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: 5cc5597acb497
Sample: 5cc5597acb497

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Summary
ID: 5cc5597acb497
Date: Sun Apr 28 08:46:05 2019
Strain: lineage1.2.1;lineage1.1.3
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
EthambutolRembB p.Asn399Asp (0.91)
Pyrazinamide
Streptomycin
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage1.2.1Indo-OceanicEAI2RD239
lineage1.1.3Indo-OceanicEAI6RD239

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6115c.876A>G1.000
gyrB6123p.Ala295Gly1.000
gyrB6127c.888G>T1.000
gyrB6172c.933C>T1.000
gyrB6190c.951A>G1.000
gyrB6214c.975G>C1.000
gyrA7391c.90C>T1.000
gyrA7394c.93T>C0.909
gyrA7412c.111C>G1.000
gyrA7422c.121C>T0.923
gyrA7433c.132G>C1.000
gyrA7451c.150C>G0.909
gyrA7457c.156T>C1.000
gyrA7469c.168C>G1.000
gyrA7472c.171T>C1.000
gyrA7475c.174A>G1.000
gyrA7480p.Phe60Tyr1.000
gyrA7484c.183T>C1.000
gyrA7490c.189C>G1.000
gyrA7502c.201C>T1.000
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>G0.967
gyrA7626c.325C>T0.950
gyrA7631c.330G>C0.941
gyrA7643c.342C>T0.938
gyrA7646c.345C>T0.938
gyrA7655c.354G>C0.900
gyrA7658c.357A>G0.900
gyrA7661c.360C>T0.900
gyrA7664c.363T>C0.900
gyrA7670c.369A>G0.900
gyrA7673c.372G>A0.900
gyrA7676c.375G>C0.900
gyrA7679c.378G>C0.909
gyrA7697c.396C>G0.941
gyrA7706c.405C>G0.938
gyrA7725c.424C>T1.000
gyrA7728c.427A>C1.000
gyrA7769c.468C>T1.000
gyrA7787c.486G>A1.000
gyrA7793c.492G>C1.000
gyrA8189c.888G>C1.000
gyrA8192c.891C>G1.000
gyrA8198c.897T>C1.000
gyrA9197c.1896G>C0.909
gyrA9230c.1929T>C0.909
gyrA9236c.1935G>C0.909
gyrA9242c.1941A>C0.909
gyrA9248c.1947G>C0.917
gyrA9252p.Val651Ile0.923
gyrA9266c.1965C>T0.933
gyrA9284c.1983T>C0.900
gyrA9296c.1995T>C0.900
gyrA9304p.Gly668Glu1.000
gyrA9326c.2025G>T1.000
gyrA9338c.2037G>A1.000
gyrA9341c.2040C>G1.000
gyrA9345c.2044A>C1.000
gyrA9383c.2082T>C1.000
gyrA9386c.2085T>C1.000
gyrA9395c.2094G>C1.000
rpoB760056c.250C>T0.833
rpoB760070c.264T>G0.929
rpoB760091c.285G>C0.929
rpoB760101c.295T>C0.933
rpoB760112c.306T>C0.933
rpoB760118c.312T>C0.933
rpoB760121c.315T>C0.933
rpoB760130p.Asp108Glu0.867
rpoB760139c.333A>G0.933
rpoB760142c.336C>G0.933
rpoB760145c.339C>G0.933
rpoB760181c.375T>A1.000
rpoB760184c.378A>G1.000
rpoB760196c.390C>G1.000
rpoB760235c.429T>C1.000
rpoB760244c.438G>C0.947
rpoB760274c.468G>A1.000
rpoB760295c.489C>T1.000
rpoB760412c.606C>T1.000
rpoB760418c.612G>C1.000
rpoB760424c.618C>G1.000
rpoB760430c.624T>C1.000
rpoB760457c.651C>T1.000
