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: 5cc5582ae566c
Sample: 5cc5582ae566c

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Summary
ID: 5cc5582ae566c
Date: Sun Apr 28 08:40:07 2019
Strain: lineage1.1.1;lineage1.2.2
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
EthambutolRembB p.His312Arg (0.91)
Pyrazinamide
StreptomycinRrrs r.190g>a (1.00), rrs r.462c>t (0.96)
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage1.1.1Indo-OceanicEAI4;EAI5RD239
lineage1.2.2Indo-OceanicEAI1RD239

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6148c.909C>G0.909
gyrB6160c.921C>G0.923
gyrB6196c.957C>T0.929
gyrB6205c.966C>T0.917
gyrB6223c.984G>C0.889
gyrA7391c.90C>T0.909
gyrA7412c.111C>G0.909
gyrA7430c.129G>A1.000
gyrA7547c.246C>T0.900
gyrA7550c.249C>T0.909
gyrA7585p.Ser95Thr1.000
gyrA7601c.300C>G0.909
gyrA7607c.306C>G0.900
gyrA7760c.459C>T0.909
gyrA7763c.462T>G0.909
gyrA7766c.465C>T0.909
gyrA7793c.492G>A0.923
gyrA7796c.495G>A1.000
gyrA7799c.498A>G1.000
gyrA7832c.531G>T1.000
gyrA7835c.534A>G1.000
gyrA9267p.Asn656Gly1.000
gyrA9284c.1983T>C1.000
gyrA9296c.1995T>C1.000
gyrA9304p.Gly668Asp1.000
gyrA9308p.Asp669Glu1.000
gyrA9323c.2022C>G1.000
rpoB760196c.390C>G1.000
rpoB760223c.417T>C1.000
rpoB760235c.429T>C1.000
rpoB760298c.492G>C0.947
rpoB760310c.504G>C0.944
rpoB760313c.507G>C0.944
rpoB760328c.522G>C0.933
rpoB760331c.525G>C0.933
rpoB760337c.531C>G0.933
rpoB760340c.534G>T0.882
rpoB760361c.555T>C0.846
rpoB760376p.Asp190Glu0.882
rpoB760381p.Thr192Met0.882
rpoB760406c.600G>C1.000
rpoB760412c.606C>T1.000
rpoB760418c.612G>C1.000
rpoB760424c.618C>G1.000
rpoB760430c.624T>C1.000
rpoB760433c.627C>T1.000
rpoB760457c.651C>T1.000
rpoB760463c.657C>T1.000
rpoB760475c.669A>G1.000
rpoB760478c.672C>A1.000
rpoB760481c.675G>C1.000
rpoB760484c.678A>G0.917
rpoB760487c.681G>C0.917
rpoB760508c.702G>C0.917
rpoB760511c.705G>C0.909
rpoB760522p.Ser239Asn0.900
rpoB760532c.726T>C0.900
rpoB760533p.Val243His0.900
rpoB760547c.741G>C0.909
rpoB760655c.849A>G1.000
rpoB760661c.855A>C1.000
rpoB760670c.864G>C1.000
rpoB760671c.865C>T1.000
rpoB760679c.873A>G1.000
rpoB760683c.877T>C1.000
rpoB760845p.Thr347His1.000
rpoB760869p.Val355Thr1.000
rpoB760877c.1071G>T1.000
rpoB760886c.1080A>G1.000
rpoB760919c.1113C>G1.000
rpoB760925c.1119T>C1.000
rpoB760928c.1122G>C1.000
rpoB760946c.1140A>G1.000
rpoB760991c.1185G>C1.000
rpoB761006c.1200C>T1.000
rpoB761015c.1209G>C1.000
rpoB761027c.1221A>G1.000
rpoB761030c.1224G>T1.000
rpoB761036c.1230G>C1.000
