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: 5cc55b294593c
Sample: 5cc55b294593c

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Summary
ID: 5cc55b294593c
Date: Sun Apr 28 08:54:53 2019
Strain: lineage1.2.1
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
StreptomycinRrrs r.190g>a (0.97), rrs r.462c>t (0.97)
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage1.2.1Indo-OceanicEAI2RD239

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6160c.921C>G1.000
gyrB6700c.1461T>C1.000
gyrB6709c.1470A>G1.000
gyrB6712c.1473G>C1.000
gyrB6724c.1485G>C1.000
gyrB6730c.1491A>G1.000
gyrB6745c.1506T>C0.917
gyrB6751c.1512G>C0.917
gyrB6760c.1521G>C0.900
gyrA7361c.60C>T1.000
gyrA7362p.Glu21Gln1.000
gyrA7391c.90C>T1.000
gyrA7412c.111C>G1.000
gyrA7430c.129G>A1.000
gyrA7433c.132G>C1.000
gyrA7442c.141G>C1.000
gyrA7457c.156T>C1.000
gyrA7463c.162G>C1.000
gyrA7496c.195C>G1.000
gyrA7514c.213C>G1.000
gyrA7526c.225G>T1.000
gyrA7532c.231T>C1.000
gyrA7541c.240C>G1.000
gyrA7547c.246C>T1.000
gyrA7550c.249C>T1.000
gyrA7585p.Ser95Thr1.000
gyrA7601c.300C>G1.000
gyrA7607c.306C>G1.000
gyrA7619c.318C>T1.000
gyrA7728c.427A>C0.917
gyrA7760c.459C>T0.917
gyrA7763c.462T>G0.923
gyrA7766c.465C>T0.923
gyrA7793c.492G>A1.000
gyrA7796c.495G>A1.000
gyrA7799c.498A>G1.000
gyrA7832c.531G>T1.000
gyrA7835c.534A>G1.000
gyrA7847c.546G>C1.000
gyrA7853c.552C>T1.000
gyrA7859c.558A>C1.000
gyrA8156c.855T>C1.000
gyrA8177c.876A>C1.000
gyrA8184p.Lys295Arg1.000
gyrA8198c.897T>C1.000
gyrA8207c.906T>C1.000
gyrA8210c.909G>A1.000
gyrA8219c.918T>C1.000
gyrA8247p.Ile316Val1.000
gyrA8264c.963T>C1.000
gyrA8267c.966G>C1.000
gyrA8283p.Ile328Leu1.000
gyrA8288c.987T>C1.000
gyrA8294c.993T>C1.000
gyrA8324c.1023T>C1.000
gyrA8330c.1029C>G1.000
gyrA8339c.1038A>G0.917
gyrA8340p.Ala347Ser0.909
gyrA8354c.1053G>C0.909
gyrA8939c.1638T>C1.000
gyrA8942c.1641G>C1.000
gyrA8946c.1645T>C1.000
gyrA8966c.1665C>G1.000
gyrA8967p.Ala556Arg1.000
gyrA8981c.1680G>C1.000
gyrA8996c.1695T>C1.000
gyrA8998p.Leu566Trp1.000
gyrA9023c.1722A>C1.000
gyrA9029c.1728T>G1.000
gyrA9032c.1731T>C1.000
gyrA9206c.1905C>G0.900
gyrA9209c.1908G>A0.900
gyrA9212c.1911G>C0.917
gyrA9230c.1929T>C0.923
gyrA9233c.1932C>G0.923
gyrA9242c.1941A>C0.923
gyrA9267p.Asn656Gly0.929
gyrA9284c.1983T>C0.938
gyrA9296c.1995T>C0.941
gyrA9304p.Gly668Asp1.000
gyrA9308p.Asp669Glu1.000
gyrA9323c.2022C>G1.000
gyrA9345c.2044A>C1.000
rpoB759570c.-237C>CG0.944
rpoB760139c.333A>T1.000
rpoB760184c.378A>G1.000
rpoB760196c.390C>G1.000
rpoB760223c.417T>C1.000
rpoB760235c.429T>C1.000
rpoB760298c.492G>C0.889
