB762086c.2280G>C1.000
rpoB762098c.2292C>G0.875
rpoB762101c.2295C>G0.176
rpoB762114p.Ile770Val1.000
rpoB762122c.2316C>T0.889
rpoB762128c.2322G>C0.875
rpoB762137c.2331C>T1.000
rpoB762140c.2334G>C1.000
rpoB762143c.2337T>C1.000
rpoB762149c.2343G>C1.000
rpoB762158c.2352G>C0.176
rpoB762161c.2355C>T1.000
rpoB762176c.2370T>C0.842
rpoB762182c.2376C>T0.833
rpoB762185c.2379G>C1.000
rpoB762218c.2412T>C0.857
rpoB762233c.2427G>C1.000
rpoB762239c.2433G>A0.818
rpoB762245c.2439G>T0.200
rpoB762881p.Met1025Ile0.938
rpoB762887c.3081G>C0.190
rpoB762896c.3090G>C0.261
rpoB762899c.3093G>C0.913
rpoB762917c.3111C>T0.174
rpoB762923c.3117C>G0.192
rpoB762929c.3123G>T1.000
rpoB762959c.3153G>C1.000
rpoB762971c.3165G>C0.970
rpoB762989c.3183G>C1.000
rpoB762995c.3189G>T1.000
rpoB763007c.3201C>T0.778
rpoB763022c.3216C>G0.800
rpoB763028c.3222T>C1.000
rpoB763031c.3225T>C0.238
rpoB763053c.3247T>C1.000
rpoB763058c.3252C>G1.000
rpoB763070c.3264T>C1.000
rpoB763074p.Thr1090Val1.000
rpoB763085c.3279C>T0.889
rpoB763094c.3288G>C0.913
rpoB763103c.3297G>C0.905
rpoB763115c.3309T>C1.000
rpoB763127c.3321G>C1.000
rpoB763160c.3354G>C1.000
rpoB763166c.3360A>G1.000
rpoB763169c.3363A>G1.000
rpoB763187c.3381C>G1.000
rpoC763474c.105C>T1.000
rpoC763486c.117T>C1.000
rpoC763492c.123G>C0.625
rpoC763528c.159G>A1.000
rpoC763531c.162G>T0.667
rpoC763546c.177A>G1.000
rpoC763570c.201G>C1.000
rpoC763597c.228G>A0.812
rpoC763615c.246G>C1.000
rpoC763619p.Arg84Lys1.000
rpoC763636c.267T>C0.923
rpoC763648c.279C>T0.875
rpoC763660c.291T>G1.000
rpoC763666c.297G>T0.950
rpoC763669c.300C>G0.955
rpoC763675c.306C>G0.857
rpoC763741c.372C>T1.000
rpoC763744c.375G>C1.000
rpoC763765c.396T>C1.000
rpoC764188c.819A>G1.000
rpoC764227c.858G>C1.000
rpoC764239c.870T>G1.000
rpoC764242c.873C>T0.900
rpoC764245c.876C>G1.000
rpoC764254c.885G>A1.000
rpoC764257c.888G>C1.000
rpoC764278c.909A>G1.000
rpoC764297p.Met310Leu1.000
rpoC764320c.951C>G0.895
rpoC764341c.972G>C0.833
rpoC764344c.975C>T0.889
rpoC764365c.996C>T1.000
rpoC764371c.1002G>C1.000
rpoC764377c.1008C>G1.000
rpoC764380c.1011G>C0.923
rpoC764387c.1018T>C1.000
rpoC764497c.1128A>G1.000
rpoC764500c.1131C>G1.000
rpoC764503c.1134G>C0.667
rpoC764509c.1140G>C1.000
rpoC764521c.1152T>C1.000
rpoC764524c.1155C>T0.312
rpoC764527c.1158C>T0.312
rpoC764533c.1164C>T0.688
rpoC764536c.1167G>T0.312
rpoC764539c.1170C>G1.000
rpoC764548c.1179G>A1.000
rpoC764554c.1185C>T0.312
rpoC764560c.1191T>C0.385
rpoC764566c.1197C>G0.385
rpoC764575c.1206T>G1.000
rpoC764576p.Ser403Arg0.385
rpoC764602c.1233C>T0.583
rpoC764605c.1236G>A0.500
rpoC764611c.1242G>T1.000
rpoC764626c.1257C>T0.500
rpoC764632c.1263T>C1.000
rpoC764650c.1281G>T1.000
rpoC764662c.1293G>C0.917
rpoC764716c.1347G>C1.000
