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: 5cc54f9840bbb
Sample: 5cc54f9840bbb

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Summary
ID: 5cc54f9840bbb
Date: Sun Apr 28 08:01:56 2019
Strain: lineage4.3;lineage2.2
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
StreptomycinRrrs r.462c>t (1.00)
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage4.3Euro-American (LAM)mainly-LAMNone
lineage2.2East-Asian (Beijing)Beijing-RD207RD105;RD207

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6256c.1017G>A1.000
gyrB6265c.1026C>T1.000
gyrB6268c.1029C>G1.000
gyrB6280c.1041T>C1.000
gyrB6292c.1053G>C1.000
gyrB6304c.1065C>G1.000
gyrB6307c.1068T>G1.000
gyrB6319c.1080G>C1.000
gyrB6751c.1512G>C1.000
gyrB6760c.1521G>C1.000
gyrB6763c.1524G>C1.000
gyrB6775c.1536G>C1.000
gyrB6793c.1554T>C1.000
gyrB6797p.Gly520Thr1.000
gyrB6811c.1572C>T1.000
gyrB6841c.1602T>C1.000
gyrB6844c.1605T>C1.000
gyrB7007c.1768C>T1.000
gyrB7010c.1771C>T1.000
gyrB7141c.1902T>C1.000
gyrB7165c.1926C>G1.000
gyrB7178c.1939T>C1.000
gyrB7186c.1947C>G1.000
gyrB7216c.1977G>C1.000
gyrB7228c.1989C>T1.000
gyrB7234c.1995C>T1.000
gyrA7391c.90C>T1.000
gyrA7394c.93T>C1.000
gyrA7406c.105G>C1.000
gyrA7427c.126G>C1.000
gyrA7442c.141G>C1.000
gyrA7451c.150C>G1.000
gyrA7457c.156T>C1.000
gyrA7475c.174A>G1.000
gyrA7480p.Phe60Tyr1.000
gyrA7484c.183T>C1.000
gyrA7514c.213C>G1.000
gyrA7523c.222C>A0.952
gyrA7532c.231T>C1.000
gyrA7541c.240C>G1.000
gyrA7547c.246C>T1.000
gyrA7562c.261C>T1.000
gyrA7571c.270G>C1.000
gyrA7585p.Ser95Thr1.000
gyrA7710c.409T>C1.000
gyrA7721c.420G>A1.000
gyrA7725c.424C>T1.000
gyrA7728c.427A>C1.000
gyrA7739c.438C>T1.000
gyrA7763c.462T>C1.000
gyrA7784c.483A>G1.000
gyrA7793c.492G>C1.000
gyrA7796c.495G>C1.000
gyrA7799c.498A>G1.000
gyrA7814c.513C>G1.000
gyrA7823c.522G>C1.000
gyrA7832c.531G>T1.000
gyrA7835c.534A>G1.000
gyrA7853c.552C>G1.000
gyrA7859c.558A>G1.000
gyrA7865c.564T>C1.000
gyrA7886c.585T>C1.000
gyrA8121c.820T>C1.000
gyrA8129c.828T>C1.000
gyrA8135c.834C>G1.000
gyrA8156c.855T>C1.000
gyrA8168c.867A>G1.000
gyrA8177c.876A>C1.000
gyrA8189c.888G>C1.000
gyrA8198c.897T>C1.000
gyrA8207c.906T>C1.000
gyrA8219c.918T>C1.000
gyrA8225c.924T>C1.000
gyrA8891c.1590G>A1.000
gyrA8897c.1596T>C1.000
gyrA8903c.1602T>C1.000
gyrA8933c.1632G>C1.000
gyrA8946c.1645T>C1.000
gyrA9204p.Ser635Thr1.000
gyrA9218c.1917C>T1.000
gyrA9224c.1923C>T1.000
gyrA9230c.1929T>C1.000
gyrA9233c.1932C>G1.000
gyrA9239c.1938C>T0.933
gyrA9252p.Val651Ile0.933
gyrA9284c.1983T>C0.941
gyrA9291c.1990C>T0.938
gyrA9296c.1995T>C0.929
gyrA9299c.1998G>C0.909
gyrA9304p.Gly668Glu1.000
gyrA9308p.Asp669Glu0.900
gyrA9323c.2022C>G0.909
gyrA9335c.2034G>C0.909
rpoB759606c.-201T>C1.000
rpoB759629c.-178T>C1.000
rpoB760091c.285G>C1.000
rpoB760101c.295T>C1.000
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>G1.000
rpoB760424c.618C>G1.000
rpoB760430c.624T>C1.000
rpoB760475c.669A>G1.000
rpoB760481c.675G>C1.000
rpoB760484c.678A>G1.000