rpoB760310c.504G>C0.867
rpoB760313c.507G>C0.933
rpoB760328c.522G>C0.917
rpoB760331c.525G>C0.917
rpoB760337c.531C>G0.917
rpoB760340c.534G>T0.846
rpoB760361c.555T>C1.000
rpoB760381p.Thr192Met1.000
rpoB760591p.Val262Ala1.000
rpoB760611c.805T>C0.941
rpoB760634c.828T>G0.950
rpoB760643c.837G>A0.944
rpoB760646c.840C>G0.944
rpoB760649c.843G>C0.947
rpoB760655c.849A>G0.947
rpoB760661c.855A>C0.947
rpoB760670c.864G>C0.944
rpoB760671c.865C>T1.000
rpoB760679c.873A>G1.000
rpoB760683c.877T>C1.000
rpoB760718c.912C>T1.000
rpoB760724c.918T>C1.000
rpoB760730c.924T>C1.000
rpoB760751c.945G>C1.000
rpoB760757c.951T>C1.000
rpoB760805c.999G>C1.000
rpoB760817c.1011A>G1.000
rpoB760820c.1014T>C1.000
rpoB760829c.1023C>T1.000
rpoB760830c.1024T>C1.000
rpoB760845p.Thr347His1.000
rpoB760869p.Val355Thr1.000
rpoB760877c.1071G>T1.000
rpoB760886c.1080A>G1.000
rpoB760919c.1113C>G1.000
rpoB760925c.1119T>C1.000
rpoB761006c.1200C>T0.900
rpoB761015c.1209G>C0.909
rpoB761027c.1221A>G0.900
rpoB761030c.1224G>T0.900
rpoB761036c.1230G>C0.900
rpoB761037c.1231T>C0.900
rpoB761057c.1251G>C0.929
rpoB761132c.1326G>T0.800
rpoB761147c.1341C>T0.909
rpoB761150c.1344A>T0.909
rpoB761153c.1347G>C0.900
rpoB761180c.1374A>C0.909
rpoB761189c.1383T>C0.900
rpoB761195c.1389G>T0.818
rpoB761207c.1401C>T0.769
rpoB761213c.1407G>C0.769
rpoB761234c.1428G>C0.750
rpoB761249c.1443A>G0.750
rpoB761255c.1449T>G0.750
rpoB761258c.1452G>A0.750
rpoB761261c.1455G>T0.800
rpoB761264c.1458C>G0.812
rpoB761273c.1467T>C0.833
rpoB761318c.1512G>C0.857
rpoB761327c.1521A>G0.857
rpoB761537c.1731C>T1.000
rpoB761570c.1764T>C1.000
rpoB761573c.1767C>G1.000
rpoB761579c.1773G>C1.000
rpoB761606c.1800C>G1.000
rpoB761612c.1806G>C1.000
rpoB761615c.1809A>C1.000
rpoB761636c.1830G>T1.000
rpoB761645c.1839C>G1.000
rpoB761648c.1842T>C1.000
rpoB761864c.2058G>C0.900
rpoB761873c.2067A>G0.900
rpoB761876c.2070C>G0.900
rpoB761879c.2073G>A0.900
rpoB761903c.2097T>G0.917
rpoB761909c.2103T>C0.900
rpoB761912c.2106T>C0.900
rpoB761915p.Asp703Glu0.818
rpoB761916p.Asp704Asn0.818
rpoB761921c.2115C>T0.833
rpoB761930c.2124G>C0.857
rpoB761954c.2148C>G0.917
rpoB761955p.Ile717Val0.923
rpoB761972c.2166C>T0.933
rpoB761990c.2184G>C0.938
rpoB762011c.2205G>C0.917
rpoB762029c.2223C>G0.933
rpoB762053c.2247T>C0.900
rpoB762056c.2250G>A0.900
rpoB762083c.2277T>C0.909
rpoB762086c.2280G>C0.909
rpoB762101c.2295C>G0.909
rpoB762114p.Ile770Val1.000
rpoB762131c.2325C>G1.000
rpoB762149c.2343G>C1.000
rpoB762167c.2361T>C1.000
rpoB762176c.2370T>C1.000
rpoB762185c.2379G>C1.000
rpoB762209c.2403C>T1.000
rpoB762212c.2406G>C1.000
