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: 5cc54feeb4bf5
Sample: 5cc54feeb4bf5

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Summary
ID: 5cc54feeb4bf5
Date: Sun Apr 28 08:06:20 2019
Strain: lineage4.3;lineage2.2;lineage4.1.1;lineage1.1.1
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
StreptomycinRrrs r.462c>t (0.95)
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage4.3Euro-American (LAM)mainly-LAMNone
lineage2.2East-Asian (Beijing)Beijing-RD207RD105;RD207
lineage4.1.1Euro-American (X-type)X1;X2;X3None
lineage1.1.1Indo-OceanicEAI4;EAI5RD239

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6256c.1017G>A0.900
gyrB6259c.1020C>T0.900
gyrB6265c.1026C>T0.900
gyrB6268c.1029C>G0.900
gyrB6280c.1041T>C0.923
gyrB6286c.1047T>C0.923
gyrB6289c.1050C>T0.923
gyrB6292c.1053G>C0.933
gyrB6307c.1068T>G0.938
gyrB6319c.1080G>C0.941
gyrB6346c.1107C>T0.933
gyrB6361c.1122G>A0.929
gyrB6362c.1123T>C0.929
gyrB6376c.1137G>A0.900
gyrB6379c.1140C>G0.900
gyrB6382c.1143A>G0.900
gyrB6388c.1149T>C0.900
gyrB6967c.1728T>C1.000
gyrB6973c.1734G>C1.000
gyrB6982c.1743A>C1.000
gyrB7007c.1768C>T1.000
gyrB7010c.1771C>T1.000
gyrB7023p.Leu595Gln1.000
gyrB7033c.1794G>C1.000
gyrA7427c.126G>C0.923
gyrA7442c.141G>C0.875
gyrA7451c.150C>G0.882
gyrA7457c.156T>C0.895
gyrA7475c.174A>G0.875
gyrA7480p.Phe60Tyr0.867
gyrA7484c.183T>C0.867
gyrA7514c.213C>G0.938
gyrA7523c.222C>A0.938
gyrA7532c.231T>C0.929
gyrA7541c.240C>G1.000
gyrA7547c.246C>T1.000
gyrA7763c.462T>C0.900
gyrA7784c.483A>G0.909
gyrA7793c.492G>C0.909
gyrA7796c.495G>C0.909
gyrA7799c.498A>G1.000
gyrA7814c.513C>G1.000
gyrA7823c.522G>C1.000
gyrA8234c.933T>C1.000
gyrA8237c.936A>G1.000
gyrA8247p.Ile316Val1.000
gyrA8264c.963T>C1.000
gyrA8267c.966G>C1.000
gyrA8270c.969G>T1.000
gyrA8276c.975G>A1.000
gyrA8283p.Ile328Leu1.000
gyrA8294c.993T>C1.000
gyrA8519c.1218A>C0.900
gyrA8520c.1219C>T0.900
gyrA8528c.1227G>C0.900
gyrA8531c.1230G>C0.917
gyrA8543c.1242C>G0.929
gyrA8546c.1245T>C0.929
gyrA8553c.1252C>A0.867
gyrA8561c.1260A>C0.882
gyrA8588c.1287G>A0.850
gyrA8603c.1302A>G0.842
gyrA8619c.1318T>C0.875
gyrA8624c.1323G>C0.875
gyrA8636c.1335A>C0.846
gyrA8642c.1341A>G0.846
gyrA8672c.1371A>G0.800
gyrA8678c.1377G>A0.800
gyrA8867c.1566A>G1.000
gyrA8870c.1569G>C1.000
gyrA8873c.1572A>C1.000
gyrA8891c.1590G>A1.000
gyrA8897c.1596T>C1.000
gyrA8903c.1602T>C1.000
gyrA8933c.1632G>C1.000
gyrA8946c.1645T>C1.000
gyrA9191c.1890G>C0.917
gyrA9200c.1899A>G0.909
gyrA9204p.Ser635Thr0.917
gyrA9218c.1917C>T0.917
gyrA9224c.1923C>T0.917
gyrA9230c.1929T>C1.000
gyrA9233c.1932C>G1.000
gyrA9239c.1938C>T1.000
gyrA9252p.Val651Ile1.000
gyrA9284c.1983T>C1.000
rpoB759606c.-201T>C0.950
rpoB759629c.-178T>C0.941
rpoB760112c.306T>C1.000
rpoB760118c.312T>G1.000
rpoB760121c.315T>C1.000
rpoB760130p.Asp108Glu1.000
rpoB760139c.333A>G1.000
rpoB760142c.336C>G1.000
rpoB760181c.375T>C1.000
rpoB760184c.378A>G1.000
rpoB760196c.390C>G1.000
rpoB760223c.417T>C1.000
rpoB760235c.429T>C1.000
rpoB760283c.477G>C1.000
rpoB760298c.492G>C1.000
rpoB760307c.501T>C1.000
rpoB760310c.504G>C1.000
rpoB760328c.522G>C1.000
rpoB760331c.525G>C1.000
rpoB760340c.534G>T1.000