rpoB760591p.Val262Ala1.000
rpoB760611c.805T>C1.000
rpoB760646c.840C>G1.000
rpoB760655c.849A>G1.000
rpoB760661c.855A>C1.000
rpoB760670c.864G>C1.000
rpoB760925c.1119T>C1.000
rpoB760928c.1122G>C1.000
rpoB760934c.1128C>T1.000
rpoB760946c.1140A>G1.000
rpoB760949c.1143C>T1.000
rpoB760982c.1176G>C1.000
rpoB760985c.1179G>C1.000
rpoB760991c.1185G>C1.000
rpoB761006c.1200C>G1.000
rpoB761015c.1209G>C1.000
rpoB761021c.1215G>C1.000
rpoB761027c.1221A>G1.000
rpoB761036c.1230G>C1.000
rpoB761037c.1231T>C1.000
rpoB761057c.1251G>C1.000
rpoB761102c.1296A>G1.000
rpoB761129c.1323G>C1.000
rpoB761132c.1326G>T0.933
rpoB761133c.1327T>C1.000
rpoB761150c.1344A>C1.000
rpoB761153c.1347G>C1.000
rpoB761165c.1359G>C1.000
rpoB761180c.1374A>C1.000
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>G1.000
rpoB761312c.1506G>C1.000
rpoB761327c.1521A>G1.000
rpoB761330c.1524G>C1.000
rpoB761354c.1548C>T1.000
rpoB761477c.1671C>G1.000
rpoB761492c.1686G>C1.000
rpoB761510c.1704T>C0.969
rpoB761537c.1731C>G0.967
rpoB761570c.1764T>C0.964
rpoB761573c.1767C>G0.926
rpoB761579c.1773G>C0.964
rpoB761588c.1782C>T0.964
rpoB761606c.1800C>G1.000
rpoB761612c.1806G>C1.000
rpoB761615c.1809A>C1.000
rpoB761636c.1830G>T1.000
rpoB761639c.1833G>A1.000
rpoB761645c.1839C>G1.000
rpoB761648c.1842T>C1.000
rpoB761657c.1851C>G1.000
rpoB761675c.1869G>C1.000
rpoB761750c.1944G>C1.000
rpoB761765c.1959T>C1.000
rpoB761772p.His656Ala1.000
rpoB761778p.Asn658Asp1.000
rpoB761791p.Arg662His1.000
rpoB761834c.2028T>C1.000
rpoB761848p.Cys681Ser1.000
rpoB761852c.2046C>G1.000
rpoB761858c.2052G>C1.000
rpoB761873c.2067A>C1.000
rpoB761885c.2079T>C1.000
rpoB761906c.2100C>G1.000
rpoB761909c.2103T>C1.000
rpoB761912c.2106T>C1.000
rpoB761915p.Asp703Glu1.000
rpoB761916p.Asp704Asn1.000
rpoB761948c.2142G>C1.000
rpoB761954c.2148C>G1.000
rpoB762008c.2202C>T1.000
rpoB762014c.2208C>T1.000
rpoB762017c.2211A>G1.000
rpoB762053c.2247T>C1.000
rpoB762062c.2256T>C1.000
rpoB762065c.2259T>C1.000
rpoB762083c.2277T>C1.000
rpoB762086c.2280G>C1.000
rpoB762101c.2295C>G1.000
rpoB762233c.2427G>C1.000
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
rpoB762398c.2592T>C1.000
rpoB762401c.2595G>C1.000
rpoB762404c.2598T>C1.000
rpoB762410c.2604T>C1.000
rpoB762416c.2610A>G1.000
rpoB762419c.2613C>G1.000
rpoB762434c.2628T>C1.000
rpoB762449c.2643C>A0.947
rpoB762467c.2661C>T1.000
rpoB762488c.2682G>C1.000
rpoB762489p.Val895Gln1.000
rpoB762509c.2703T>G1.000
rpoB762510p.Ala902Pro1.000
rpoB762521c.2715C>T1.000
rpoB762857c.3051C>G1.000
rpoB762860c.3054G>C1.000
rpoB762863c.3057T>C1.000
rpoB762929c.3123G>C1.000
rpoB762989c.3183G>C1.000
rpoB763013c.3207C>G1.000
rpoB763028c.3222T>C1.000
rpoB763031c.3225T>G1.000
rpoB763034c.3228C>G1.000
rpoB763040c.3234C>G1.000
rpoB763070c.3264T>C1.000
rpoB763085c.3279C>G1.000
rpoB763115c.3309T>C1.000
rpoB763136c.3330C>T1.000
rpoB763148c.3342G>C1.000
rpoB763158c.3352C>T1.000
rpoB763166c.3360A>G1.000
rpoB763190c.3384C>T1.000
rpoB763214c.3408T>C1.000