rpoB762233c.2427G>C1.000
rpoB762254c.2448T>C1.000
rpoB762491c.2685T>G1.000
rpoB762789p.Leu995Met1.000
rpoB762795p.Asp997Asn1.000
rpoB762799p.Ala998Gly1.000
rpoB762813p.Met1003Val1.000
rpoB762818c.3012C>G1.000
rpoB762827c.3021G>T1.000
rpoB762839c.3033G>A1.000
rpoB762857c.3051C>G1.000
rpoB762920c.3114C>T1.000
rpoB762926c.3120C>G1.000
rpoB762929c.3123G>T1.000
rpoB762995c.3189G>T1.000
rpoB763013c.3207C>G1.000
rpoB763028c.3222T>C1.000
rpoB763031c.3225T>G1.000
rpoB763034c.3228C>A1.000
rpoB763040c.3234C>G1.000
rpoB763053c.3247T>C1.000
rpoB763070c.3264T>C1.000
rpoB763085c.3279C>G1.000
rpoB763094c.3288G>C1.000
rpoB763103c.3297G>C1.000
rpoB763115c.3309T>C1.000
rpoB763127c.3321G>T1.000
rpoB763139c.3333C>T1.000
rpoB763142c.3336C>G1.000
rpoB763166c.3360A>G1.000
rpoB763169c.3363A>G1.000
rpoB763193c.3387C>T1.000
rpoC763468c.99G>C1.000
rpoC763486c.117T>C1.000
rpoC763492c.123G>C1.000
rpoC763546c.177A>G1.000
rpoC763570c.201G>C1.000
rpoC763594c.225C>T1.000
rpoC763603c.234C>T1.000
rpoC763618c.249C>T1.000
rpoC763624c.255C>G1.000
rpoC763633c.264T>C1.000
rpoC763660c.291T>G1.000
rpoC763666c.297G>C1.000
rpoC763669c.300C>G1.000
rpoC763696c.327T>C1.000
rpoC763699c.330G>T1.000
rpoC763702c.333C>G1.000
rpoC763708c.339G>T1.000
rpoC763717c.348T>C1.000
rpoC763732c.363C>T1.000
rpoC763735c.366G>C0.909
rpoC763747c.378G>A1.000
rpoC763765c.396T>C1.000
rpoC763781p.Ser138Ala1.000
rpoC763792p.Glu141Asp1.000
rpoC763801c.432C>G1.000
rpoC763807c.438T>C1.000
rpoC763836p.Ala156Val1.000
rpoC763900c.531G>C1.000
rpoC763930c.561G>A1.000
rpoC763945c.576T>C1.000
rpoC763948c.579G>C1.000
rpoC763949p.Arg194Lys1.000
rpoC763972c.603C>T1.000
rpoC763987c.618C>T1.000
rpoC763991p.Ile208Leu1.000
rpoC763996c.627T>C1.000
rpoC764002c.633C>T1.000
rpoC764011c.642T>C1.000
rpoC764024c.655T>C1.000
rpoC764044c.675T>C1.000
rpoC764059c.690G>T1.000
rpoC764074c.705C>T1.000
rpoC764077c.708C>G1.000
rpoC764083c.714A>G1.000
rpoC764152c.783C>T1.000
rpoC764159c.790C>T1.000
rpoC764278c.909A>G1.000
rpoC764311c.942C>G1.000
rpoC764338c.969G>A1.000
rpoC764353c.984G>C1.000
rpoC764365c.996C>T1.000
rpoC764371c.1002G>C1.000
rpoC764380c.1011G>C1.000
rpoC764387c.1018T>C1.000
rpoC764485c.1116G>C1.000
rpoC764497c.1128A>G1.000
rpoC764500c.1131C>G1.000
rpoC764521c.1152T>C1.000
rpoC764536c.1167G>C1.000
rpoC764539c.1170C>G0.923
rpoC764548c.1179G>A0.923
rpoC764554c.1185C>T0.929
rpoC764560c.1191T>C0.917
rpoC764566c.1197C>G0.909
rpoC764581c.1212T>C0.909
rpoC764593c.1224C>T0.923
rpoC764605c.1236G>C0.923
rpoC764611c.1242G>T0.923
rpoC764632c.1263T>C0.929