rpoB760361c.555T>C1.000
rpoB760370c.564C>G1.000
rpoB760376p.Asp190Glu1.000
rpoB760380p.Thr192Leu1.000
rpoB760406c.600G>C1.000
rpoB760412c.606C>G0.955
rpoB760424c.618C>G1.000
rpoB760430c.624T>C1.000
rpoB760475c.669A>G1.000
rpoB760481c.675G>C1.000
rpoB760484c.678A>G1.000
rpoB760591p.Val262Ala0.818
rpoB760611c.805T>C0.857
rpoB760634c.828T>C0.846
rpoB760646c.840C>G0.846
rpoB760655c.849A>G0.846
rpoB760661c.855A>C0.833
rpoB760670c.864G>C0.857
rpoB760674c.868T>C0.857
rpoB760679c.873A>G0.867
rpoB760683c.877T>C0.867
rpoB760718c.912C>T1.000
rpoB760724c.918T>C1.000
rpoB760730c.924T>C1.000
rpoB760751c.945G>C0.900
rpoB760869p.Val355Ile0.933
rpoB760886c.1080A>G0.955
rpoB760925c.1119T>C1.000
rpoB760928c.1122G>C1.000
rpoB760931c.1125C>G1.000
rpoB760934c.1128C>T1.000
rpoB760946c.1140A>G1.000
rpoB760982c.1176G>C0.966
rpoB760985c.1179G>C0.964
rpoB760991c.1185G>C0.967
rpoB761006c.1200C>G0.967
rpoB761015c.1209G>C0.933
rpoB761021c.1215G>C0.935
rpoB761027c.1221A>G0.931
rpoB761036c.1230G>C0.897
rpoB761037c.1231T>C0.893
rpoB761057c.1251G>C0.931
rpoB761102c.1296A>G0.939
rpoB761129c.1323G>C0.957
rpoB761132c.1326G>T0.955
rpoB761133c.1327T>C0.955
rpoB761150c.1344A>C1.000
rpoB761153c.1347G>C1.000
rpoB761165c.1359G>C1.000
rpoB761180c.1374A>C0.944
rpoB761189c.1383T>C1.000
rpoB761195c.1389G>C1.000
rpoB761207c.1401C>T1.000
rpoB761213c.1407G>C1.000
rpoB761219c.1413G>C1.000
rpoB761249c.1443A>G1.000
rpoB761255c.1449T>G1.000
rpoB761261c.1455G>T1.000
rpoB761306c.1500C>G0.950
rpoB761312c.1506G>C0.950
rpoB761327c.1521A>G0.947
rpoB761330c.1524G>C0.933
rpoB761354c.1548C>T0.917
rpoB761360c.1554T>C0.909
rpoB761362p.Ser519Thr0.900
rpoB761375c.1569G>C0.900
rpoB761408c.1602G>C0.909
rpoB761414c.1608A>G0.909
rpoB761510c.1704T>C1.000
rpoB761537c.1731C>G1.000
rpoB761570c.1764T>C1.000
rpoB761573c.1767C>G1.000
rpoB761579c.1773G>C1.000
rpoB761588c.1782C>T1.000
rpoB761606c.1800C>G1.000
rpoB761612c.1806G>C1.000
rpoB761615c.1809A>C1.000
rpoB761636c.1830G>T0.944
rpoB761645c.1839C>G1.000
rpoB761648c.1842T>C1.000
rpoB761657c.1851C>G1.000
rpoB761675c.1869G>C1.000
rpoB761885c.2079T>C0.909
rpoB761906c.2100C>G0.900
rpoB761909c.2103T>C0.800
rpoB761912c.2106T>C0.800
rpoB761915p.Asp703Glu0.800
rpoB761916p.Asp704Asn0.800
rpoB761948c.2142G>C0.882
rpoB761954c.2148C>G0.882
rpoB762008c.2202C>T0.962
rpoB762014c.2208C>T0.962
rpoB762017c.2211A>G0.962
rpoB762053c.2247T>C1.000
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
rpoB762140c.2334G>C1.000
rpoB762143c.2337T>C1.000
rpoB762149c.2343G>C1.000
rpoB762167c.2361T>C1.000
rpoB762176c.2370T>C1.000
rpoB762185c.2379G>C1.000
rpoB762206c.2400C>G1.000
rpoB762233c.2427G>C1.000
rpoB762246c.2440C>T1.000
rpoB762254c.2448T>G1.000
rpoB762257c.2451C>G1.000
rpoB762266c.2460T>C1.000
rpoB762284c.2478G>C1.000
rpoB762293c.2487T>C1.000
rpoB762314c.2508C>T1.000
rpoB762317c.2511A>G1.000
rpoB762329c.2523G>C1.000
rpoB762338c.2532T>C1.000
rpoB762347c.2541T>C1.000
rpoB762362p.Glu852Asp1.000
rpoB762369c.2563T>C1.000
rpoB762434c.2628T>C1.000
rpoB762449c.2643C>A1.000
rpoB762857c.3051C>G0.917
rpoB762860c.3054G>C0.917
rpoB762863c.3057T>C0.923