rpoB761037c.1231T>C1.000
rpoB761057c.1251G>C1.000
rpoB761180c.1374A>C1.000
rpoB761189c.1383T>C1.000
rpoB761195c.1389G>T1.000
rpoB761207c.1401C>T1.000
rpoB761213c.1407G>C1.000
rpoB761234c.1428G>C1.000
rpoB761249c.1443A>G1.000
rpoB761255c.1449T>G1.000
rpoB761273c.1467T>C0.917
rpoB761318c.1512G>C0.900
rpoB761465c.1659G>T1.000
rpoB761510c.1704T>C1.000
rpoB761537c.1731C>T0.941
rpoB761570c.1764T>C0.900
rpoB761645c.1839C>G0.900
rpoB761873c.2067A>G1.000
rpoB761876c.2070C>G1.000
rpoB761879c.2073G>A1.000
rpoB761903c.2097T>G1.000
rpoB761990c.2184G>C1.000
rpoB762011c.2205G>C1.000
rpoB762029c.2223C>G1.000
rpoB762053c.2247T>C1.000
rpoB762056c.2250G>A1.000
rpoB762062c.2256T>C1.000
rpoB762065c.2259T>C1.000
rpoB762083c.2277T>C1.000
rpoB762086c.2280G>C1.000
rpoB762101c.2295C>G1.000
rpoB762114p.Ile770Val1.000
rpoB762131c.2325C>G1.000
rpoB762134c.2328C>G1.000
rpoB762143c.2337T>C1.000
rpoB762149c.2343G>C1.000
rpoB762167c.2361T>C1.000
rpoB762209c.2403C>T1.000
rpoB762212c.2406G>C1.000
rpoB762233c.2427G>C1.000
rpoB762254c.2448T>C1.000
rpoB762284c.2478G>C1.000
rpoB762293c.2487T>C1.000
rpoB762296c.2490G>A1.000
rpoB762449c.2643C>A1.000
rpoB762470c.2664G>C1.000
rpoB762491c.2685T>G1.000
rpoB762507p.Leu901Met0.867
rpoB762510p.Ala902Pro0.857
rpoB762533c.2727T>C0.923
rpoB762536c.2730T>C0.917
rpoB762537c.2731T>C0.917
rpoB762551c.2745C>T0.900
rpoB762575c.2769C>T0.818
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>T0.947
rpoB762995c.3189G>T1.000
rpoB763013c.3207C>G1.000
rpoB763094c.3288G>C0.818
rpoB763103c.3297G>C0.818
rpoB763115c.3309T>C0.818
rpoB763127c.3321G>T0.846
rpoB763139c.3333C>T0.846
rpoB763142c.3336C>G0.846
rpoB763166c.3360A>G0.867
rpoB763169c.3363A>G0.867
rpoB763193c.3387C>T0.867
rpoB763202c.3396A>G0.800
rpoC763468c.99G>C0.900
rpoC763486c.117T>C0.909
rpoC763492c.123G>C0.909
rpoC763546c.177A>G0.929
rpoC763570c.201G>C0.938
rpoC763594c.225C>T0.933
rpoC763603c.234C>T0.933
rpoC763618c.249C>T0.923
rpoC763624c.255C>G0.923
rpoC763633c.264T>C0.923
rpoC763660c.291T>G0.917
rpoC763666c.297G>C0.917
rpoC763669c.300C>G0.917
rpoC763930c.561G>A0.900
rpoC764152c.783C>T1.000
rpoC764159c.790C>T1.000
rpoC764338c.969G>A1.000
rpoC764353c.984G>C1.000
rpoC764387c.1018T>C1.000
rpoC764446c.1077T>C1.000
rpoC764449c.1080G>C1.000
rpoC764458c.1089G>C1.000
rpoC764461c.1092A>G1.000
rpoC764485c.1116G>C1.000
rpoC764497c.1128A>G1.000
rpoC764500c.1131C>G1.000
rpoC764521c.1152T>C1.000
rpoC764536c.1167G>C1.000
rpoC764539c.1170C>G1.000
rpoC764593c.1224C>T0.933