rpoC764746c.1377G>T1.000
rpoC764749c.1380G>C1.000
rpoC764752c.1383G>C1.000
rpoC764758c.1389C>G1.000
rpoC764764p.His465Gln1.000
rpoC764767c.1398G>A0.941
rpoC764797c.1428G>C0.958
rpoC764803c.1434C>T1.000
rpoC764824c.1455T>C0.967
rpoC764869c.1500C>T1.000
rpoC764872c.1503A>T1.000
rpoC764875c.1506C>G1.000
rpoC764878c.1509C>G1.000
rpoC764887c.1518G>T1.000
rpoC764888c.1519T>C1.000
rpoC764893c.1524T>C1.000
rpoC764902c.1533C>G0.889
rpoC764935c.1566T>C1.000
rpoC764939c.1570C>T0.909
rpoC764947c.1578G>C0.909
rpoC764948c.1579T>C1.000
rpoC764968c.1599T>C1.000
rpoC765004c.1635G>T0.905
rpoC765007c.1638T>G1.000
rpoC765008c.1639T>C1.000
rpoC765019c.1650A>G1.000
rpoC765028c.1659C>G0.905
rpoC765034c.1665T>A1.000
rpoC765040c.1671T>C1.000
rpoC765041c.1672T>C1.000
rpoC765047c.1678T>C1.000
rpoC765052c.1683C>G1.000
rpoC765055c.1686C>G0.944
rpoC765073c.1704G>C0.950
rpoC765076c.1707A>G1.000
rpoC765079c.1710T>G1.000
rpoC765082c.1713G>T1.000
rpoC765103c.1734G>T1.000
rpoC765121c.1752G>T1.000
rpoC765481c.2112C>T0.182
rpoC765493c.2124G>C0.818
rpoC765496c.2127C>T0.818
rpoC765499c.2130C>G1.000
rpoC765502c.2133G>A0.182
rpoC765525p.Ala719Val1.000
rpoC765529c.2160C>T0.818
rpoC765541c.2172C>G0.818
rpoC765875p.Val836Ile1.000
rpoC765886c.2517C>G1.000
rpoC765892c.2523T>A1.000
rpoC765898c.2529C>T0.818
rpoC765907c.2538G>C0.818
rpoC765908p.Leu847Ala1.000
rpoC766375c.3006C>G1.000
rpoC766381c.3012C>T1.000
rpoC766384c.3015A>G1.000
rpoC766390c.3021C>T0.923
rpoC766402c.3033C>G0.923
rpoC766408c.3039C>T1.000
rpoC766426c.3057C>T1.000
rpoC766435p.Glu1022Asp1.000
rpoC766456c.3087C>G1.000
rpoC766459c.3090G>T1.000
rpoC766462c.3093G>C0.909
rpoC767059c.3690T>G1.000
rpoC767062c.3693C>T0.900
rpoC767065c.3696G>C0.900
rpoC767080c.3711G>C1.000
rpoC767087p.Cys1240Ser1.000
rrs1471923r.78t>c1.000
rrs1471924r.79c>cca0.955
rrs1471925r.80t>g1.000
rrs1471929r.84c>g0.905
rrs1471930r.85g>c0.905
rrs1471931r.86g>t0.905
rrs1471932r.87a>g1.000
rrs1471934r.89a>g1.000
rrs1471979r.134t>c0.781
rrs1471980r.135g>c0.226
rrs1471981r.136c>a0.226
rrs1471986r.141c>t0.774
rrs1472075r.230a>g1.000
rrs1472106r.261g>a1.000
rrs1472108r.263c>t1.000
rrs1472137r.292g>a0.962
rrs1472150r.305t>a1.000
rrs1472151r.306c>t0.962
rrs1472172r.327t>c1.000
rrs1472251r.406g>a1.000
rrs1472286r.441c>g0.781
rrs1472288r.443a>t0.774
rrs1472289r.444t>g0.172
rrs1472290r.445c>g0.172
rrs1472297r.452ggtccgggttctct>g1.000
rrs1472311r.466c>t0.172
rrs1472312r.467ggat>g1.000
rrs1472315r.470t>g1.000
rrs1472324r.479g>c0.162
rrs1472325r.480g>c0.162
rrs1472326r.481t>a0.838
rrs1472328r.483g>c0.838
rrs1472382r.537g>a0.918
rrs1472422r.577t>c1.000
rrs1472435r.590t>c1.000
rrs1472438r.593t>c1.000
rrs1472439r.594c>t1.000