rpoB760493c.687C>A1.000
rpoB760520c.714C>G1.000
rpoB760522p.Ser239Asn1.000
rpoB760526c.720G>A1.000
rpoB760532c.726T>C1.000
rpoB760533p.Val243Thr1.000
rpoB760547c.741G>C1.000
rpoB760563p.Arg253Met1.000
rpoB760591p.Val262Ala1.000
rpoB760601c.795C>T0.947
rpoB760611c.805T>C1.000
rpoB760622c.816C>T1.000
rpoB760646c.840C>G1.000
rpoB760649c.843G>C1.000
rpoB760655c.849A>G1.000
rpoB760661c.855A>C1.000
rpoB760670c.864G>C1.000
rpoB760674c.868T>C1.000
rpoB760679c.873A>G1.000
rpoB760683c.877T>C1.000
rpoB760724c.918T>C1.000
rpoB760730c.924T>C1.000
rpoB760748c.942C>G1.000
rpoB760757c.951T>C1.000
rpoB760759p.Val318Ala1.000
rpoB760769c.963C>G1.000
rpoB760793c.987A>G1.000
rpoB760805c.999G>C1.000
rpoB760817c.1011A>G0.909
rpoB760820c.1014T>C0.917
rpoB760826c.1020C>G0.917
rpoB760830c.1024T>C0.917
rpoB760841c.1035T>C0.900
rpoB760845p.Thr347Pro0.900
rpoB760856c.1050C>G0.917
rpoB760931c.1125C>G1.000
rpoB760937c.1131G>A1.000
rpoB760946c.1140A>G1.000
rpoB760973c.1167G>C1.000
rpoB761051c.1245G>T0.900
rpoB761150c.1344A>C1.000
rpoB761168c.1362C>G1.000
rpoB761180c.1374A>C1.000
rpoB761240c.1434C>T0.929
rpoB761249c.1443A>G1.000
rpoB761255c.1449T>C1.000
rpoB761261c.1455G>T1.000
rpoB761264c.1458C>G1.000
rpoB761282c.1476C>G0.952
rpoB761327c.1521A>G1.000
rpoB761345c.1539G>T1.000
rpoB761354c.1548C>T1.000
rpoB761360c.1554T>C1.000
rpoB761362p.Ser519Thr1.000
rpoB761374p.Val523Glu1.000
rpoB761414c.1608A>G1.000
rpoB761423c.1617T>C1.000
rpoB761432c.1626C>T1.000
rpoB761435c.1629T>C1.000
rpoB761438c.1632G>C1.000
rpoB761444c.1638T>C1.000
rpoB761452p.Val549Glu1.000
rpoB761457p.Pro551Ser1.000
rpoB761465c.1659G>A1.000
rpoB761471c.1665C>T1.000
rpoB761477c.1671C>T1.000
rpoB761492c.1686G>C0.933
rpoB761504c.1698C>G0.938
rpoB761510c.1704T>C0.941
rpoB761531c.1725C>G0.947
rpoB761537c.1731C>G0.947
rpoB761558c.1752C>G0.895
rpoB761570c.1764T>C0.895
rpoB761573c.1767C>G0.895
rpoB761579c.1773G>C0.900
rpoB761606c.1800C>G0.909
rpoB761612c.1806G>T0.938
rpoB761615c.1809A>C0.941
rpoB761636c.1830G>T1.000
rpoB761645c.1839C>A1.000
rpoB761648c.1842T>C1.000
rpoB761666c.1860G>C1.000
rpoB761690c.1884G>C1.000
rpoB761725p.Glu640Ala1.000
rpoB761732c.1926C>G1.000
rpoB761735c.1929C>G1.000
rpoB761750c.1944G>C1.000
rpoB762008c.2202C>G1.000
rpoB762014c.2208C>T1.000
rpoB762047c.2241G>A1.000
rpoB762053c.2247T>C1.000
rpoB762062c.2256T>C1.000
rpoB762065c.2259T>C1.000
rpoB762083c.2277T>C1.000
rpoB762086c.2280G>C1.000
rpoB762101c.2295C>G1.000
rpoB762281c.2475G>A0.900
rpoB762284c.2478G>C0.900