rpoC764605c.1236G>C0.812
rpoC764611c.1242G>T0.850
rpoC764632c.1263T>C0.850
rpoC764650c.1281G>T0.864
rpoC764713c.1344G>A0.895
rpoC764716c.1347G>C0.905
rpoC764746c.1377G>C0.964
rpoC764764c.1395T>C1.000
rpoC764803c.1434C>T1.000
rpoC764809c.1440C>T1.000
rpoC764812c.1443C>G1.000
rpoC764815c.1446A>G1.000
rpoC764824c.1455T>C1.000
rpoC764911c.1542A>G1.000
rpoC764932c.1563C>G1.000
rpoC765007c.1638T>G1.000
rpoC765008c.1639T>C1.000
rpoC765016c.1647C>G1.000
rpoC765019c.1650A>G1.000
rpoC765034c.1665T>C1.000
rpoC765089c.1720T>C0.800
rpoC765383p.Met672Leu1.000
rpoC765409c.2040T>C1.000
rpoC765412c.2043T>C1.000
rpoC765421c.2052C>G1.000
rpoC765451c.2082C>T1.000
rpoC765454c.2085C>G1.000
rpoC765478c.2109T>C1.000
rpoC765496c.2127C>T1.000
rpoC765499c.2130C>G1.000
rpoC765508c.2139C>G1.000
rpoC765517c.2148C>G1.000
rpoC765583c.2214G>T1.000
rpoC765688c.2319G>C1.000
rpoC765694c.2325G>C1.000
rpoC765961c.2592G>A0.900
rpoC765967c.2598C>T0.909
rpoC765979c.2610C>G0.909
rpoC765994c.2625A>T0.917
rpoC766009c.2640G>C1.000
rpoC766010c.2641T>A1.000
rpoC766027c.2658G>T1.000
rpoC766280p.Ser971Gly1.000
rpoC766291c.2922G>C1.000
rpoC766297c.2928G>C1.000
rpoC766309c.2940G>A1.000
rpoC766312c.2943T>G1.000
rpoC766315c.2946C>G1.000
rpoC766348c.2979A>G1.000
rpoC766351c.2982C>G1.000
rpoC766363c.2994G>C1.000
rpoC766366c.2997C>G1.000
rpoC766381c.3012C>T1.000
rpoC766384c.3015A>G1.000
rpoC766393c.3024C>G1.000
rpoC766462c.3093G>C1.000
rpoC766484p.Val1039Ile1.000
rpoC766504c.3135G>C1.000
rpoC766513c.3144C>T1.000
rpoC766528c.3159T>G1.000
rpoC766534c.3165C>G1.000
rpoC766549c.3180G>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.Ser1100Ala1.000
rpoC766672c.3303T>C1.000
rpoC766690c.3321G>T0.875
rpoC766714c.3345G>C0.941
rpoC766726c.3357T>C0.941
rpoC766738c.3369G>T0.941
rpoC766750c.3381C>G1.000
rpoC766753c.3384C>T0.917
rpoC766765c.3396A>C0.923
rpoC766774c.3405T>C0.917
rpoC766798c.3429C>G0.909
rpoC766801c.3432C>G0.917
rpoC766804c.3435A>G0.923
rpoC766843c.3474T>C0.929
rpoC766846c.3477C>T0.929
rpoC766864c.3495G>C0.938
rpoC766894c.3525T>C0.917
rpoC766895c.3526T>C0.917
rpoC766900c.3531T>C0.909
rpoC766903c.3534C>T0.909
rpoC766918c.3549C>T1.000
rpoC766948c.3579G>C1.000
rpoC766963c.3594T>C1.000
rpoC766972c.3603G>C1.000
rpoC766978c.3609C>A1.000
rpoC766996c.3627C>T1.000
rpoC767008c.3639G>C1.000
rpoC767033c.3664T>A1.000
rpoC767059c.3690T>G0.944
rpoC767062c.3693C>A0.941
rpoC767098c.3729T>C0.955
rpoC767119c.3750A>G0.955
rpoC767134c.3765C>A0.955
rpoC767167c.3798C>G1.000