rpoC764650c.1281G>T0.929
rpoC764713c.1344G>A0.938
rpoC764716c.1347G>C0.929
rpoC764746c.1377G>C0.938
rpoC764764c.1395T>C0.947
rpoC764803c.1434C>T0.938
rpoC764809c.1440C>T0.923
rpoC764812c.1443C>G0.923
rpoC764815c.1446A>G0.923
rpoC764824c.1455T>C0.917
rpoC764875c.1506C>G1.000
rpoC764893c.1524T>C1.000
rpoC764896c.1527C>T1.000
rpoC764911c.1542A>G1.000
rpoC764932c.1563C>G1.000
rpoC765007c.1638T>G0.909
rpoC765008c.1639T>C0.909
rpoC765016c.1647C>G0.909
rpoC765019c.1650A>G0.909
rpoC765047c.1678T>C0.900
rpoC765052c.1683C>G0.900
rpoC765055c.1686C>G0.900
rpoC765451c.2082C>T0.900
rpoC765478c.2109T>C0.900
rpoC765517c.2148C>G0.909
rpoC765529c.2160C>T0.909
rpoC765541c.2172C>G1.000
rpoC765556c.2187G>C1.000
rpoC765562c.2193G>C1.000
rpoC765583c.2214G>T1.000
rpoC765604c.2235C>T1.000
rpoC765607c.2238C>G1.000
rpoC765611p.His748Ala1.000
rpoC765619c.2250G>A1.000
rpoC765631p.Asp754Glu1.000
rpoC765640c.2271A>G1.000
rpoC765658c.2289C>T1.000
rpoC765676c.2307G>A1.000
rpoC765772c.2403C>G1.000
rpoC765778c.2409C>G1.000
rpoC765781p.Asp804Glu1.000
rpoC765784c.2415C>G1.000
rpoC765796c.2427C>T1.000
rpoC765811c.2442T>C0.917
rpoC765826c.2457T>C0.933
rpoC765844c.2475C>A0.941
rpoC765875p.Val836Ile0.938
rpoC765883c.2514C>G0.938
rpoC765886c.2517C>G0.950
rpoC765892c.2523T>C0.950
rpoC765934c.2565C>G0.929
rpoC765937c.2568T>C0.933
rpoC765946c.2577C>T0.933
rpoC765947c.2578T>C0.933
rpoC765961c.2592G>A1.000
rpoC765967c.2598C>T1.000
rpoC765979c.2610C>G1.000
rpoC766348c.2979A>G1.000
rpoC766363c.2994G>C1.000
rpoC766366c.2997C>G1.000
rpoC766381c.3012C>T1.000
rpoC766384c.3015A>G1.000
rpoC766393c.3024C>G1.000
rpoC766408c.3039C>T0.933
rpoC766426c.3057C>T0.933
rpoC766429c.3060C>G0.929
rpoC766447c.3078T>C0.938
rpoC766456c.3087C>G0.938
rpoC766459c.3090G>T0.938
rpoC766462c.3093G>C0.938
rpoC766484p.Val1039Ile0.933
rpoC766504c.3135G>C1.000
rpoC766513c.3144C>T1.000
rpoC766528c.3159T>G1.000
rpoC766534c.3165C>G1.000
rpoC766549c.3180G>C1.000
rpoC766565p.Ile1066Val1.000
rpoC766573c.3204T>C1.000
rpoC766607p.Ile1080Leu1.000
rpoC766618c.3249G>T1.000
rpoC766624c.3255G>C1.000
rpoC766645c.3276A>G1.000
rpoC766651c.3282T>C1.000
rpoC766657c.3288A>G1.000
rpoC766667p.Ser1100Ala0.933
rpoC766672c.3303T>C1.000
rpoC766690c.3321G>T0.938
rpoC766714c.3345G>C1.000
rpoC766726c.3357T>C1.000
rpoC766738c.3369G>T0.944
rpoC766750c.3381C>G0.923
rpoC766753c.3384C>T0.923
rpoC766765c.3396A>C1.000
rpoC766774c.3405T>C0.941
rpoC766798c.3429C>G0.917
rpoC766801c.3432C>G0.923
rpoC766804c.3435A>G0.923
rpoC766843c.3474T>C0.933
rpoC766846c.3477C>T0.933
rpoC766864c.3495G>C0.929