rrs1472445r.600a>at1.000
rrs1472448r.603t>tg1.000
rrs1472450r.605acg>a1.000
rrs1472462r.617t>c1.000
rrs1472463r.618g>a1.000
rrs1472464r.619a>g1.000
rrs1472471r.626g>a1.000
rrs1472489r.644a>t0.980
rrs1472497r.652g>a0.985
rrs1472530r.685g>a0.985
rrs1472580r.735c>t1.000
rrs1472612r.767g>t0.986
rrs1472672r.827gt>g0.972
rrs1472675r.830t>c0.983
rrs1472677r.832c>t0.982
rrs1472680r.835c>t0.982
rrs1472682r.837t>a1.000
rrs1472683r.838t>c1.000
rrs1472686r.841g>a0.717
rrs1472836r.991g>a1.000
rrs1472840r.995a>c1.000
rrs1472841r.996g>a1.000
rrs1472846r.1001c>ca1.000
rrs1472849r.1004ct>c1.000
rrs1472857r.1012a>g1.000
rrs1472859r.1014g>c1.000
rrs1472860r.1015c>t1.000
rrs1472873r.1028c>t1.000
rrs1472874r.1029c>t1.000
rrs1472875r.1030t>g1.000
rrs1472880r.1035g>a1.000
rrs1472956r.1111t>c1.000
rrs1472957r.1112c>t1.000
rrs1472958r.1113a>g0.957
rrs1472960r.1115g>a0.957
rrs1472969r.1124a>g0.957
rrs1472970r.1125c>g0.957
rrs1472973r.1128a>t0.957
rrs1472977r.1132g>c0.917
rrs1472978r.1133t>c0.917
rrs1472986r.1141c>t0.875
rrs1472988r.1143t>c0.917
rrs1472989r.1144g>a0.917
rrs1472990r.1145a>g1.000
rrs1473081r.1236c>t0.941
rrs1473088r.1243a>g0.941
rrs1473099r.1254t>g0.897
rrs1473100r.1255g>a1.000
rrs1473104r.1259c>t1.000
rrs1473110r.1265t>g1.000
rrs1473111r.1266a>g1.000
rrs1473121r.1276t>c0.899
rrs1473123r.1278a>t0.921
rrs1473130r.1285g>a0.931
rrs1473145r.1300c>t1.000
rrs1473166r.1321g>a1.000
rrs1473202r.1357c>t0.169
rrs1473276r.1431a>g1.000
rrs1473290r.1445c>t1.000
rrs1473291r.1446g>gt1.000
rrs1473301r.1456t>c0.173
rrl1473719r.62g>t1.000
rrl1473724r.67t>c1.000
rrl1473731r.74t>g1.000
rrl1473732r.75g>t0.867
rrl1473743r.86c>t0.972
rrl1473750r.93c>a0.972
rrl1473756r.99g>t0.972
rrl1473757r.100t>g0.972
rrl1473758r.101g>t0.972
rrl1473768r.111a>g0.977
rrl1473770r.113t>g0.977
rrl1473806r.149c>t0.967
rrl1473811r.154c>a0.960
rrl1473812r.155g>c0.960
rrl1473815r.158t>g0.960
rrl1473822r.165a>g1.000
rrl1473828r.171g>gct0.957
rrl1473832r.175c>t1.000
rrl1473835r.178ga>g1.000
rrl1473844r.187c>t1.000
rrl1473870r.213g>a1.000
rrl1473876r.219g>a1.000
rrl1473898r.241c>t1.000
rrl1473899r.242a>g1.000
rrl1473916r.259c>a1.000
rrl1473922r.265a>g1.000
rrl1473923r.266c>g1.000
rrl1473934r.277g>a0.950
rrl1473935r.278c>t0.950
rrl1473936r.279a>g1.000
rrl1473943r.286g>t1.000
rrl1473945r.288t>a1.000
rrl1473946r.289a>t1.000
rrl1473968r.311c>t1.000
rrl1473971r.314g>t0.900
rrl1474130r.473c>t1.000
rrl1474140r.483c>t1.000
rrl1474151r.494c>t1.000
rrl1474174r.517a>g0.962
rrl1474179r.522c>ct0.962
rrl1474181r.524c>t0.885
rrl1474183r.526t>c0.923
rrl1474184r.527c>t1.000
rrl1474185r.528ga>g0.963
rrl1474186r.529a>g0.960
rrl1474201r.544t>c1.000
rrl1474218r.561t>a1.000