rpoC767173c.3804C>G1.000
rpoC767180p.Ala1271Gln1.000
rpoC767191c.3822C>G1.000
rpoC767206c.3837C>G1.000
rpoC767209c.3840T>C1.000
rpoC767212c.3843G>C1.000
rpsL781649c.90T>C1.000
rpsL781655c.96T>C1.000
rpsL781658c.99A>G1.000
rpsL781715c.156T>C1.000
rpsL781718c.159C>T1.000
rpsL781721c.162C>T1.000
rpsL781728c.169T>C1.000
rpsL781742c.183C>T1.000
rpsL781754c.195G>C1.000
rpsL781763c.204C>G1.000
rpsL781778c.219C>T1.000
rpsL781808c.249C>T1.000
rpsL781829c.270G>C1.000
rpsL781832c.273T>C1.000
rpsL781865c.306G>C1.000
rpsL781868c.309T>C1.000
rpsL781871c.312G>T1.000
rpsL781880c.321C>G1.000
rplC800796c.-13A>C1.000
rplC800801c.-8A>G1.000
rplC801423c.615G>C1.000
rplC801427p.Met207Val1.000
rplC801438c.630T>C1.000
rplC801461653G>A1.000
embR1416330p.Val340Ile0.800
embR1416340c.1008G>C0.833
embR1416343c.1005C>G0.833
embR1416379c.969G>C0.917
embR1416388c.960T>C0.909
rrs1471918r.73a>t1.000
rrs1471922r.77gt>g1.000
rrs1471925r.80t>c1.000
rrs1471931r.86ga>g1.000
rrs1471934r.89a>g1.000
rrs1471938r.93t>a1.000
rrs1471970r.125g>a1.000
rrs1471984r.139t>a1.000
rrs1472019r.174g>a1.000
rrs1472030r.185g>a1.000
rrs1472032r.187g>a1.000
rrs1472034r.189t>c1.000
rrs1472042r.197t>c1.000
rrs1472053r.208agc>a1.000
rrs1472061r.216a>t1.000
rrs1472075r.230a>g1.000
rrs1472108r.263c>t1.000
rrs1472113r.268t>c1.000
rrs1472225r.380c>a0.939
rrs1472314r.469a>g0.955
rrs1472315r.470t>c0.955
rrs1472489r.644a>t1.000
rrs1472755r.910g>a1.000
rrs1472847r.1002g>c1.000
rrs1472848r.1003t>g1.000
rrs1472849r.1004c>g1.000
rrs1472850r.1005t>c1.000
rrs1472857r.1012a>g1.000
rrs1472858r.1013g>t1.000
rrs1472859r.1014g>c1.000
rrs1472860r.1015c>g1.000
rrs1472969r.1124a>g0.958
rrs1472970r.1125c>g0.957
rrs1472977r.1132g>c0.955
rrs1472978r.1133t>c0.957
rrs1473120r.1275c>ct0.892
rrs1473123r.1278a>t1.000
rrs1473288r.1443c>ct0.893
rrs1473289r.1444t>ta0.926
rrs1473290r.1445c>t0.962
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
rrl1474127r.470g>a1.000
rrl1474139r.482c>t1.000
rrl1474140r.483c>t1.000
rrl1474151r.494c>t1.000
rrl1474181r.524c>t1.000
rrl1474266r.609t>c0.963
rrl1474290r.633ttttcctctccggagg>t0.957
rrl1474306r.649a>c0.846
rrl1474308r.651g>t0.846
rrl1474310r.653t>g0.929
rrl1474362r.705a>g1.000
rrl1474447r.790g>a0.957
rrl1474639r.982g>a1.000
rrl1474716r.1059a>c0.958
rrl1474794r.1137c>a0.893
rrl1474812r.1155g>a0.929
rrl1474831r.1174a>g0.943
rrl1474957r.1300c>t0.929
rrl1474968r.1311g>a1.000
rrl1475006r.1349a>g1.000
rrl1475007r.1350c>t1.000
rrl1475013r.1356g>a1.000
rrl1475018r.1361g>t1.000