rpoC766894c.3525T>C1.000
rpoC766895c.3526T>C1.000
rpoC766900c.3531T>C1.000
rpoC766903c.3534C>T1.000
rpoC766918c.3549C>T0.900
rpoC766933c.3564A>G0.900
rpoC766945c.3576A>C0.900
rpoC766948c.3579G>C0.909
rpoC766972c.3603G>C0.900
rpoC766978c.3609C>A0.917
rpoC766996c.3627C>T1.000
rpoC767008c.3639G>C0.923
rpoC767033c.3664T>A0.944
rpoC767059c.3690T>G0.941
rpoC767062c.3693C>A0.941
rpoC767098c.3729T>C0.950
rpoC767119c.3750A>G0.957
rpoC767134c.3765C>A0.947
rpoC767167c.3798C>G1.000
rpoC767173c.3804C>G1.000
rpoC767191c.3822C>G1.000
rpsL781649c.90T>C1.000
rpsL781655c.96T>C1.000
rpsL781658c.99A>G1.000
rpsL781715c.156T>C1.000
rpsL781718c.159C>T1.000
rpsL781721c.162C>T0.947
rpsL781728c.169T>C0.950
rpsL781742c.183C>T0.952
rpsL781754c.195G>C0.955
rpsL781763c.204C>G0.952
rpsL781778c.219C>T0.955
rpsL781808c.249C>T0.957
rpsL781829c.270G>C1.000
rpsL781832c.273T>C1.000
rpsL781865c.306G>C1.000
rpsL781868c.309T>C1.000
rpsL781871c.312G>T1.000
rpsL781880c.321C>G1.000
rpsL781892c.333A>G1.000
rplC800796c.-13A>C0.950
rplC800801c.-8A>G0.947
rplC800815c.7C>A0.950
rplC800820c.12G>A0.950
rplC800829c.21C>G0.952
rplC800844c.36T>C0.944
rplC800865c.57A>G1.000
rplC800867p.Ser20Asn1.000
rplC800873p.Arg22Lys1.000
rplC800877c.69A>C1.000
rplC800880c.72A>G1.000
rplC800889c.81C>T1.000
embR1416310c.1038C>T0.909
embR1416313c.1035T>C0.909
embR1416316c.1032G>C0.909
embR1416330p.Val340Ile0.923
embR1416340c.1008G>C0.923
embR1416343c.1005C>G0.923
embR1416379c.969G>C1.000
embR1416388c.960T>C1.000
rrs1471866r.21c>t0.960
rrs1471918r.73a>t0.972
rrs1471925r.80t>c0.971
rrs1471934r.89a>g0.971
rrs1471938r.93t>a0.971
rrs1471970r.125g>a0.982
rrs1471984r.139t>a1.000
rrs1472019r.174g>a0.980
rrs1472030r.185g>a1.000
rrs1472032r.187g>a0.969
rrs1472034r.189t>c1.000
rrs1472042r.197t>c0.975
rrs1472053r.208agc>a1.000
rrs1472061r.216a>t1.000
rrs1472075r.230a>g1.000
rrs1472108r.263c>t1.000
rrs1472113r.268t>c1.000
rrs1472225r.380c>a1.000
rrs1472314r.469a>g0.973
rrs1472315r.470t>c0.973
rrs1472489r.644a>t0.969
rrs1472755r.910g>a1.000
rrs1472847r.1002g>c0.867
rrs1472848r.1003t>g0.867
rrs1472849r.1004c>g0.867
rrs1472850r.1005t>c0.867
rrs1472857r.1012a>g0.867
rrs1472858r.1013g>t0.867
rrs1472859r.1014g>c0.867
rrs1472860r.1015c>g0.867
rrs1472969r.1124a>g1.000
rrs1472970r.1125c>g1.000
rrs1472977r.1132g>c1.000
rrs1472978r.1133t>c1.000
rrs1473120r.1275c>ct0.846
rrs1473123r.1278a>t0.919
rrs1473288r.1443c>ct0.744
rrs1473290r.1445c>t0.939
rrl1473653c.-5T>A1.000
rrl1473758r.101g>t1.000
rrl1473806r.149c>t1.000
rrl1473813r.156c>t1.000
rrl1473815r.158t>c1.000