rpoB763226c.3420A>G1.000
rpoB763227c.3421C>T1.000
rpoB763238c.3432T>C1.000
rpoB763253c.3447G>C1.000
rpoB763256c.3450G>A1.000
rpoB763268c.3462C>G1.000
rpoB763283c.3477T>C1.000
rpoB763284c.3478C>T1.000
rpoC763351c.-19T>C1.000
rpoC763352c.-18T>A1.000
rpoC763402c.33C>G1.000
rpoC763411c.42T>G1.000
rpoC763414c.45T>C1.000
rpoC763441c.72C>T1.000
rpoC763444c.75T>C1.000
rpoC763456c.87A>G1.000
rpoC763486c.117T>G0.950
rpoC763528c.159G>A1.000
rpoC763546c.177A>G1.000
rpoC763570c.201G>C1.000
rpoC763573c.204G>C1.000
rpoC763594c.225C>T1.000
rpoC763633c.264T>C1.000
rpoC763636c.267T>C1.000
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
rpoC763936c.567C>G1.000
rpoC763945c.576T>C1.000
rpoC764024c.655T>C1.000
rpoC764032p.Asp221Glu1.000
rpoC764040p.Ser224Thr1.000
rpoC764044c.675T>C1.000
rpoC764059c.690G>T1.000
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>G0.960
rpoC764257c.888G>C1.000
rpoC764266c.897T>C1.000
rpoC764269c.900G>C1.000
rpoC764272c.903G>C1.000
rpoC764278c.909A>G1.000
rpoC764338c.969G>A1.000
rpoC764353c.984G>C1.000
rpoC764365c.996C>T1.000
rpoC764489c.1120C>T1.000
rpoC764497c.1128A>G1.000
rpoC764510c.1141C>T1.000
rpoC764521c.1152T>C1.000
rpoC764554c.1185C>T1.000
rpoC764560c.1191T>C1.000
rpoC764566c.1197C>G1.000
rpoC764575c.1206T>G1.000
rpoC764581c.1212T>C1.000
rpoC764593c.1224C>T1.000
rpoC764611c.1242G>T1.000
rpoC764650c.1281G>C1.000
rpoC764651c.1282T>A1.000
rpoC764752c.1383G>C1.000
rpoC764764c.1395T>C1.000
rpoC764809c.1440C>T1.000
rpoC764815c.1446A>G1.000
rpoC764827c.1458G>C1.000
rpoC764858c.1489T>C1.000
rpoC764872c.1503A>G1.000
rpoC764888c.1519T>C1.000
rpoC764911c.1542A>G1.000
rpoC764932c.1563C>A1.000
rpoC764935c.1566T>C1.000
rpoC764948c.1579T>C1.000
rpoC764968c.1599T>C1.000
rpoC764995c.1626C>G1.000
rpoC765019c.1650A>G1.000
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
rpoC765292c.1923G>C1.000
rpoC765298c.1929G>C1.000
rpoC765300p.Val644Ala1.000
rpoC765319c.1950A>G1.000
rpoC765326p.His653Ala1.000
rpoC765329p.Ser654Gly1.000
rpoC765346c.1977C>G1.000
rpoC765349c.1980T>C1.000
rpoC765352c.1983G>C1.000
rpoC765383p.Met672Leu1.000
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.Ala905Gln1.000
rpoC766096c.2727G>C1.000
rpoC766129c.2760C>G1.000
rpoC766135c.2766G>A1.000
rpoC766141c.2772C>T1.000
rpoC766142c.2773C>T1.000
rpoC766312c.2943T>G1.000
rpoC766327c.2958C>A1.000
rpoC766345c.2976T>C1.000
rpoC766348c.2979A>G1.000
rpoC766357c.2988C>T1.000
rpoC766363c.2994G>C1.000
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
rpoC766483c.3114G>C1.000
rpoC766484p.Val1039Ile1.000
rpoC766492c.3123T>C1.000
rpoC766522c.3153C>G1.000
rpoC766528c.3159T>C1.000
rpoC766531c.3162G>C1.000
rpoC766540p.Asp1057Glu1.000
rpoC766549c.3180G>C1.000
rpoC766657c.3288A>G1.000
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>C1.000
rpoC766864c.3495G>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>C1.000
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>C1.000