rrl1475019r.1362t>a1.000
rrl1475028r.1371g>a1.000
rrl1475061r.1404c>a1.000
rrl1475062r.1405a>t1.000
rrl1475202r.1545g>c1.000
rrl1475315r.1658a>c0.958
rrl1475355r.1698c>t0.974
rrl1475369r.1712g>c0.971
rrl1475402r.1745c>t0.971
rrl1475429r.1772g>a1.000
rrl1475479r.1822c>t1.000
rrl1475480r.1823a>t1.000
rrl1475505r.1848g>a1.000
rrl1475526r.1869c>a1.000
rrl1475573r.1916g>a1.000
rrl1475599r.1942a>g1.000
rrl1475604r.1947a>c1.000
rrl1475606r.1949t>c1.000
rrl1475619r.1962c>t1.000
rrl1475622r.1965g>t1.000
rrl1475635r.1978g>a1.000
rrl1475637r.1980t>g1.000
rrl1475659r.2002g>a1.000
rrl1475760r.2103c>t0.909
rrl1475763r.2106c>t0.913
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
rrl1476131r.2474c>t1.000
rrl1476214r.2557g>t0.944
rrl1476215r.2558c>t0.944
rrl1476297r.2640c>t1.000
rrl1476299r.2642c>t1.000
rrl1476580r.2923g>a0.969
rrl1476597r.2940g>a0.964
rrl1476608r.2951c>t0.963
rrl1476619r.2962c>t0.966
rrl1476628r.2971t>a0.966
rrl1476689r.3032a>t0.957
rrl1476692r.3035t>a0.955
rrl1476695r.3038t>a0.950
rrl1476710r.3053c>a0.900
rrl1476720r.3063g>t0.933
rrl1476723r.3066t>a0.923
rrl1476725r.3068c>t0.923
rrl1476726r.3069a>g0.923
rrl1476732r.3075t>c0.923
rrl1476759r.3102t>c0.909
fabG11673710p.Leu91Val1.000
fabG11673724c.285A>G1.000
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
inhA1674699c.498C>T1.000
inhA1674703c.502T>C1.000
inhA1674718c.517A>C1.000
inhA1674726c.525G>C1.000
inhA1674732c.531C>T1.000
inhA1674756c.555T>C1.000
inhA1674762c.561T>C1.000
inhA1674870c.669T>C1.000
inhA1674879c.678T>A1.000
inhA1674888c.687C>T1.000
inhA1674942c.741T>C1.000
inhA1674945p.Asp248Glu1.000
inhA1674957c.756G>A1.000
inhA1674963c.762G>C1.000
rpsA1833784c.243C>T1.000
rpsA1833802c.261A>G1.000
rpsA1833811c.270G>T1.000
rpsA1833817c.276C>G1.000
rpsA1833820c.279G>A1.000
rpsA1833856c.315A>G1.000
rpsA1833859c.318C>T1.000
rpsA1833874c.333T>C1.000
rpsA1833894p.Ala118Glu1.000
rpsA1833928c.387G>C1.000
rpsA1833979c.438T>C1.000
rpsA1833988c.447C>G1.000
rpsA1834051c.510G>A1.000
rpsA1834099c.558C>G1.000
rpsA1834102c.561T>C1.000
rpsA1834123c.582C>G1.000
rpsA1834297c.756C>G1.000
rpsA1834303c.762T>G1.000
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
rpsA1834498c.957C>T1.000
rpsA1834513c.972C>G1.000
rpsA1834528c.987T>C1.000
rpsA1834546c.1005T>C1.000
rpsA1834606c.1065C>T1.000
rpsA1834609c.1068T>C1.000
rpsA1834612c.1071G>T1.000
rpsA1834633c.1092A>G1.000
rpsA1834639c.1098T>C1.000
rpsA1834654c.1113G>A1.000
rpsA1834690c.1149T>C1.000