rrl1473839r.182g>t1.000
rrl1473876r.219g>a1.000
rrl1473899r.242a>t1.000
rrl1473923r.266c>a1.000
rrl1473937r.280c>t1.000
rrl1473943r.286g>t1.000
rrl1473945r.288t>a1.000
rrl1473946r.289a>t1.000
rrl1473980r.323aggat>a0.958
rrl1473987r.330g>gatct1.000
rrl1473995r.338g>t1.000
rrl1474001r.344c>t1.000
rrl1474007r.350a>g1.000
rrl1474016r.359c>a1.000
rrl1474018r.361g>a1.000
rrl1474029r.372g>a1.000
rrl1474051r.394t>c1.000
rrl1474061r.404t>c1.000
rrl1474090r.433c>t1.000
rrl1474093r.436g>a1.000
rrl1474103r.446a>t1.000
rrl1474127r.470g>a1.000
rrl1474139r.482c>t1.000
rrl1474140r.483c>t1.000
rrl1474151r.494c>t1.000
rrl1474181r.524c>t1.000
rrl1474266r.609t>c0.971
rrl1474290r.633ttttcctctccggagg>t0.933
rrl1474306r.649a>c0.842
rrl1474308r.651g>t0.842
rrl1474310r.653t>g0.864
rrl1474362r.705a>g0.956
rrl1474414r.757c>t0.857
rrl1474447r.790g>a0.971
rrl1474639r.982g>a0.962
rrl1474716r.1059a>c0.943
rrl1474794r.1137c>a1.000
rrl1474812r.1155g>a1.000
rrl1474831r.1174a>g1.000
rrl1474957r.1300c>t0.952
rrl1474968r.1311g>a0.952
rrl1475006r.1349a>g0.952
rrl1475007r.1350c>t0.952
rrl1475013r.1356g>a0.955
rrl1475018r.1361g>t1.000
rrl1475019r.1362t>a1.000
rrl1475028r.1371g>a1.000
rrl1475061r.1404c>a1.000
rrl1475062r.1405a>t0.971
rrl1475202r.1545g>c0.938
rrl1475213r.1556c>t0.933
rrl1475315r.1658a>c0.906
rrl1475355r.1698c>t0.947
rrl1475369r.1712g>c0.944
rrl1475402r.1745c>t0.979
rrl1475429r.1772g>a0.957
rrl1475479r.1822c>t0.955
rrl1475480r.1823a>t0.955
rrl1475505r.1848g>a0.971
rrl1475526r.1869c>a0.962
rrl1475573r.1916g>a0.970
rrl1475599r.1942a>g0.967
rrl1475604r.1947a>c0.969
rrl1475606r.1949t>c0.969
rrl1475619r.1962c>t0.971
rrl1475622r.1965g>t0.971
rrl1475635r.1978g>a0.968
rrl1475637r.1980t>g0.968
rrl1475659r.2002g>a0.971
rrl1475760r.2103c>t0.968
rrl1475763r.2106c>t0.968
rrl1475975r.2318c>t1.000
rrl1475977r.2320a>g1.000
rrl1475988r.2331a>t1.000
rrl1476030r.2373a>g1.000
rrl1476032r.2375c>t1.000
rrl1476040r.2383c>t1.000
rrl1476046r.2389g>a1.000
rrl1476049r.2392c>t1.000
rrl1476086r.2429g>a1.000
rrl1476089r.2432t>c1.000
rrl1476095r.2438c>g1.000
rrl1476103r.2446c>g1.000
rrl1476105r.2448g>a1.000
rrl1476106r.2449a>t1.000
rrl1476110r.2453g>c1.000
rrl1476115r.2458t>c1.000
rrl1476117r.2460g>c1.000
rrl1476131r.2474c>t1.000
rrl1476214r.2557g>t1.000
rrl1476215r.2558c>t1.000
rrl1476297r.2640c>t0.955
rrl1476299r.2642c>t0.955
rrl1476580r.2923g>a0.972
rrl1476597r.2940g>a0.971
rrl1476608r.2951c>t0.973
rrl1476619r.2962c>t0.976
rrl1476628r.2971t>a0.977
rrl1476689r.3032a>t0.941
rrl1476692r.3035t>a0.941
rrl1476695r.3038t>a0.939