rrl1474249r.592g>t1.000
rrl1474348r.691c>t1.000
rrl1474351r.694g>c0.150
rrl1474353r.696a>c0.850
rrl1474354r.697c>t1.000
rrl1474355r.698a>c0.850
rrl1474356r.699t>c0.150
rrl1474359r.702c>g1.000
rrl1474362r.705a>g1.000
rrl1474387r.730c>t1.000
rrl1474496r.839c>t1.000
rrl1474497r.840g>c1.000
rrl1474506r.849c>g1.000
rrl1474507r.850g>t1.000
rrl1474529r.872a>c0.976
rrl1474530r.873g>a0.975
rrl1474537r.880g>a1.000
rrl1474539r.882c>t0.974
rrl1474540r.883t>g0.975
rrl1474627r.970g>c0.838
rrl1474628r.971c>t0.838
rrl1474632r.975g>t0.972
rrl1474635r.978c>ctt1.000
rrl1474637r.980ccg>c1.000
rrl1474721r.1064g>a0.886
rrl1474722r.1065t>g0.865
rrl1474734r.1077g>t1.000
rrl1474740r.1083g>c1.000
rrl1474747r.1090c>g1.000
rrl1474749r.1092c>t1.000
rrl1474760r.1103a>g1.000
rrl1474794r.1137c>t1.000
rrl1474803r.1146g>a0.988
rrl1474812r.1155g>a0.987
rrl1474823r.1166c>g1.000
rrl1474824r.1167a>g0.986
rrl1474830r.1173a>g1.000
rrl1474903r.1246t>c0.981
rrl1474904r.1247g>c1.000
rrl1474913r.1256t>c1.000
rrl1474932r.1275c>t0.976
rrl1475031r.1374g>t1.000
rrl1475064r.1407g>a1.000
rrl1475076r.1419c>a1.000
rrl1475079r.1422t>c1.000
rrl1475080r.1423g>t1.000
rrl1475081r.1424c>g1.000
rrl1475090r.1433a>t0.976
rrl1475114r.1457c>t1.000
rrl1475116r.1459g>a1.000
rrl1475505r.1848g>a0.969
rrl1475526r.1869c>a1.000
rrl1475531r.1874c>t0.980
rrl1475538r.1881t>a1.000
rrl1475539r.1882a>t1.000
rrl1475545r.1888t>g1.000
rrl1475550r.1893a>g1.000
rrl1475649r.1992a>g1.000
rrl1475655r.1998t>a1.000
rrl1475659r.2002g>a1.000
rrl1475699r.2042c>t0.962
rrl1475753r.2096c>g1.000
rrl1475758r.2101a>t0.789
rrl1475759r.2102c>t0.167
rrl1475769r.2112t>c0.773
rrl1475775r.2118g>t1.000
rrl1475883r.2226a>t0.924
rrl1475884r.2227a>g0.924
rrl1475897r.2240t>c1.000
rrl1475916r.2259c>g1.000
rrl1475975r.2318c>t0.944
rrl1475977r.2320a>g1.000
rrl1475988r.2331a>g1.000
rrl1475997r.2340a>t1.000
rrl1476056r.2399g>a0.952
rrl1476086r.2429g>a1.000
rrl1476088r.2431a>t1.000
rrl1476099r.2442a>g1.000
rrl1476105r.2448ga>g1.000
rrl1476115r.2458t>c1.000
rrl1476131r.2474c>t1.000
rrl1476160r.2503t>c0.167
rrl1476194r.2537a>g0.947
rrl1476200r.2543a>t1.000
rrl1476201r.2544c>t1.000
rrl1476214r.2557g>t0.908
rrl1476215r.2558c>t0.917
rrl1476224r.2567a>g1.000
rrl1476245r.2588c>t1.000
rrl1476251r.2594t>g0.933
rrl1476256r.2599a>t1.000
rrl1476260r.2603a>g1.000
rrl1476281r.2624t>c1.000
rrl1476297r.2640c>a1.000
rrl1476298r.2641c>a1.000
rrl1476301r.2644a>t1.000
rrl1476309r.2652g>t1.000
rrl1476428r.2771c>t1.000
rrl1476524r.2867c>t1.000
rrl1476531r.2874t>c0.500
rrl1476567r.2910c>t0.122
rrl1476584r.2927c>t1.000
rrl1476585r.2928a>g1.000
rrl1476594r.2937c>t1.000
rrl1476603r.2946g>a1.000
rrl1476608r.2951c>t0.946
rrl1476614r.2957a>t1.000