rpoB762293c.2487T>C0.917
rpoB762317c.2511A>G1.000
rpoB762338c.2532T>C1.000
rpoB762341c.2535G>C1.000
rpoB762347c.2541T>C1.000
rpoB762362p.Glu852Asp1.000
rpoB762369c.2563T>C0.929
rpoB762848c.3042G>A1.000
rpoB762857c.3051C>G1.000
rpoB762860c.3054G>C1.000
rpoB762917c.3111C>T0.950
rpoB762929c.3123G>T0.947
rpoB762962c.3156C>T0.913
rpoB762983c.3177C>G0.900
rpoB762995c.3189G>T0.889
rpoB763031c.3225T>C1.000
rpoB763034c.3228C>G0.889
rpoB763040c.3234C>G0.941
rpoB763050c.3244C>T1.000
rpoB763055c.3249G>A1.000
rpoB763070c.3264T>C1.000
rpoB763082c.3276C>T1.000
rpoB763085c.3279C>G1.000
rpoB763115c.3309T>C1.000
rpoB763127c.3321G>C1.000
rpoB763166c.3360A>G1.000
rpoC763351c.-19T>C1.000
rpoC763352c.-18T>A1.000
rpoC763402c.33C>T1.000
rpoC763409c.40C>T1.000
rpoC763414c.45T>G1.000
rpoC763441c.72C>T1.000
rpoC763444c.75T>C1.000
rpoC763456c.87A>G1.000
rpoC763486c.117T>G1.000
rpoC763528c.159G>A1.000
rpoC763546c.177A>G1.000
rpoC763570c.201G>C1.000
rpoC763594c.225C>T1.000
rpoC763603c.234C>T1.000
rpoC763618c.249C>T1.000
rpoC763636c.267T>C1.000
rpoC763660c.291T>G1.000
rpoC763669c.300C>G1.000
rpoC763675c.306C>G1.000
rpoC763703c.334T>A1.000
rpoC763709c.340C>T1.000
rpoC763714c.345G>C1.000
rpoC763726c.357C>T1.000
rpoC763732c.363C>G1.000
rpoC763741c.372C>T1.000
rpoC763744c.375G>C1.000
rpoC763762c.393C>T1.000
rpoC763765c.396T>G1.000
rpoC763771c.402C>T1.000
rpoC763780c.411C>G1.000
rpoC763801c.432C>G0.955
rpoC763807c.438T>C0.913
rpoC763836p.Ala156Val0.913
rpoC763851p.Ala161Gly0.867
rpoC763855c.486C>T0.867
rpoC763858c.489A>G0.867
rpoC763872p.Gly168Ala0.867
rpoC763876p.Glu169Asp0.875
rpoC763879c.510A>G0.867
rpoC763888c.519G>C0.909
rpoC763891c.522G>C0.909
rpoC763894c.525A>G0.917
rpoC763900c.531G>A0.917
rpoC763936c.567C>G0.933
rpoC763939c.570G>A0.933
rpoC763951c.582G>A1.000
rpoC763963c.594C>G1.000
rpoC763967p.Gly200Ser1.000
rpoC763972c.603C>T1.000
rpoC763987c.618C>T1.000
rpoC763996c.627T>C1.000
rpoC764005c.636G>C1.000
rpoC764024c.655T>C1.000
rpoC764040p.Ser224Thr1.000
rpoC764044c.675T>G1.000
rpoC764059c.690G>T1.000
rpoC764083c.714A>G1.000
rpoC764098c.729A>G1.000
rpoC764101c.732C>G1.000
rpoC764317c.948C>G1.000
rpoC764320c.951C>G1.000
rpoC764365c.996C>T1.000
rpoC764497c.1128A>G1.000
rpoC764503c.1134G>C1.000
rpoC764521c.1152T>C1.000
rpoC764527c.1158C>T1.000
rpoC764530c.1161C>G1.000
rpoC764536c.1167G>T1.000
rpoC764539c.1170C>G1.000
rpoC764554c.1185C>T1.000
rpoC764575c.1206T>G0.938
rpoC764578c.1209C>G0.933
rpoC764605c.1236G>A0.962