rpoB762929c.3123G>C0.970
rpoB762989c.3183G>C0.971
rpoB762995c.3189G>T0.971
rpoB763013c.3207C>G0.971
rpoB763028c.3222T>C0.963
rpoB763031c.3225T>G1.000
rpoB763034c.3228C>G0.968
rpoB763040c.3234C>G0.971
rpoB763070c.3264T>C1.000
rpoB763085c.3279C>G1.000
rpoB763115c.3309T>C1.000
rpoB763136c.3330C>T0.966
rpoB763148c.3342G>C0.958
rpoB763158c.3352C>T0.944
rpoB763166c.3360A>G0.944
rpoB763190c.3384C>T0.941
rpoB763214c.3408T>C1.000
rpoB763226c.3420A>G1.000
rpoB763227c.3421C>T1.000
rpoB763238c.3432T>C1.000
rpoC763402c.33C>G0.941
rpoC763411c.42T>G0.944
rpoC763414c.45T>C0.889
rpoC763441c.72C>T1.000
rpoC763444c.75T>C1.000
rpoC763456c.87A>G1.000
rpoC763486c.117T>G1.000
rpoC763528c.159G>A0.966
rpoC763546c.177A>G0.964
rpoC763570c.201G>C0.955
rpoC763573c.204G>C0.955
rpoC763594c.225C>T0.966
rpoC763603c.234C>T0.962
rpoC763636c.267T>C0.960
rpoC763660c.291T>G1.000
rpoC763675c.306C>G1.000
rpoC763696c.327T>C1.000
rpoC763702c.333C>G1.000
rpoC763717c.348T>C1.000
rpoC763723c.354G>C1.000
rpoC763732c.363C>G1.000
rpoC763741c.372C>T1.000
rpoC763744c.375G>C1.000
rpoC763765c.396T>C1.000
rpoC763774c.405G>C1.000
rpoC763807c.438T>C1.000
rpoC763816c.447C>G1.000
rpoC763835p.Ala156Met1.000
rpoC763853p.Val162Ile1.000
rpoC763858c.489A>G1.000
rpoC763872p.Gly168Ala1.000
rpoC763876p.Glu169Asp1.000
rpoC763879c.510A>G1.000
rpoC763888c.519G>C1.000
rpoC763891c.522G>C1.000
rpoC763894c.525A>G1.000
rpoC763900c.531G>C1.000
rpoC763945c.576T>C0.929
rpoC763948c.579G>A0.923
rpoC763949c.580C>A0.923
rpoC763954c.585C>G0.923
rpoC763963c.594C>T0.929
rpoC764002c.633C>G0.900
rpoC764005c.636G>C0.900
rpoC764083c.714A>G1.000
rpoC764098c.729A>G1.000
rpoC764101c.732C>G1.000
rpoC764102p.Val245Ile1.000
rpoC764112p.Tyr248Phe1.000
rpoC764116c.747C>T1.000
rpoC764131c.762T>C1.000
rpoC764140c.771C>T1.000
rpoC764188c.819A>G1.000
rpoC764195p.Ser276Ile1.000
rpoC764203c.834G>C1.000
rpoC764206c.837T>C1.000
rpoC764215c.846A>G1.000
rpoC764236c.867G>A1.000
rpoC764248c.879C>G1.000
rpoC764257c.888G>C1.000
rpoC764266c.897T>C1.000
rpoC764269c.900G>C1.000
rpoC764272c.903G>C0.938
rpoC764278c.909A>G0.950
rpoC764338c.969G>A0.952
rpoC764353c.984G>C0.950
rpoC764365c.996C>T0.947
rpoC764405c.1036A>C1.000
rpoC764419c.1050C>G1.000
rpoC764428c.1059G>C1.000
rpoC764431c.1062G>C1.000
rpoC764434c.1065A>G1.000
rpoC764446c.1077T>C0.909
rpoC764449c.1080G>C0.909
rpoC764452c.1083T>C0.909
rpoC764458c.1089G>C0.909
rpoC764461c.1092A>G0.909
rpoC764489c.1120C>T0.955
rpoC764497c.1128A>G0.952
rpoC764510c.1141C>T0.947
rpoC764521c.1152T>C0.947
rpoC764527c.1158C>T0.947
rpoC764536c.1167G>C0.947
rpoC764539c.1170C>G0.947
rpoC764554c.1185C>T0.944
rpoC764560c.1191T>C1.000
rpoC764566c.1197C>G0.933
rpoC764575c.1206T>G0.867
rpoC764581c.1212T>C0.867
rpoC764593c.1224C>T0.938
rpoC764611c.1242G>T0.923
rpoC764650c.1281G>C0.929
rpoC764651c.1282T>A0.929
rpoC764752c.1383G>C1.000
rpoC764764c.1395T>C1.000
rpoC764809c.1440C>T1.000
rpoC764815c.1446A>G1.000
rpoC764827c.1458G>C0.969
rpoC764858c.1489T>C0.969
rpoC764872c.1503A>G0.962
rpoC764888c.1519T>C0.969
rpoC764911c.1542A>G0.941
rpoC764932c.1563C>A0.963
rpoC764935c.1566T>C0.964
rpoC764948c.1579T>C1.000