rpsL781631c.72G>C1.000
rpsL781649c.90T>C1.000
rpsL781655c.96T>C1.000
rpsL781682c.123T>C1.000
rpsL781700c.141G>C1.000
rpsL781703c.144G>T1.000
rpsL781715c.156T>C1.000
rpsL781728c.169T>C1.000
rpsL781736c.177T>C1.000
rpsL781742c.183C>T1.000
rpsL781748c.189C>G1.000
rpsL781754c.195G>C1.000
rpsL781760c.201T>C1.000
rpsL781772c.213C>A0.933
rpsL781808c.249C>T1.000
rpsL781811c.252C>T1.000
rpsL781832c.273T>C1.000
rpsL781838c.279G>C1.000
rpsL781841c.282C>G1.000
rpsL781865c.306G>C1.000
rpsL781868c.309T>C1.000
rpsL781871c.312G>C1.000
rpsL781877c.318T>C1.000
rpsL781892c.333A>G1.000
rpsL781898c.339A>T1.000
rpsL781916c.357T>C1.000
rpsL781929p.Gly124Ser1.000
rplC800844c.36T>C0.909
rrs1471923r.78t>c1.000
rrs1471925r.80t>c1.000
rrs1471932r.87a>g1.000
rrs1471934r.89a>g1.000
rrs1471969r.124t>c1.000
rrs1471970r.125g>a1.000
rrs1472044r.199g>t1.000
rrs1472045r.200t>a1.000
rrs1472053r.208agc>a1.000
rrs1472061r.216a>t1.000
rrs1472075r.230a>g1.000
rrs1472108r.263c>t1.000
rrs1472969r.1124a>g1.000
rrs1472970r.1125c>g1.000
rrs1472977r.1132g>c1.000
rrs1472978r.1133t>c1.000
rrs1473105r.1260g>a1.000
rrs1473120r.1275c>ct1.000
rrs1473123r.1278a>t1.000
rrs1473145r.1300c>t1.000
rrs1473166r.1321g>a1.000
rrs1473290r.1445c>t1.000
rrl1473651c.-7GT>G1.000
rrl1473658r.1t>a1.000
rrl1473659r.2t>a1.000
rrl1473668r.11c>t1.000
rrl1473756r.99g>a1.000
rrl1473758r.101g>t1.000
rrl1473806r.149c>t1.000
rrl1473877r.220g>a1.000
rrl1473898r.241c>t1.000
rrl1473943r.286g>t1.000
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>t1.000
rrl1474151r.494c>t1.000
rrl1474181r.524c>t1.000
rrl1474249r.592g>t1.000
rrl1474291r.634tttcctctccggagga>t1.000
rrl1474308r.651g>t1.000
rrl1474310r.653t>g1.000
rrl1474356r.699t>c1.000
rrl1474362r.705a>g1.000
rrl1474376r.719t>c0.952
rrl1474639r.982g>a1.000
rrl1474794r.1137c>t1.000
rrl1474812r.1155g>a1.000
rrl1474823r.1166c>t1.000
rrl1474831r.1174a>g1.000
rrl1474904r.1247g>a1.000
rrl1474956r.1299c>t1.000
rrl1474960r.1303c>g1.000
rrl1474963r.1306g>t1.000
rrl1474964r.1307t>a1.000
rrl1474965r.1308g>c1.000
rrl1474970r.1313g>a1.000
rrl1475006r.1349a>t1.000
rrl1475061r.1404c>t1.000
rrl1475088r.1431a>t1.000
rrl1475199r.1542g>a1.000
rrl1475206r.1549c>t0.947
rrl1475209r.1552g>c1.000
rrl1475213r.1556c>t1.000
rrl1475249r.1592t>c1.000
rrl1475252r.1595c>t1.000
rrl1475266r.1609t>c1.000
rrl1475267r.1610g>a1.000
rrl1475275r.1618c>t1.000
rrl1475276r.1619t>c1.000
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>t1.000
rrl1475505r.1848g>a1.000
rrl1475526r.1869c>a1.000
rrl1475599r.1942a>g1.000
rrl1475608r.1951t>c1.000
rrl1475642r.1985t>c1.000
rrl1475657r.2000a>g1.000
rrl1475659r.2002g>t1.000
rrl1475758r.2101ac>a1.000
rrl1475763r.2106c>t1.000
rrl1475765r.2108ag>a1.000
rrl1475881r.2224t>c1.000
rrl1475988r.2331a>g1.000
rrl1476031r.2374c>t1.000
rrl1476032r.2375c>a1.000
rrl1476033r.2376t>c1.000
rrl1476034r.2377c>a1.000
rrl1476045r.2388g>t1.000
rrl1476047r.2390g>t1.000
