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: 5cc54c3b71404
Sample: 5cc54c3b71404

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Summary
ID: 5cc54c3b71404
Date: Sun Apr 28 07:47:38 2019
Strain: lineage4.2.1;lineage1.2.1
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
EthambutolRembB p.His312Arg (1.00), embB p.Tyr384Asn (1.00)
Pyrazinamide
Streptomycin
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage4.2.1Euro-American (TUR)H3;H4None
lineage1.2.1Indo-OceanicEAI2RD239

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB5254c.15A>G1.000
gyrB5284c.45G>A1.000
gyrB5287c.48T>C1.000
gyrB5293c.54C>G1.000
gyrB5302c.63A>G1.000
gyrB5305c.66G>A1.000
gyrB5308c.69G>A1.000
gyrB5341c.102T>C1.000
gyrB5359c.120C>T1.000
gyrB5363c.124T>C1.000
gyrB5377c.138T>C1.000
gyrB5422c.183T>C1.000
gyrB5425c.186A>G1.000
gyrB5426p.Thr63Ala0.909
gyrB5431c.192A>C1.000
gyrB5434c.195G>A1.000
gyrB5436p.Asn66Ser1.000
gyrB5440c.201A>G1.000
gyrB5449c.210T>C1.000
gyrB5455c.216T>C1.000
gyrB5470c.231C>G1.000
gyrB5824c.585A>G1.000
gyrB5836c.597C>T1.000
gyrB5851c.612G>C1.000
gyrB5860c.621C>T1.000
gyrB5869c.630C>T1.000
gyrB5870p.Glu211Gln1.000
gyrB5873c.634A>C1.000
gyrB5884c.645A>G1.000
gyrB5902c.663A>G1.000
gyrB6145c.906C>T1.000
gyrB6178c.939C>T1.000
gyrB6181c.942C>G1.000
gyrA7523c.222C>A1.000
gyrA7532c.231T>C1.000
gyrA7541c.240C>G1.000
gyrA7547c.246C>T1.000
gyrA7585p.Ser95Thr1.000
gyrA7595c.294C>G1.000
gyrA7601c.300C>G1.000
gyrA7619c.318C>T1.000
gyrA7622c.321C>T1.000
gyrA7631c.330G>C1.000
gyrA7652c.351C>G1.000
gyrA7766c.465C>T1.000
gyrA7769c.468C>T1.000
gyrA7784c.483A>G1.000
gyrA7787c.486G>A1.000
gyrA7799c.498A>G1.000
gyrA7832c.531G>T1.000
gyrA7835c.534A>C1.000
gyrA7838c.537C>T1.000
gyrA7850c.549C>G1.000
gyrA8375c.1074G>C1.000
gyrA8382p.Leu361Met1.000
gyrA8393c.1092T>C1.000
gyrA8399c.1098T>C1.000
gyrA8402p.Asp367Glu1.000
gyrA8471c.1170T>C1.000
gyrA8486c.1185T>C1.000
gyrA8531c.1230G>A1.000
gyrA8655p.Ile452Val1.000
gyrA8981c.1680G>C1.000
gyrA8987c.1686C>G1.000
gyrA8998p.Leu566Trp1.000
gyrA9003c.1702C>T1.000
gyrA9017c.1716C>T1.000
gyrA9023c.1722A>C1.000
gyrA9029c.1728T>G1.000
gyrA9050p.Asp583Glu1.000
gyrA9065c.1764C>G1.000
gyrA9068c.1767G>C1.000
gyrA9071c.1770G>C1.000
gyrA9080c.1779G>C1.000
gyrA9089c.1788G>C1.000
gyrA9101c.1800A>G1.000
gyrA9119c.1818A>G1.000
gyrA9257c.1956C>T1.000
gyrA9284c.1983T>G1.000
rpoB759583c.-224T>G1.000
rpoB759587c.-220T>A1.000
rpoB759606c.-201T>C1.000
rpoB759635c.-172C>T1.000
rpoB760106c.300G>C1.000
rpoB760112c.306T>C1.000
rpoB760118c.312T>C1.000
rpoB760121c.315T>C1.000
rpoB760172c.366G>C1.000
rpoB760193c.387C>G1.000
rpoB760196c.390C>G1.000
rpoB760202c.396G>A1.000
rpoB760223c.417T>C1.000
rpoB760235c.429T>C1.000
rpoB760256c.450C>T1.000
rpoB760298c.492G>C1.000
rpoB760307c.501T>C1.000
rpoB760328c.522G>C1.000
rpoB760340c.534G>T1.000
rpoB760343c.537G>C1.000
rpoB760361c.555T>C1.000
rpoB760625c.819C>A1.000
rpoB760868c.1062C>G1.000
rpoB760919c.1113C>G1.000
rpoB760920c.1114C>T1.000
rpoB760928c.1122G>C1.000
rpoB760946c.1140A>G1.000
rpoB760971c.1165C>A1.000