rpoC764968c.1599T>C0.966
rpoC764995c.1626C>G0.966
rpoC765019c.1650A>G0.967
rpoC765034c.1665T>C1.000
rpoC765040c.1671T>C1.000
rpoC765041c.1672T>C1.000
rpoC765047c.1678T>C1.000
rpoC765053c.1684T>A1.000
rpoC765073c.1704G>C1.000
rpoC765076c.1707A>G1.000
rpoC765079c.1710T>G1.000
rpoC765082c.1713G>C1.000
rpoC765089c.1720T>C1.000
rpoC765103c.1734G>T1.000
rpoC765346c.1977C>G0.900
rpoC765383p.Met672Leu0.933
rpoC765404p.Leu679Val1.000
rpoC765409c.2040T>C1.000
rpoC765421c.2052C>G1.000
rpoC765478c.2109T>C1.000
rpoC765499c.2130C>G1.000
rpoC765529c.2160C>T1.000
rpoC765541c.2172C>G1.000
rpoC765553c.2184C>T1.000
rpoC765556c.2187G>C1.000
rpoC765559c.2190G>C1.000
rpoC765580c.2211G>C1.000
rpoC765613p.His748Gln1.000
rpoC765625c.2256C>G1.000
rpoC765631p.Asp754Glu1.000
rpoC765700c.2331T>C1.000
rpoC765734c.2365T>C1.000
rpoC765739c.2370G>T1.000
rpoC765751c.2382C>G1.000
rpoC765753p.Asp795Ala1.000
rpoC765772c.2403C>G1.000
rpoC765784c.2415C>G1.000
rpoC765787c.2418C>T1.000
rpoC765793c.2424C>G1.000
rpoC765796c.2427C>T1.000
rpoC765811c.2442T>C1.000
rpoC765814c.2445A>G1.000
rpoC765826c.2457T>C1.000
rpoC765835c.2466C>T1.000
rpoC765850c.2481G>C1.000
rpoC765883c.2514C>G1.000
rpoC765886c.2517C>G1.000
rpoC765892c.2523T>C1.000
rpoC765937c.2568T>C1.000
rpoC765967c.2598C>T1.000
rpoC765982c.2613C>G1.000
rpoC765994c.2625A>T1.000
rpoC766010c.2641T>A1.000
rpoC766021c.2652G>C1.000
rpoC766027c.2658G>C1.000
rpoC766030c.2661C>G1.000
rpoC766036c.2667C>T1.000
rpoC766043p.Gln892Glu1.000
rpoC766054c.2685C>G1.000
rpoC766082p.Ala905Gln0.933
rpoC766096c.2727G>C1.000
rpoC766123c.2754C>T1.000
rpoC766345c.2976T>C0.900
rpoC766348c.2979A>G0.900
rpoC766357c.2988C>T0.917
rpoC766363c.2994G>C0.917
rpoC766381c.3012C>T1.000
rpoC766384c.3015A>G1.000
rpoC766408c.3039C>G1.000
rpoC766411c.3042C>G1.000
rpoC766426c.3057C>T1.000
rpoC766447c.3078T>C1.000
rpoC766462c.3093G>C1.000
rpoC766468c.3099G>A1.000
rpoC766486c.3117A>C1.000
rpoC766492c.3123T>C1.000
rpoC766522c.3153C>G1.000
rpoC766528c.3159T>C1.000
rpoC766531c.3162G>C1.000
rpoC766540p.Asp1057Glu1.000
rpoC766549c.3180G>C1.000
rpoC766573c.3204T>C1.000
rpoC766607p.Ile1080Leu1.000
rpoC766630c.3261G>C1.000
rpoC766657c.3288A>G1.000
rpoC766660c.3291G>C1.000
rpoC766672c.3303T>C1.000
rpoC766673p.Gly1102Asn1.000
rpoC766726c.3357T>C1.000
rpoC766738c.3369G>C1.000
rpoC766765c.3396A>C1.000
rpoC766774c.3405T>C1.000
rpoC766801c.3432C>G1.000
rpoC766804c.3435A>G1.000
rpoC766861c.3492G>T1.000
rpoC766864c.3495G>C1.000
rpoC766876c.3507C>T1.000
rpoC766882c.3513C>T1.000
rpoC766894c.3525T>C1.000
rpoC766900c.3531T>C1.000
rpoC766933c.3564A>G1.000
rpoC766945c.3576A>G1.000
rpoC766963c.3594T>C1.000
rpoC766972c.3603G>C1.000
rpoC766996c.3627C>T1.000
rpoC767009c.3640T>A1.000
rpoC767014c.3645G>C1.000
rpoC767033c.3664T>A1.000
rpoC767059c.3690T>G1.000
rpoC767062c.3693C>A1.000
rpoC767098c.3729T>C1.000
rpoC767119c.3750A>G1.000
rpoC767134c.3765C>A1.000
rpoC767158c.3789T>G1.000
rpoC767180p.Ala1271Gln1.000
rpoC767191c.3822C>G1.000
rpoC767206c.3837C>G1.000
rpoC767209c.3840T>C1.000
rpoC767212c.3843G>C1.000
rpoC767221c.3852C>G1.000
rpoC767230c.3861G>C1.000
rpoC767233c.3864T>C1.000