rrl1476048r.2391g>a1.000
rrl1476049r.2392c>t1.000
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
fabG11673523c.84G>T0.929
fabG11673535c.96A>G1.000
fabG11673547c.108T>C1.000
fabG11673568c.129C>G1.000
fabG11673574c.135C>G1.000
fabG11673580c.141T>G1.000
fabG11673710p.Leu91Ile1.000
fabG11673716p.Ala93Lys1.000
fabG11673733p.Met98Ile1.000
fabG11673748c.309A>G1.000
fabG11673749p.Lys104Arg1.000
fabG11673758p.Lys107Glu1.000
fabG11673890p.Ala151Ser1.000
fabG11673901c.462A>G1.000
fabG11673905p.Ser156Ala1.000
fabG11673916c.477A>C1.000
fabG11673917p.Val160Leu1.000
fabG11673922c.483T>C1.000
fabG11673941p.Ala168Ser1.000
fabG11673955c.516G>C1.000
fabG11673961c.522A>C1.000
fabG11673985c.546C>G1.000
fabG11674006p.Asp189Glu1.000
fabG11674079p.Pro214Ala1.000
rpsA1833532c.-10A>C1.000
rpsA1833554p.Thr5Ala1.000
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>C1.000
rpsA1833841c.300C>G1.000
rpsA1833847c.306C>G1.000
rpsA1833856c.315A>G1.000
rpsA1833874c.333T>C1.000
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
rpsA1834102c.561T>C1.000
rpsA1834105c.564C>G1.000
rpsA1834108c.567C>G1.000
rpsA1834123c.582C>G1.000
rpsA1834195c.654G>C1.000
rpsA1834210c.669C>T1.000
rpsA1834222c.681T>C1.000
rpsA1834231c.690T>C1.000
rpsA1834234c.693G>C1.000
rpsA1834249c.708T>C1.000
rpsA1834261c.720A>G1.000
rpsA1834262c.721T>A1.000
rpsA1834303c.762T>C1.000
rpsA1834306c.765T>C1.000
rpsA1834333c.792C>T1.000
rpsA1834348c.807T>C1.000
rpsA1834366c.825A>G1.000
rpsA1834396c.855G>C1.000
rpsA1834411c.870T>C1.000
rpsA1834417c.876G>C1.000
rpsA1834423c.882G>C1.000
rpsA1834435c.894G>C1.000
rpsA1834451c.910T>C1.000
rpsA1834465c.924T>C1.000
rpsA1834468c.927A>G1.000
rpsA1834489c.948T>C1.000
rpsA1834513c.972C>G1.000
rpsA1834528c.987T>C1.000
rpsA1834540c.999G>C0.933
rpsA1834546c.1005T>C1.000
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
kasA2518162c.48G>A1.000
kasA2518174c.60A>G1.000
kasA2518190p.Ser26Ala1.000
kasA2518199p.Ile29Val1.000
kasA2518220c.106C>T1.000
kasA2518234c.120G>A1.000
kasA2518248p.Ala45Val1.000
kasA2518480c.366T>C1.000
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
kasA2518783c.669T>C1.000
kasA2518789c.675G>C1.000
kasA2518792c.678C>A1.000
kasA2518795c.681C>G1.000
kasA2518825c.711T>C1.000
kasA2518864c.750G>C1.000
kasA2518879c.765A>G1.000
kasA2518885c.771T>C1.000
kasA2518898c.784T>C1.000
kasA2518906c.792A>G1.000
kasA2519062c.948T>G1.000
kasA2519068c.954C>T1.000
kasA2519072p.Ala320Thr1.000
kasA2519107c.993T>C1.000
kasA2519108p.Asp332Gln1.000
kasA2519116c.1002C>G1.000
kasA2519122c.1008G>C1.000
kasA2519137c.1023T>G1.000
ahpC2726303c.111T>C1.000
ahpC2726638p.Ala149Val1.000
ahpC2726645c.453C>G1.000
ahpC2726657c.465A>C1.000
ahpC2726669p.Asp159Glu1.000
folC2747335c.264C>A0.900
folC2747343p.Val86Ile0.909
folC2747355p.Val82Ile1.000
folC2747362c.237C>G1.000
thyX3067349c.597C>G1.000
thyX3067373c.573G>C1.000
thyX3067388c.558G>C1.000
thyX3067391c.555C>G1.000
thyX3067394c.552C>G1.000