rpoC764626c.1257C>T0.962
rpoC764650c.1281G>T0.962
rpoC764668c.1299C>T0.964
rpoC764686c.1317C>T0.929
rpoC764746c.1377G>C0.952
rpoC764749c.1380G>C0.950
rpoC764752c.1383G>C0.952
rpoC764764c.1395T>C0.958
rpoC764782c.1413C>T0.960
rpoC764797c.1428G>C0.963
rpoC764803c.1434C>T0.964
rpoC764809c.1440C>T0.964
rpoC764815c.1446A>G0.966
rpoC764824c.1455T>C0.960
rpoC764858c.1489T>C0.962
rpoC764887c.1518G>C1.000
rpoC764888c.1519T>C1.000
rpoC764902c.1533C>T1.000
rpoC764911c.1542A>G1.000
rpoC764923c.1554A>G1.000
rpoC764932c.1563C>G1.000
rpoC764941c.1572G>A1.000
rpoC764948c.1579T>C1.000
rpoC764968c.1599T>C1.000
rpoC765007c.1638T>G1.000
rpoC765008c.1639T>C1.000
rpoC765013c.1644C>T1.000
rpoC765019c.1650A>G1.000
rpoC765367c.1998C>G0.909
rpoC765370c.2001G>C0.909
rpoC765383p.Met672Leu0.818
rpoC765391c.2022C>T0.833
rpoC765406c.2037G>T0.846
rpoC765409c.2040T>C0.846
rpoC765412c.2043T>C0.857
rpoC765421c.2052C>G0.867
rpoC765452p.Ala695Ser0.889
rpoC765466c.2097C>T0.889
rpoC765478c.2109T>C0.842
rpoC765493c.2124G>C0.812
rpoC765499c.2130C>G0.833
rpoC765508c.2139C>G0.895
rpoC765517c.2148C>G0.882
rpoC765529c.2160C>T0.944
rpoC765541c.2172C>G0.938
rpoC765553c.2184C>T0.941
rpoC765556c.2187G>C0.944
rpoC765562c.2193G>C0.941
rpoC765578c.2209C>T0.947
rpoC765622p.Glu751Asp1.000
rpoC765625c.2256C>T1.000
rpoC765628c.2259G>C1.000
rpoC765658c.2289C>T1.000
rpoC765700c.2331T>C1.000
rpoC765728p.Gln787Lys1.000
rpoC765734c.2365T>C1.000
rpoC765739c.2370G>C1.000
rpoC765752p.Asp795Ser1.000
rpoC765772c.2403C>G1.000
rpoC765826c.2457T>C0.909
rpoC765835c.2466C>T0.929
rpoC765883c.2514C>G0.941
rpoC765886c.2517C>G0.944
rpoC765892c.2523T>C0.950
rpoC765934c.2565C>T0.952
rpoC765967c.2598C>T0.952
rpoC765982c.2613C>G0.957
rpoC765994c.2625A>T0.957
rpoC766012c.2643C>G0.950
rpoC766021c.2652G>C0.952
rpoC766061p.Val898Ile0.941
rpoC766082p.Ala905Gln0.917
rpoC766093c.2724C>A0.917
rpoC766095p.Thr909Ser0.917
rpoC766105c.2736C>T1.000
rpoC766282c.2913C>T1.000
rpoC766288c.2919C>G1.000
rpoC766309c.2940G>A1.000
rpoC766315c.2946C>G1.000
rpoC766321c.2952C>G1.000
rpoC766348c.2979A>G1.000
rpoC766369c.3000C>G1.000
rpoC766381c.3012C>T1.000
rpoC766384c.3015A>G1.000
rpoC766393c.3024C>G1.000
rpoC766402c.3033C>G1.000
rpoC766408c.3039C>T1.000
rpoC766426c.3057C>T1.000
rpoC766456c.3087C>G1.000
rpoC766486c.3117A>G1.000
rpoC766492c.3123T>C1.000
rpoC766522c.3153C>G1.000
rpoC766528c.3159T>C1.000
rpoC766530p.Arg1054Gln1.000
rpoC766549c.3180G>C1.000
rpoC766573c.3204T>C1.000
rpoC766585c.3216T>C1.000
rpoC766594c.3225G>C1.000