rrl1476619r.2962c>t1.000
rrl1476628r.2971t>a1.000
rrl1476629r.2972c>a1.000
rrl1476630r.2973a>g1.000
rrl1476661r.3004a>g1.000
rrl1476665r.3008t>g1.000
rrl1476666r.3009c>t1.000
rrl1476675r.3018c>g1.000
rpsA1833664c.123C>G1.000
rpsA1833676c.135A>G1.000
rpsA1833679c.138G>C1.000
rpsA1833682c.141C>T0.909
rpsA1833694c.153G>T1.000
rpsA1833697c.156C>G1.000
rpsA1833709c.168C>T1.000
rpsA1833734p.Ala65Ser1.000
rpsA1833748c.207C>G1.000
rpsA1833770p.Asn77Ser1.000
rpsA1833781c.240T>C1.000
rpsA1833782p.Ser81Asn1.000
rpsA1833802c.261A>G0.950
rpsA1833805c.264C>T0.947
rpsA1833808c.267G>T0.947
rpsA1833811c.270G>T1.000
rpsA1833832c.291G>A1.000
rpsA1833838c.297G>C1.000
rpsA1833847c.306C>G1.000
rpsA1833856c.315A>G1.000
rpsA1833859c.318C>T1.000
rpsA1833862c.321G>T1.000
rpsA1833874c.333T>C1.000
rpsA1833894p.Ala118Glu1.000
rpsA1833928c.387G>C1.000
rpsA1833949c.408T>C1.000
rpsA1833961c.420C>G0.842
rpsA1833970c.429G>C1.000
rpsA1833979c.438T>C1.000
rpsA1833985c.444G>C1.000
rpsA1833988c.447C>G1.000
rpsA1833991c.450C>A0.150
rpsA1833997c.456G>C0.875
rpsA1834009c.468C>T0.846
rpsA1834012c.471G>C1.000
rpsA1834015c.474G>C0.154
rpsA1834021c.480C>T1.000
rpsA1834030c.489C>G1.000
rpsA1834051c.510G>A0.818
rpsA1834066c.525G>A0.810
rpsA1834069c.528G>C1.000
rpsA1834093c.552G>C0.833
rpsA1834099c.558C>G1.000
rpsA1834105c.564C>T0.818
rpsA1834108c.567C>G0.818
rpsA1834114c.573G>C0.818
rpsA1834183c.642T>C1.000
rpsA1834210c.669C>T1.000
rpsA1834231c.690T>C1.000
rpsA1834234c.693G>C1.000
rpsA1834246c.705G>C1.000
rpsA1834249c.708T>C1.000
rpsA1834261c.720A>C1.000
rpsA1834264c.723G>T0.941
rpsA1834279c.738C>T1.000
rpsA1834282c.741C>T1.000
rpsA1834294c.753G>T1.000
rpsA1834300p.Gln253His1.000
rpsA1834327c.786G>T1.000
rpsA1834339c.798C>T1.000
rpsA1834340p.Met267Leu1.000
rpsA1834348c.807T>C0.929
rpsA1834354c.813G>T1.000
rpsA1834357c.816T>G1.000
rpsA1834366c.825A>G1.000
rpsA1834375c.834G>A1.000
rpsA1834396c.855G>T1.000
rpsA1834399p.His286Gln1.000
rpsA1834411c.870T>C1.000
rpsA1834423c.882G>T1.000
rpsA1834451c.910T>C1.000
rpsA1834468c.927A>G1.000
rpsA1834483p.Glu314Asp1.000
rpsA1834486p.Glu315Asp1.000
rpsA1834489c.948T>C1.000
rpsA1834498c.957C>T0.857
rpsA1834501c.960G>C1.000
rpsA1834513c.972C>G0.158
rpsA1834528c.987T>C0.833
rpsA1834540c.999G>C0.842
rpsA1834543c.1002C>G0.842
rpsA1834546c.1005T>C0.842
rpsA1834552c.1011G>T1.000
rpsA1834555c.1014T>C1.000
rpsA1834600c.1059G>C1.000
rpsA1834612c.1071G>T1.000
rpsA1834619c.1078T>C1.000
rpsA1834622c.1081T>A1.000
rpsA1834633c.1092A>G1.000
rpsA1834639c.1098T>C1.000
rpsA1834667p.Ala376Ser1.000
rpsA1834690c.1149T>C1.000
rpsA1834732c.1191T>C1.000
rpsA1834738c.1197A>G1.000

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;