rpsL781571c.12C>T1.000
rpsL781595c.36T>C1.000
rpsL781605p.Ile16Val1.000
rpsL781608p.Ser17Ala1.000
rpsL781628c.69T>C0.947
rpsL781631c.72G>C0.955
rpsL781649c.90T>C0.966
rpsL781655c.96T>C0.966
rpsL781700c.141G>C0.968
rpsL781703c.144G>T0.938
rpsL781715c.156T>C0.970
rpsL781728c.169T>C0.970
rpsL781736c.177T>C1.000
rpsL781742c.183C>T0.969
rpsL781748c.189C>G0.969
rpsL781754c.195G>C0.969
rpsL781760c.201T>C0.971
rpsL781772c.213C>A1.000
rpsL781808c.249C>T0.969
rpsL781811c.252C>T0.970
rpsL781832c.273T>C0.969
rpsL781838c.279G>C1.000
rpsL781841c.282C>G1.000
rpsL781865c.306G>C0.950
rpsL781868c.309T>C0.947
rpsL781871c.312G>C0.950
rpsL781877c.318T>C0.958
rpsL781892c.333A>G0.958
rpsL781898c.339A>T0.958
rpsL781916c.357T>C0.958
rpsL781929p.Gly124Ser0.952
rplC800794c.-15A>G0.933
rplC800796c.-13A>G0.938
rplC800814c.6A>G0.905
rplC800817c.9A>T0.905
rplC800844c.36T>C0.889
rplC800865c.57A>G0.818
rplC800867p.Ser20Asn0.818
rplC800874c.66A>G0.818
rplC800875p.Val23Ile0.818
rplC800880c.72A>G0.818
rplC800889c.81C>G0.818
rplC800892c.84G>C0.818
rplC800907c.99C>G0.818
rplC801168c.360C>G1.000
rplC801171c.363A>G1.000
rplC801174c.366T>C1.000
rplC801195c.387G>C1.000
rplC801207c.399C>T1.000
rplC801246c.438C>T1.000
rplC801300c.492C>G1.000
rplC801309c.501C>G1.000
rplC801312c.504G>C1.000
rplC801321c.513C>T1.000
rplC801324c.516T>C1.000
rplC801339c.531T>C1.000
rplC801341p.Leu178Gln1.000
rplC801348c.540T>G1.000
rplC801357c.549T>C1.000
rplC801367p.Ala187Thr1.000
rplC801402c.594T>C1.000
rplC801405c.597T>C1.000
rplC801423c.615G>C1.000
rplC801426c.618C>G1.000
rplC801427p.Met207Val1.000
rrs1471923r.78t>c0.941
rrs1471925r.80t>c0.941
rrs1471932r.87a>g0.950
rrs1471934r.89a>g0.950
rrs1471969r.124t>c0.966
rrs1471970r.125g>a0.968
rrs1472044r.199g>t1.000
rrs1472045r.200t>a1.000
rrs1472053r.208agc>a1.000
rrs1472061r.216a>t1.000
rrs1472075r.230a>g1.000
rrs1472108r.263c>t0.971
rrs1472969r.1124a>g1.000
rrs1472970r.1125c>g1.000
rrs1472977r.1132g>c1.000
rrs1472978r.1133t>c1.000
rrs1473105r.1260g>a0.975
rrs1473120r.1275c>ct0.892
rrs1473123r.1278a>t0.944
rrs1473145r.1300c>t0.977
rrs1473166r.1321g>a0.978
rrs1473290r.1445c>t0.980
rrl1473651c.-7GT>G1.000
rrl1473658r.1t>a1.000
rrl1473659r.2t>a1.000
rrl1473668r.11c>t1.000
rrl1473756r.99g>a0.971
rrl1473758r.101g>t0.969
rrl1473806r.149c>t0.967
rrl1473877r.220g>a1.000
rrl1473898r.241c>t1.000
rrl1473943r.286g>t0.962
rrl1473945r.288t>a1.000
rrl1473946r.289a>t1.000
rrl1473986r.329t>c1.000
rrl1473987r.330g>a1.000
rrl1473995r.338g>t1.000
rrl1474001r.344c>t1.000
rrl1474009r.352a>g1.000
rrl1474012r.355c>t1.000
rrl1474093r.436g>t1.000
rrl1474099r.442g>a1.000
rrl1474103r.446a>t1.000
rrl1474140r.483c>t0.962
rrl1474151r.494c>t0.966
rrl1474181r.524c>t0.971
rrl1474249r.592g>t1.000
rrl1474291r.634tttcctctccggagga>t1.000
rrl1474308r.651g>t0.929
rrl1474310r.653t>g0.966
rrl1474356r.699t>c0.973
rrl1474362r.705a>g0.974
rrl1474376r.719t>c0.974
rrl1474427r.770a>c0.909
rrl1474429r.772g>c0.909
rrl1474432r.775c>g1.000
rrl1474639r.982g>a1.000
rrl1474794r.1137c>t1.000
rrl1474812r.1155g>a1.000
rrl1474823r.1166c>t1.000
rrl1474831r.1174a>g0.960
rrl1474904r.1247g>a0.912