rpoC766607p.Ile1080Leu1.000
rpoC766630c.3261G>T1.000
rpoC766660c.3291G>A1.000
rpoC766666c.3297C>G1.000
rpoC766672c.3303T>C1.000
rpoC766700c.3331C>T1.000
rpoC766726c.3357T>C0.938
rpoC766733c.3364C>T0.929
rpoC766738c.3369G>C0.929
rpoC766741c.3372G>C0.933
rpoC766750c.3381C>G0.929
rpoC766765c.3396A>C0.941
rpoC766774c.3405T>C0.933
rpoC766798c.3429C>G0.933
rpoC766801c.3432C>G0.933
rpoC766804c.3435A>G0.875
rpoC766843c.3474T>G0.895
rpoC766864c.3495G>C0.889
rpoC766876c.3507C>T0.889
rpoC766883p.Ser1172Ala0.938
rpoC766894c.3525T>C0.929
rpoC766895c.3526T>C0.929
rpoC766900c.3531T>C1.000
rpoC766903c.3534C>T1.000
rpoC766918c.3549C>T1.000
rpoC766933c.3564A>G1.000
rpoC766945c.3576A>G1.000
rpoC766963c.3594T>G0.917
rpoC766996c.3627C>G0.938
rpoC767002c.3633G>C0.938
rpoC767009c.3640T>A0.909
rpoC767014c.3645G>C0.917
rpoC767033c.3664T>A0.933
rpoC767059c.3690T>G0.933
rpoC767062c.3693C>A0.933
rpoC767098c.3729T>C0.941
rpoC767119c.3750A>G0.941
rpoC767134c.3765C>A0.941
rpoC767149c.3780C>T0.923
rpoC767158c.3789T>A0.929
rpoC767167c.3798C>G0.933
rpoC767180p.Ala1271Gln0.933
rpoC767191c.3822C>G0.938
rpoC767206c.3837C>G0.938
rpoC767209c.3840T>C0.933
rpoC767221c.3852C>G0.941
rpoC767230c.3861G>C0.938
rpoC767233c.3864T>C1.000
rpoC767263c.3894T>G1.000
rpoC767264p.Ala1299Gln1.000
rpoC767278c.3909T>C1.000
rpoC767281c.3912C>G1.000
rpoC767284c.3915C>T1.000
rpsL781595c.36T>C1.000
rpsL781598c.39G>C1.000
rpsL781605p.Ile16Val1.000
rpsL781608p.Ser17Ala1.000
rpsL781616c.57C>T0.933
rpsL781628c.69T>C0.933
rpsL781655c.96T>C0.889
rpsL781658c.99A>G0.889
rpsL781682c.123T>C0.962
rpsL781715c.156T>C1.000
rpsL781718c.159C>G1.000
rpsL781721c.162C>T1.000
rpsL781728c.169T>C1.000
rpsL781736c.177T>C1.000
rpsL781751c.192G>C1.000
rpsL781754c.195G>C1.000
rpsL781760c.201T>C1.000
rpsL781766c.207C>T1.000
rpsL781772c.213C>G1.000
rpsL781793c.234G>C1.000
rpsL781808c.249C>T1.000
rpsL781832c.273T>G0.923
rpsL781835c.276T>C1.000
rpsL781859c.300T>G1.000
rplC801357c.549T>C1.000
rplC801372c.564G>A1.000
rplC801385c.577C>T1.000
rrs1471923r.78t>c0.933
rrs1471925r.80t>c0.923
rrs1471932r.87a>g0.917
rrs1471934r.89a>g0.923
rrs1471970r.125g>a1.000
rrs1472030r.185g>t1.000
rrs1472031r.186g>t1.000
rrs1472033r.188a>g1.000
rrs1472034r.189t>c1.000
rrs1472040r.195t>c1.000
rrs1472053r.208agc>a1.000
rrs1472061r.216a>t1.000
rrs1472075r.230a>g1.000
rrs1472286r.441c>g0.895
rrs1472289r.444t>g0.889
rrs1472290r.445c>g0.889
rrs1472313r.468g>a0.889
rrs1472315r.470t>g0.941
rrs1472324r.479g>c0.895