rpsA1834732c.1191T>C1.000
kasA2518219c.105T>C0.909
kasA2518220c.106C>T0.909
kasA2518234c.120G>A0.909
kasA2518247p.Ala45Thr0.929
kasA2518261p.Glu49Asp0.933
kasA2518268p.Thr52Ser0.933
kasA2518273c.159G>A0.929
kasA2518279c.165T>C0.929
kasA2518282c.168A>G0.929
kasA2518283p.Ala57Pro0.929
kasA2518287p.Val58Ala0.929
kasA2518300c.186T>A0.944
kasA2518312p.Asp66Glu1.000
kasA2518323p.Ser70Ile1.000
kasA2518336c.222A>G1.000
kasA2518339c.225C>G1.000
kasA2518492c.378C>T0.800
kasA2518504c.390T>C0.800
kasA2518506p.Ala131Glu0.800
kasA2518519c.405G>C0.800
kasA2518528c.414C>G0.800
kasA2518534c.420G>C0.818
kasA2518672c.558G>C0.900
kasA2518678c.564C>T0.900
kasA2518705c.591T>C0.900
kasA2518717c.603C>T0.909
kasA2518723c.609G>A0.900
kasA2518747c.633C>G1.000
kasA2518765c.651G>C0.900
kasA2518768c.654C>G0.900
kasA2518783c.669T>C0.909
kasA2518792c.678C>G0.818
kasA2518795c.681C>G0.818
folC2747104c.495G>A0.909
folC2747110c.489A>G0.909
folC2747113c.486G>C0.909
thyX3067373c.573G>C0.900
thyX3067391c.555C>G0.900
thyX3067394c.552C>G0.900
thyX3067418c.528G>C1.000
thyX3067433c.513G>C1.000
thyX3067439c.507T>C1.000
thyX3067445c.501G>A1.000
thyX3067742c.204T>C0.900
thyX3067762p.Arg62Ser0.917
thyX3067765p.Leu61Ile1.000
thyX3067781c.165G>C1.000
thyX3067789p.Lys53Arg1.000
thyX3067790c.156G>C1.000
thyX3067849p.Pro33Ser1.000
thyX3067850c.96T>G1.000
thyX3067853c.93G>C1.000
thyX3067874c.72G>C1.000
ald3086826p.Val3Ile0.900
ald3086831c.12T>C0.900
fbiA3640302c.-241T>A0.923
fbiA3640305c.-238A>G0.923
fbiA3640347c.-196A>G0.895
fbiA3640365c.-178C>G0.867
embC4240780c.918T>C0.818
embC4240783c.921G>C0.818
embC4240789c.927T>C0.833
embC4240819c.957A>G0.846
embC4240831c.969T>G0.833
embC4241050c.1188T>G1.000
embC4241053c.1191G>T1.000
embC4241059c.1197G>A1.000
embC4241119c.1257C>G1.000
embA4244695p.Lys488Thr1.000
embA4244699c.1467C>G1.000
embA4244702c.1470C>G1.000
embA4244708c.1476C>G1.000
embA4244747c.1515T>C1.000
embA4244764p.Val511Ala1.000
embA4245149c.1917C>G0.900
embA4245153p.Ile641Val0.900
embA4245845c.2613T>C0.900
embA4245848c.2616C>G0.900
embA4245851c.2619G>C0.900
embB4247434c.921C>G0.909
embB4247437c.924A>C0.909
embB4247491c.978G>C0.929
embB4247497c.984T>C0.929
embB4247945c.1432T>C1.000
embB4247948p.Val479Leu1.000
embB4248064c.1551G>C1.000
embB4248070c.1557T>C1.000
embB4248130c.1617G>C1.000
embB4248133c.1620C>G1.000
embB4248142c.1629T>C1.000
embB4248143c.1630T>C1.000
embB4248149p.Thr546Ala1.000
embB4248157c.1644A>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;