rrl1474956r.1299c>t0.882
rrl1474960r.1303c>g0.875
rrl1474963r.1306g>t0.875
rrl1474964r.1307t>a0.875
rrl1474965r.1308g>c0.844
rrl1474970r.1313g>a0.889
rrl1475006r.1349a>t0.886
rrl1475061r.1404c>t0.935
rrl1475088r.1431a>t0.951
rrl1475199r.1542g>a0.974
rrl1475206r.1549c>t0.917
rrl1475209r.1552g>c0.957
rrl1475213r.1556c>t0.957
rrl1475249r.1592t>c0.973
rrl1475252r.1595c>t0.971
rrl1475266r.1609t>c0.939
rrl1475267r.1610g>a0.969
rrl1475275r.1618c>t0.969
rrl1475276r.1619t>c0.968
rrl1475291r.1634a>c1.000
rrl1475313r.1656g>a1.000
rrl1475315r.1658a>t1.000
rrl1475355r.1698c>t1.000
rrl1475369r.1712g>t1.000
rrl1475402r.1745c>t1.000
rrl1475419r.1762c>t1.000
rrl1475436r.1779c>t1.000
rrl1475483r.1826c>t0.973
rrl1475505r.1848g>a0.971
rrl1475526r.1869c>a0.974
rrl1475599r.1942a>g0.938
rrl1475608r.1951t>c0.941
rrl1475642r.1985t>c0.935
rrl1475657r.2000a>g0.933
rrl1475659r.2002g>t0.935
rrl1475758r.2101ac>a1.000
rrl1475763r.2106c>t1.000
rrl1475765r.2108ag>a1.000
rrl1475881r.2224t>c1.000
rrl1475988r.2331a>g1.000
rrl1476086r.2429g>a1.000
rrl1476089r.2432t>c1.000
rrl1476095r.2438c>g1.000
rrl1476106r.2449a>t1.000
rrl1476115r.2458t>c1.000
rrl1476117r.2460g>c1.000
rrl1476224r.2567a>g1.000
rrl1476281r.2624t>c1.000
rrl1476583r.2926g>a1.000
rrl1476584r.2927c>t1.000
rrl1476594r.2937c>t1.000
rrl1476597r.2940g>a1.000
rrl1476603r.2946g>a1.000
rrl1476608r.2951c>g1.000
rrl1476628r.2971t>a1.000
rrl1476689r.3032a>t1.000
rrl1476690r.3033c>t1.000
rrl1476693r.3036g>a1.000
rrl1476695r.3038t>a1.000
rrl1476716r.3059a>c1.000
rrl1476726r.3069a>g1.000
rrl1476732r.3075t>c1.000
rrl1476750r.3093t>c1.000
rrl1476755r.3098g>a1.000
fabG11673710p.Leu91Ile1.000
fabG11673716p.Ala93Lys1.000
fabG11673733p.Met98Ile1.000
fabG11673955c.516G>C1.000
fabG11673961c.522A>C1.000
fabG11673985c.546C>A1.000
fabG11674006p.Asp189Glu1.000
fabG11674018c.579G>C0.909
fabG11674021c.582G>C0.900
fabG11674024c.585T>C0.900
fabG11674033c.594T>C0.900
fabG11674037p.Gln200Ala0.900
fabG11674042c.603G>C0.900
fabG11674049p.Gln204Asp0.909
fabG11674054c.615T>C0.917
fabG11674060c.621A>G0.923
fabG11674063c.624G>C0.929
fabG11674079p.Pro214Ala0.947
fabG11674090c.651C>T0.950
fabG11674114c.675T>A1.000
fabG11674123c.684T>C1.000
fabG11674126c.687G>C1.000
fabG11674132c.693T>C1.000
fabG11674136p.Ser233Ala1.000
fabG11674141c.702T>C1.000
inhA1674480c.279T>C1.000
inhA1674486c.285T>C1.000
inhA1674504c.303C>G1.000
inhA1674507c.306G>C1.000
inhA1674672c.471C>G1.000
inhA1674703c.502T>C1.000
inhA1674708c.507G>A1.000
rpsA1833568c.27G>C1.000
rpsA1833589c.48A>T1.000
rpsA1833595c.54T>C1.000
rpsA1833661c.120A>G1.000
rpsA1833667c.126C>G1.000
rpsA1833721c.180A>G1.000
rpsA1833724c.183C>G1.000
rpsA1833727c.186G>C1.000
rpsA1833742c.201A>G1.000
rpsA1833745c.204G>C1.000
rpsA1833748c.207C>G1.000
rpsA1833787c.246C>G1.000
rpsA1833790c.249T>C1.000
rpsA1833802c.261A>G1.000
rpsA1833811c.270G>T1.000
rpsA1833838c.297G>C0.944
rpsA1833841c.300C>G0.944
rpsA1833847c.306C>G0.909
rpsA1833856c.315A>G0.955
rpsA1833874c.333T>C0.952
rpsA1833928c.387G>C1.000
rpsA1833940c.399C>G1.000
rpsA1833971c.430C>T1.000
rpsA1833979c.438T>C1.000
rpsA1834000c.459G>C1.000