rrs1472325r.480g>c0.895
rrs1472328r.483g>c0.900
rrs1472460r.615t>c0.800
rrs1472461r.616g>c0.800
rrs1472463r.618g>c0.800
rrs1472464r.619a>g0.800
rrs1472489r.644a>g1.000
rrs1472686r.841g>a0.964
rrs1472969r.1124a>g1.000
rrs1472970r.1125c>g1.000
rrs1472977r.1132g>c0.944
rrs1472978r.1133t>c0.944
rrs1473105r.1260g>a0.964
rrs1473120r.1275c>ct0.852
rrs1473123r.1278a>t1.000
rrs1473288r.1443c>t1.000
rrs1473290r.1445c>t1.000
rrs1473291r.1446g>t1.000
rrl1473396c.-262A>AG0.750
rrl1473401c.-257G>A1.000
rrl1473403c.-255C>T1.000
rrl1473408c.-250C>T1.000
rrl1473659r.2t>c1.000
rrl1473668r.11c>t1.000
rrl1473676r.19g>a1.000
rrl1473758r.101g>t1.000
rrl1473797r.140g>t1.000
rrl1473806r.149c>t1.000
rrl1473813r.156c>t1.000
rrl1473831r.174g>a0.957
rrl1473876r.219g>a1.000
rrl1473887r.230t>a0.957
rrl1473888r.231t>a1.000
rrl1473899r.242a>t1.000
rrl1473918r.261c>t1.000
rrl1473943r.286g>c1.000
rrl1473945r.288t>a1.000
rrl1473946r.289a>t1.000
rrl1473981r.324g>t0.947
rrl1473994r.337c>t0.889
rrl1473995r.338g>t0.889
rrl1474001r.344c>t0.889
rrl1474009r.352a>g0.889
rrl1474011r.354g>a0.882
rrl1474018r.361g>a0.889
rrl1474030r.373g>a0.889
rrl1474061r.404t>c0.941
rrl1474089r.432c>t0.909
rrl1474093r.436g>a0.900
rrl1474100r.443c>t0.909
rrl1474103r.446a>t0.909
rrl1474130r.473c>t0.938
rrl1474140r.483c>t0.938
rrl1474151r.494c>t0.947
rrl1474181r.524c>t0.955
rrl1474249r.592g>t1.000
rrl1474291r.634tttcctctccggagga>t1.000
rrl1474308r.651g>t0.941
rrl1474310r.653t>g0.941
rrl1474447r.790g>a0.952
rrl1474627r.970g>a1.000
rrl1474632r.975g>t1.000
rrl1474639r.982g>a1.000
rrl1474717r.1060a>t1.000
rrl1474753r.1096a>g1.000
rrl1474760r.1103a>g1.000
rrl1474783r.1126g>a1.000
rrl1474794r.1137c>t1.000
rrl1474812r.1155g>a1.000
rrl1474831r.1174a>g1.000
rrl1474945r.1288c>t1.000
rrl1474952r.1295acatcc>a1.000
rrl1475018r.1361g>a1.000
rrl1475027r.1370g>t1.000
rrl1475028r.1371g>t1.000
rrl1475061r.1404c>t1.000
rrl1475313r.1656g>a1.000
rrl1475315r.1658a>t1.000
rrl1475355r.1698c>t1.000
rrl1475369r.1712g>t1.000
rrl1475401r.1744ac>a1.000
rrl1475404r.1747a>g1.000
rrl1475405r.1748a>t1.000
rrl1475419r.1762c>t1.000
rrl1475429r.1772g>a1.000
rrl1475453r.1796t>a1.000
rrl1475480r.1823a>g0.917
rrl1475483r.1826c>t0.917
rrl1475487r.1830c>t0.900
rrl1475505r.1848g>a0.923
rrl1475526r.1869c>a0.938
rrl1475599r.1942a>g1.000
rrl1475604r.1947a>c1.000
rrl1475605r.1948a>t1.000
rrl1475608r.1951t>c1.000
rrl1475617r.1960c>g1.000
rrl1475625r.1968g>c1.000
rrl1475637r.1980t>a1.000
rrl1475642r.1985t>c1.000