thyX3067439c.507T>C1.000
thyX3067445c.501G>C1.000
thyX3067457c.489G>C1.000
thyX3067462c.484G>A1.000
thyX3067465p.Ile161Val1.000
thyX3067475c.471T>C1.000
thyX3067490c.456G>C1.000
thyX3067493c.453T>C1.000
thyX3067515p.Ser144Thr1.000
thyX3067577c.369C>T1.000
thyX3067583c.363G>C1.000
thyX3067602p.Arg115His1.000
thyX3067611p.Lys112Thr1.000
thyX3067619c.327T>G1.000
thyX3067631c.315G>C1.000
thyX3067634c.312G>C1.000
thyX3067652c.294A>G1.000
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
thyX3067738p.Phe70Leu1.000
thyX3067739c.207A>G1.000
thyX3067754c.192G>A1.000
thyX3067762p.Arg62Lys1.000
thyX3067765p.Leu61Ile1.000
thyX3067772c.174G>C0.909
thyX3067781c.165G>C1.000
thyX3067793c.153A>G1.000
thyX3067802c.144G>C1.000
thyX3067898p.Asp16Glu1.000
thyX3067935p.Thr4Ile1.000
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
embC4241089c.1227C>G1.000
embC4241095c.1233C>T1.000
embC4241107c.1245G>C0.955
embC4241140c.1278A>G1.000
embC4241146c.1284C>G1.000
embC4241158c.1296T>C1.000
embC4241161c.1299C>G1.000
embC4241162c.1300T>C1.000
embC4241170c.1308G>C1.000
embC4241173c.1311C>T1.000
embC4241203c.1341T>C1.000
embC4241206c.1344G>C1.000
embA4244534c.1302T>C1.000
embA4244537c.1305T>G1.000
embA4244543c.1311C>G1.000
embA4244547p.Ile439Val1.000
embA4244557p.Arg442Thr1.000
embA4244582c.1350T>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
embA4245182c.1950T>C1.000
embA4245189c.1957C>T1.000
embA4245198p.Leu656Ile1.000
embA4245207c.1975T>C1.000
embA4245215c.1983A>C1.000
embA4245222p.Tyr664Gln1.000
embA4245764c.2532G>C1.000
embA4245772p.Asn847Thr1.000
embA4245785c.2553G>C1.000
embB4247470c.957T>C1.000
embB4247491c.978G>C1.000
embB4247512c.999T>C1.000
embB4247539c.1026T>C1.000
embB4247797c.1284C>G1.000
embB4247800c.1287A>T1.000
embB4247803c.1290G>C1.000
embB4247815c.1302C>G1.000
embB4247819p.Val436Ile1.000
embB4247830c.1317A>G1.000
embB4247839c.1326G>C1.000
embB4247875c.1362G>C1.000
embB4247876c.1363C>T1.000
embB4247881c.1368G>C1.000
embB4247887c.1374C>T1.000
embB4247899p.Met462Ile1.000
embB4247905c.1392G>C1.000
embB4247909c.1396T>C1.000
embB4247914c.1401G>C1.000
embB4247932c.1419C>G1.000
embB4247940p.Leu476Trp1.000
embB4247945c.1432T>C1.000
embB4247951p.Ser480Ala1.000
embB4247974c.1461C>G1.000
embB4248046c.1533A>G1.000
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>C1.000
embB4248220c.1707A>C1.000
embB4248298c.1785C>T1.000
embB4248304c.1791G>C1.000
embB4248316c.1803C>G1.000
embB4248319c.1806A>G1.000
embB4248343c.1830G>C1.000
embB4248350c.1837T>C1.000
embB4248355c.1842A>G1.000
embB4248373c.1860C>G1.000
embB4248382c.1869C>G1.000
embB4248386c.1873C>A1.000
embB4249469p.Leu986Met1.000
embB4249486c.2973T>G1.000
embB4249498c.2985G>C1.000
ethA4327396c.78A>G1.000
ethA4327399p.Asp25Glu1.000
ethA4327423c.51G>C1.000
ethA4327435c.39T>G1.000
ethA4327438c.36A>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
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