rpsA1834021c.480C>T1.000
rpsA1834030c.489C>G1.000
rpsA1834099c.558C>G1.000
rpsA1834177c.636A>C0.900
rpsA1834189c.648G>C0.923
rpsA1834195c.654G>C0.923
rpsA1834210c.669C>T0.929
rpsA1834222c.681T>C0.933
rpsA1834231c.690T>C0.933
rpsA1834234c.693G>C0.933
rpsA1834249c.708T>C0.938
rpsA1834261c.720A>G1.000
rpsA1834262c.721T>A1.000
rpsA1834303c.762T>C0.957
rpsA1834306c.765T>C0.957
rpsA1834333c.792C>T0.944
rpsA1834348c.807T>C0.889
rpsA1834366c.825A>G0.846
rpsA1834396c.855G>C0.818
rpsA1834435c.894G>C1.000
rpsA1834451c.910T>C1.000
rpsA1834465c.924T>C1.000
rpsA1834468c.927A>G1.000
rpsA1834489c.948T>C1.000
rpsA1834528c.987T>C1.000
rpsA1834540c.999G>C1.000
rpsA1834546c.1005T>C1.000
rpsA1834555c.1014T>G1.000
rpsA1834609c.1068T>C1.000
rpsA1834618c.1077G>C1.000
rpsA1834633c.1092A>G1.000
rpsA1834639c.1098T>C1.000
rpsA1834654p.Glu371Asp1.000
rpsA1834690c.1149T>C1.000
rpsA1834732c.1191T>C1.000
rpsA1834733p.Ala398Ser1.000
rpsA1834738c.1197A>G1.000
rpsA1834753c.1212T>C1.000
rpsA1834765p.Glu408Asp1.000
rpsA1834775p.Ala412Thr1.000
rpsA1834780c.1239A>G1.000
rpsA1834786c.1245A>G1.000
rpsA1834789c.1248T>C1.000
rpsA1834792c.1251G>C1.000
katG2155661p.Val151Ile1.000
katG2155680c.432C>G1.000
katG2155691c.421A>G1.000
katG2155695c.417G>C1.000
katG2155704c.408G>C1.000
katG2155716c.396A>C0.929
katG2155722c.390C>G0.917
katG2155728c.384C>G0.909
kasA2518162c.48G>A0.923
kasA2518174c.60A>G0.882
kasA2518190p.Ser26Ala0.941
kasA2518199p.Ile29Val0.941
kasA2518220c.106C>T1.000
kasA2518234c.120G>A1.000
kasA2518248p.Ala45Val1.000
kasA2518261p.Glu49Asp1.000
kasA2518263p.Phe50Tyr1.000
kasA2518265p.Val51Ile1.000
kasA2518483c.369C>G1.000
kasA2518504c.390T>C1.000
kasA2518506p.Ala131Glu1.000
kasA2518519c.405G>C1.000
kasA2518528c.414C>G1.000
kasA2518540c.426T>C1.000
kasA2518561c.447T>C1.000
kasA2518567c.453G>C1.000
kasA2518570c.456G>C1.000
kasA2518574p.Ile154Val1.000
kasA2518579c.465T>C1.000
kasA2518588c.474T>C1.000
kasA2518591c.477G>C0.909
kasA2518768c.654C>T1.000
kasA2518777c.663C>T1.000
kasA2518783c.669T>C1.000
kasA2518789c.675G>C1.000
kasA2518792c.678C>A1.000
kasA2518795c.681C>G1.000
kasA2518825c.711T>C1.000
kasA2518864c.750G>C0.947
kasA2518879c.765A>G0.944
kasA2518885c.771T>C0.944
kasA2518898c.784T>C0.933
kasA2518906c.792A>G0.923
kasA2518910p.Leu266Met0.909
kasA2518921c.807T>C0.900
kasA2519107c.993T>C1.000
kasA2519108p.Asp332Gln1.000
kasA2519116c.1002C>G1.000
kasA2519122c.1008G>C1.000
kasA2519158c.1044C>T0.900
kasA2519167c.1053T>G0.900
kasA2519173c.1059C>G0.900
thyX3067439c.507T>C1.000
thyX3067442c.504G>A1.000
thyX3067457c.489G>C1.000
thyX3067465p.Ile161Val1.000
thyX3067475c.471T>C1.000
thyX3067652c.294A>G0.900
thyX3067661c.285G>C1.000
thyX3067685c.261T>G1.000
thyX3067693p.Ile85Leu1.000
thyX3067694c.252C>G1.000
thyX3067718c.228G>C1.000
thyX3067721c.225A>G1.000
thyX3067727c.219T>G1.000
thyX3067736c.210G>A1.000
thyX3067765p.Leu61Ile1.000
thyX3067772c.174G>C1.000
thyX3067781c.165G>C1.000
thyX3067793c.153A>G1.000
thyX3067799c.147C>T1.000
thyX3067802c.144G>C1.000
thyX3067814c.132A>G1.000
thyX3067850c.96T>G1.000
thyX3067869p.Thr26Ser1.000
thyX3067874c.72G>C1.000