rrl1475657r.2000a>g1.000
rrl1475659r.2002g>a1.000
rrl1475760r.2103c>t1.000
rrl1475763r.2106c>t1.000
rrl1475881r.2224t>c1.000
rrl1475988r.2331a>g1.000
rrl1475999r.2342g>t1.000
rrl1476077r.2420t>c1.000
rrl1476086r.2429g>a0.917
rrl1476089r.2432t>c1.000
rrl1476095r.2438c>t1.000
rrl1476106r.2449a>t1.000
rrl1476115r.2458t>c0.941
rrl1476214r.2557g>t1.000
rrl1476215r.2558c>t1.000
rrl1476251r.2594t>c0.917
rrl1476580r.2923g>a0.967
rrl1476597r.2940g>a0.963
rrl1476619r.2962c>t0.960
rrl1476628r.2971t>a0.958
rrl1476689r.3032a>t0.938
rrl1476690r.3033c>t0.938
rrl1476693r.3036g>a0.938
rrl1476695r.3038t>a0.938
rrl1476716r.3059a>c0.923
inhA1674480c.279T>C0.917
inhA1674489c.288G>T0.929
inhA1674507c.306G>A0.933
inhA1674534c.333G>C1.000
inhA1674549c.348G>C1.000
inhA1674555c.354G>A1.000
inhA1674561c.360C>T1.000
rpsA1833589c.48A>T1.000
rpsA1833613c.72C>A1.000
rpsA1833619c.78A>C1.000
rpsA1833661c.120A>G0.933
rpsA1833667c.126C>G0.929
rpsA1833703c.162C>T1.000
rpsA1833724c.183C>G0.941
rpsA1833727c.186G>C0.938
rpsA1833745c.204G>C1.000
rpsA1833790c.249T>C1.000
rpsA1833793c.252C>T1.000
rpsA1833802c.261A>G1.000
rpsA1833832c.291G>A1.000
rpsA1833838c.297G>C1.000
rpsA1833841c.300C>G1.000
rpsA1833847c.306C>G1.000
rpsA1833856c.315A>G1.000
rpsA1833859c.318C>T1.000
rpsA1833874c.333T>C0.909
rpsA1833895c.354G>C0.929
rpsA1833928c.387G>C0.933
rpsA1833949c.408T>C0.933
rpsA1833970c.429G>A0.895
rpsA1833979c.438T>C0.889
rpsA1834000c.459G>C0.875
rpsA1834015c.474G>C0.882
rpsA1834021c.480C>T0.900
rpsA1834102c.561T>C0.950
rpsA1834105c.564C>T0.952
rpsA1834150c.609G>C1.000
rpsA1834153c.612T>C1.000
rpsA1834154p.Asn205Gln1.000
rpsA1834157c.616T>C1.000
rpsA1834162c.621A>G1.000
rpsA1834165c.624A>G1.000
rpsA1834177c.636A>C1.000
rpsA1834186c.645C>G1.000
rpsA1834189c.648G>C1.000
rpsA1834195c.654G>C1.000
rpsA1834222c.681T>C1.000
rpsA1834225c.684C>G1.000
rpsA1834231c.690T>G0.944
rpsA1834249c.708T>C0.941
rpsA1834261c.720A>G0.938
rpsA1834264c.723G>C0.938
rpsA1834297c.756C>T0.955
rpsA1834303c.762T>G0.955
rpsA1834306c.765T>C0.955
rpsA1834336c.795C>G0.955
rpsA1834348c.807T>C1.000
rpsA1834357c.816T>C1.000
rpsA1834366c.825A>G1.000
rpsA1834375c.834G>A1.000
rpsA1834396c.855G>T0.960
rpsA1834411c.870T>C1.000
rpsA1834417c.876G>C1.000
rpsA1834423c.882G>T1.000
rpsA1834451c.910T>C1.000
rpsA1834456c.915T>G1.000
rpsA1834465c.924T>C1.000
rpsA1834468c.927A>G1.000
rpsA1834477c.936C>T1.000
rpsA1834489c.948T>C1.000
rpsA1834519c.978G>C1.000
rpsA1834546c.1005T>C1.000
rpsA1834555c.1014T>G1.000