rrl1476710r.3053c>a0.935
rrl1476720r.3063g>t0.895
rrl1476723r.3066t>a0.889
rrl1476725r.3068c>t0.889
rrl1476726r.3069a>g0.889
rrl1476732r.3075t>c0.941
rrl1476759r.3102t>c1.000
inhA1674414c.213G>C1.000
inhA1674416p.Ala72Asp1.000
inhA1674421c.220T>C1.000
inhA1674443p.Ala81Val1.000
inhA1674450c.249G>C1.000
inhA1674452p.Ala84Glu1.000
inhA1674471c.270G>C1.000
inhA1674474c.273G>C1.000
inhA1674480c.279T>C1.000
inhA1674486c.285T>C1.000
inhA1674489c.288G>A1.000
inhA1674503p.Thr101Ser1.000
inhA1674542p.Ala114Glu1.000
inhA1674546c.345T>C1.000
inhA1674756c.555T>C0.909
inhA1674762c.561T>C1.000
inhA1674942c.741T>C1.000
inhA1674945p.Asp248Glu1.000
inhA1674957c.756G>A1.000
inhA1674963c.762G>C1.000
rpsA1833589c.48A>T1.000
rpsA1833593p.Ser18Thr0.917
rpsA1833661c.120A>G0.923
rpsA1833664c.123C>A0.923
rpsA1833724c.183C>G1.000
rpsA1833727c.186G>C1.000
rpsA1833745c.204G>C1.000
rpsA1833784c.243C>T1.000
rpsA1833802c.261A>G1.000
rpsA1833811c.270G>T1.000
rpsA1833817c.276C>G1.000
rpsA1833820c.279G>A1.000
rpsA1833856c.315A>G0.905
rpsA1833859c.318C>T0.909
rpsA1833874c.333T>C0.913
rpsA1833894p.Ala118Glu0.920
rpsA1833928c.387G>C1.000
rpsA1833979c.438T>C1.000
rpsA1833988c.447C>G1.000
rpsA1834000c.459G>C1.000
rpsA1834012c.471G>C1.000
rpsA1834015c.474G>C1.000
rpsA1834021c.480C>T1.000
rpsA1834030c.489C>G1.000
rpsA1834051c.510G>A1.000
rpsA1834261c.720A>G0.909
rpsA1834264c.723G>C0.900
rpsA1834297c.756C>G0.929
rpsA1834303c.762T>G0.929
rpsA1834306c.765T>C1.000
rpsA1834348c.807T>C1.000
rpsA1834366c.825A>G1.000
rpsA1834372c.831G>A1.000
rpsA1834378c.837T>C1.000
rpsA1834396c.855G>C1.000
rpsA1834411c.870T>C1.000
rpsA1834423c.882G>T1.000
rpsA1834451c.910T>C1.000
rpsA1834456c.915T>C1.000
rpsA1834459c.918G>C1.000
rpsA1834468c.927A>G1.000
rpsA1834489c.948T>C1.000
rpsA1834513c.972C>G0.923
rpsA1834528c.987T>C0.917
rpsA1834546c.1005T>C0.929
rpsA1834606c.1065C>T0.900
rpsA1834609c.1068T>C0.900
rpsA1834612c.1071G>T0.909
rpsA1834633c.1092A>G0.929
rpsA1834639c.1098T>C0.938
rpsA1834654c.1113G>A0.944
rpsA1834666c.1125G>C1.000
rpsA1834669c.1128G>C1.000
rpsA1834690c.1149T>C1.000
rpsA1834732c.1191T>C1.000
katG2155673c.439G>A1.000
katG2155691c.421A>G1.000
katG2155704c.408G>C1.000
katG2155716c.396A>G1.000
kasA2518219c.105T>C1.000
kasA2518220c.106C>T1.000
kasA2518234c.120G>A1.000
kasA2518247p.Ala45Thr1.000
kasA2518609p.Met165Ile1.000
folC2747061p.Arg180Ser1.000
folC2747062c.537T>G1.000
folC2747065c.534G>A1.000
folC2747074c.525C>G1.000
folC2747083c.516C>T1.000
folC2747086c.513T>C1.000
folC2747089c.510C>G1.000
folC2747104c.495G>A1.000