thyX3067898p.Asp16Glu1.000
thyX3067935p.Thr4Ile1.000
thyA3074181c.291T>C1.000
thyA3074187c.285A>G1.000
thyA3074205p.Glu89Asp1.000
thyA3074214c.258A>G1.000
thyA3074241c.231G>C1.000
thyA3074244c.228T>C1.000
thyA3074254p.His73Arg1.000
thyA3074262c.210A>G1.000
thyA3074267p.Ile69Val1.000
thyA3074268c.204A>G1.000
fbiA3640347c.-196A>G1.000
fbiA3640349c.-194A>G1.000
fbiA3640350c.-193C>T1.000
fbiA3640365c.-178C>G1.000
embC4240780c.918T>C1.000
embC4240783c.921G>C1.000
embC4240789c.927T>C1.000
embC4240819c.957A>G1.000
embC4240828c.966G>A1.000
embC4240831c.969T>G1.000
embC4241017c.1155T>C1.000
embC4241023c.1161T>G0.900
embC4241032c.1170G>C1.000
embC4241038c.1176G>C1.000
embC4241047c.1185C>G1.000
embC4241050c.1188T>G1.000
embC4241053c.1191G>C0.933
embC4241089c.1227C>G1.000
embC4241095c.1233C>T1.000
embC4241107c.1245G>C1.000
embC4241140c.1278A>G1.000
embC4241146c.1284C>G1.000
embC4241158c.1296T>C1.000
embC4241449c.1587C>G1.000
embC4241453p.Ile531Val1.000
embC4241479c.1617C>G1.000
embC4241480c.1618T>C1.000
embC4241488c.1626G>C1.000
embA4245053c.1821G>C1.000
embA4245060c.1828T>C1.000
embA4245083c.1851A>C1.000
embA4245089c.1857G>C1.000
embA4245101c.1869G>C1.000
embA4245137c.1905T>C1.000
embA4245146c.1914G>A1.000
embA4245149c.1917C>G1.000
embA4245153p.Ile641Val1.000
embA4245182c.1950T>C1.000
embA4245189c.1957C>T1.000
embA4245198p.Leu656Ile1.000
embA4245207c.1975T>C1.000
embA4245215c.1983A>C1.000
embA4245222p.Tyr664Gln1.000
embA4245242c.2010C>T1.000
embB4247464c.951C>G1.000
embB4247470c.957T>C1.000
embB4247491c.978G>C1.000
embB4247497c.984T>C1.000
embB4247512c.999T>C1.000
embB4247539c.1026T>C1.000
embB4247554c.1041T>C1.000
embB4247566c.1053C>A0.917
embB4247572c.1059A>G1.000
embB4247899p.Met462Ile0.900
embB4247905c.1392G>C0.900
embB4247914c.1401G>C0.900
embB4247932c.1419C>G0.917
embB4247951p.Ser480Ala0.909
embB4247974c.1461C>G1.000
embB4248007c.1494C>G1.000
embB4248011p.Ser500Arg1.000
embB4248014p.Thr501Ala1.000
embB4248035p.Val508Ile1.000
embB4248040c.1527C>G1.000
embB4248041p.Ala510Thr1.000
embB4248044p.Lys511Ala1.000
embB4248070c.1557T>C1.000
embB4248085c.1572T>C1.000
embB4248097c.1584C>G1.000
embB4248130c.1617G>C1.000
embB4248142c.1629T>C1.000
embB4248143c.1630T>C1.000
embB4248157c.1644A>G1.000
embB4248172c.1659G>C0.958
embB4248199c.1686A>G1.000
embB4248200p.Ile563Val1.000
embB4248205c.1692C>G1.000
embB4248206p.Ser565Gly1.000
embB4248220c.1707A>C1.000
embB4248304c.1791G>C1.000
embB4248319c.1806A>G1.000
embB4248343c.1830G>C1.000
embB4248350c.1837T>C1.000
embB4248373c.1860C>G1.000
embB4248457c.1944T>C1.000
embB4248472c.1959T>C1.000
embB4248475c.1962G>C1.000
embB4249369c.2856T>C0.917
embB4249375c.2862G>C0.917
embB4249381c.2868A>G0.923
embB4249417c.2904A>G0.929
embB4249441c.2928A>G0.900
embB4249444c.2931T>C0.900
embB4249447c.2934G>C0.900
embB4249469p.Leu986Met0.933
ethA4327396c.78A>T0.933
ethA4327399p.Asp25Glu0.933
ethA4327423c.51G>C0.933
ethA4327435c.39T>G0.933
ethA4327438c.36A>G0.933
ethA4327452p.Val8Leu0.917
ethA4327453c.21A>G0.917
ethA4327459c.15G>A0.917
ethA4327468c.6G>A0.917

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;