rpsA1834603c.1062G>A1.000
rpsA1834609c.1068T>C1.000
rpsA1834612c.1071G>A1.000
rpsA1834633c.1092A>G1.000
rpsA1834639c.1098T>C1.000
rpsA1834654c.1113G>A0.882
rpsA1834690c.1149T>C0.875
rpsA1834699p.Glu386Asp0.875
rpsA1834732c.1191T>C0.833
kasA2518190p.Ser26Ala1.000
kasA2518199p.Ile29Val1.000
kasA2518219c.105T>C1.000
kasA2518220c.106C>T1.000
kasA2518245p.His44Arg1.000
kasA2518248p.Ala45Val1.000
kasA2518261p.Glu49Asp1.000
kasA2518783c.669T>C1.000
kasA2518789c.675G>C1.000
kasA2518795c.681C>A1.000
kasA2518798c.684G>C1.000
kasA2518825c.711T>C1.000
kasA2518840c.726C>G1.000
thyX3067685c.261T>C0.900
thyX3067693p.Ile85Val0.900
thyX3067694c.252C>G0.900
thyX3067718c.228G>C0.917
thyX3067727c.219T>G0.929
thyX3067739c.207A>G0.857
thyX3067742c.204T>G0.846
thyX3067762p.Arg62Lys0.800
thyX3067765p.Leu61Ile0.818
thyA3073854c.618G>A1.000
thyA3073863c.609A>G1.000
thyA3073889p.Ser195Asp1.000
thyA3073892c.580A>G1.000
thyA3073905c.567G>C1.000
thyA3073944c.528G>A1.000
thyA3073953c.519A>G1.000
thyA3073956c.516C>G1.000
thyA3073959c.513A>G1.000
thyA3073977c.495T>C1.000
thyA3073989c.483A>G1.000
thyA3074001c.471G>C1.000
thyA3074004c.468A>G1.000
thyA3074037c.435G>C1.000
fbiA3640347c.-196A>G1.000
fbiA3640365c.-178C>G1.000
alr3841001c.420T>C1.000
alr3841013c.408G>C1.000
alr3841018p.Leu135Val1.000
alr3841033p.Val130Ile1.000
alr3841036p.Gln129Glu1.000
alr3841037c.384C>G1.000
alr3841055c.366G>C1.000
alr3841079c.342A>G1.000
alr3841088c.333G>A1.000
alr3841100c.321T>C1.000
alr3841106c.315A>G1.000
panD4044177c.105G>C1.000
panD4044180c.102G>A1.000
panD4044188c.94A>G1.000
panD4044195c.87A>G1.000
panD4044225c.57G>A1.000
panD4044233p.Cys17Gln1.000
panD4044237c.45C>G1.000
embC4241095c.1233C>T1.000
embC4241101c.1239G>C1.000
embC4241121p.Ser420Asn1.000
embC4241137c.1275G>C1.000
embC4241146c.1284C>G1.000
embC4241394p.Lys511Ser0.846
embC4241452c.1590G>C1.000
embC4241455c.1593C>T1.000
embC4241461c.1599C>G1.000
embA4245125c.1893G>C1.000
embA4245137c.1905T>C1.000
embA4245149c.1917C>G1.000
embB4247572c.1059A>C0.889
embB4247590c.1077A>G0.917
embB4247684c.1171T>C0.909
embB4248007c.1494C>A1.000
embB4248157c.1644A>G1.000
embB4248161c.1648C>T1.000
embB4248169c.1656C>G1.000
embB4248190c.1677G>C1.000
embB4248200p.Ile563Val1.000
embB4248206p.Ser565Gly1.000
embB4248211c.1698G>A1.000
embB4248220c.1707A>C1.000
embB4248241c.1728C>T1.000
embB4248277c.1764G>C1.000
embB4248298c.1785C>T1.000
embB4248304c.1791G>C1.000

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;