folC2747110c.489A>G1.000
folC2747113c.486G>C1.000
thyX3067649c.297G>A0.818
thyX3067652c.294A>G0.818
thyX3067661c.285G>C0.818
thyX3067685c.261T>C0.833
thyX3067688c.258C>G0.833
thyX3067694c.252C>G0.818
thyX3067721c.225A>G0.900
thyX3067724c.222C>T0.900
thyX3067727c.219T>G0.900
thyX3067742c.204T>C1.000
thyX3067762p.Arg62Ser1.000
thyX3067765p.Leu61Ile1.000
thyX3067781c.165G>C1.000
ald3086826p.Val3Ile1.000
ald3086831c.12T>C1.000
ald3086849c.30A>G1.000
ald3086885c.66C>A1.000
ald3086891c.72G>C1.000
ald3087346p.Ala176Gly0.900
ald3087368c.549A>C0.900
ald3087382p.Asn188Ser0.900
fbiA3640260c.-283TC>T1.000
fbiA3640262c.-281G>A1.000
fbiA3640268c.-275T>G1.000
fbiA3640270c.-273G>T1.000
fbiA3640302c.-241T>A1.000
fbiA3640303c.-240TA>T1.000
fbiA3640305c.-238A>G1.000
fbiA3640347c.-196A>G1.000
fbiA3640365c.-178C>G1.000
embC4240789c.927T>C0.917
embC4240819c.957A>G1.000
embC4240831c.969T>G1.000
embC4240859p.Leu333Met1.000
embC4240867c.1005T>G1.000
embC4240870c.1008T>C1.000
embC4240875p.Ser338Thr1.000
embC4240885c.1023T>C1.000
embC4240897c.1035C>G1.000
embC4240900c.1038A>G1.000
embC4240903c.1041C>T1.000
embC4240909c.1047G>C1.000
embC4240911p.Ala350Val1.000
embC4241614c.1752A>G0.900
embC4241617c.1755G>A0.900
embC4241626c.1764T>C0.900
embA4244747c.1515T>C0.833
embA4244764p.Val511Ala0.833
embA4244768p.Glu512Asp0.833
embA4244771c.1539G>C0.909
embA4244780c.1548C>G0.909
embA4244792c.1560G>C0.909
embA4245083c.1851A>G1.000
embA4245086c.1854C>G1.000
embA4245089c.1857G>T1.000
embA4245101c.1869G>C1.000
embA4245125c.1893G>C1.000
embA4245128c.1896G>C1.000
embA4245137c.1905T>C1.000
embA4245149c.1917C>G1.000
embA4245153p.Ile641Val1.000
embA4245182c.1950T>C1.000
embA4245200c.1968C>G1.000
embA4245202p.Thr657Ile1.000
embA4245206c.1974A>G1.000
embA4245215c.1983A>C1.000
embA4245224c.1992T>C1.000
embB4247677c.1164C>G1.000
embB4247683c.1170C>G1.000
embB4247684c.1171T>C1.000
embB4247689c.1176G>C1.000
embB4247725c.1212G>C0.933
embB4247728c.1215G>A0.933
embB4247746c.1233C>A0.923
embB4247755c.1242C>G0.917
embB4247779c.1266C>G0.909
embB4248097c.1584C>G0.800
embB4248098p.Ile529Phe0.800
embB4248106c.1593C>G0.800
embB4248130c.1617G>C0.917
embB4248133c.1620C>G0.917
embB4248142c.1629T>C0.833
embB4248143c.1630T>C0.833
embB4248149p.Thr546Ala0.833
embB4248157c.1644A>G0.833
embB4248220c.1707A>G0.909
embB4249321c.2808A>G0.909
embB4249323p.Ala937Asp0.909
embB4249339c.2826T>C0.909
embB4249342c.2829C>G0.909
embB4249345c.2832C>A0.909
embB4249351c.2838C>A0.900
embB4249369c.2856T>C0.900

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;