rpoB760994c.1188G>A1.000
rpoB761006c.1200C>T1.000
rpoB761015c.1209G>C1.000
rpoB761027c.1221A>G1.000
rpoB761036c.1230G>A1.000
rpoB761037c.1231T>C1.000
rpoB761051c.1245G>C1.000
rpoB761066c.1260G>C1.000
rpoB761096c.1290G>C1.000
rpoB761097c.1291A>T1.000
rpoB761102c.1296A>G1.000
rpoB761132c.1326G>C1.000
rpoB761133c.1327T>C1.000
rpoB761168c.1362C>G1.000
rpoB761180c.1374A>C1.000
rpoB761183c.1377T>G1.000
rpoB761234c.1428G>C1.000
rpoB761249c.1443A>G1.000
rpoB761255c.1449T>G1.000
rpoB761261c.1455G>T1.000
rpoB761273c.1467T>C1.000
rpoB761300c.1494G>A1.000
rpoB761318c.1512G>C1.000
rpoB761327c.1521A>G1.000
rpoB761408c.1602G>C1.000
rpoB761423c.1617T>C1.000
rpoB761435c.1629T>C1.000
rpoB761438c.1632G>T1.000
rpoB761441p.Asp545Glu1.000
rpoB761444c.1638T>C1.000
rpoB761447c.1641C>G1.000
rpoB761471c.1665C>G1.000
rpoB761483c.1677G>C1.000
rpoB761492c.1686G>C1.000
rpoB761502p.Pro566Ala1.000
rpoB761510c.1704T>G1.000
rpoB761537c.1731C>G1.000
rpoB761954c.2148C>G1.000
rpoB761990c.2184G>C1.000
rpoB762218c.2412T>G1.000
rpoB762224c.2418C>G1.000
rpoB762236c.2430G>A1.000
rpoB762284c.2478G>C1.000
rpoB762293c.2487T>C1.000
rpoB762776c.2970C>T1.000
rpoB762782c.2976T>C0.933
rpoB762799p.Ala998Gly1.000
rpoB762812c.3006C>G1.000
rpoB762813p.Met1003Val1.000
rpoB762827c.3021G>C1.000
rpoB762830c.3024C>T1.000
rpoB762857c.3051C>G1.000
rpoB762860c.3054G>T1.000
rpoB762899c.3093G>C1.000
rpoB762929c.3123G>C1.000
rpoB762995c.3189G>C1.000
rpoB763028c.3222T>C1.000
rpoB763031c.3225T>G0.923
rpoB763034c.3228C>G1.000
rpoB763040c.3234C>G1.000
rpoB763050c.3244C>T1.000
rpoB763070c.3264T>C1.000
rpoB763076c.3270C>T1.000
rpoB763085c.3279C>G1.000
rpoB763094c.3288G>C1.000
rpoB763115c.3309T>C1.000
rpoB763124c.3318C>T1.000
rpoB763127c.3321G>C1.000
rpoB763169c.3363A>G1.000
rpoC763375c.6C>A1.000
rpoC763408c.39T>C1.000
rpoC763411c.42T>G1.000
rpoC763414c.45T>C1.000
rpoC763430c.61A>C1.000
rpoC763435c.66A>G1.000
rpoC763444c.75T>C1.000
rpoC763456c.87A>G1.000
rpoC763468c.99G>C1.000
rpoC763486c.117T>C1.000
rpoC763505c.136C>T1.000
rpoC763561c.192G>A1.000
rpoC763600c.231C>T1.000
rpoC763606c.237C>T1.000
rpoC763618c.249C>A1.000
rpoC763633c.264T>C1.000
rpoC763636c.267T>G1.000
rpoC763639c.270G>A1.000
rpoC763658c.289C>T1.000
rpoC763666c.297G>A1.000
rpoC763696c.327T>C1.000
rpoC763699c.330G>C1.000
rpoC763702c.333C>G1.000
rpoC763708c.339G>C1.000
rpoC763714c.345G>C1.000
rpoC763717c.348T>C1.000
rpoC763732c.363C>G1.000
rpoC763735c.366G>C1.000
rpoC763744c.375G>C1.000
rpoC763765c.396T>C1.000
rpoC763771c.402C>T1.000
rpoC763781p.Ser138Ala1.000
rpoC763801c.432C>G1.000
rpoC763807c.438T>C1.000
rpoC763813c.444C>G1.000
rpoC763819c.450G>C1.000
rpoC764161c.792G>C1.000
rpoC764203c.834G>C1.000
rpoC764206p.Asp279Glu1.000
rpoC764217p.Asn283Ser1.000
rpoC764278c.909A>G1.000
rpoC764284c.915G>C1.000
rpoC764317c.948C>T1.000
rpoC764344c.975C>T1.000
rpoC764587c.1218C>G1.000
rpoC764674c.1305G>A1.000
rpoC764681c.1312C>T1.000
rpoC764746c.1377G>T1.000
rpoC764752c.1383G>C1.000
rpoC764755c.1386C>T1.000
rpoC764764c.1395T>C1.000
rpoC764767c.1398G>C1.000
rpoC764791c.1422C>G1.000
rpoC764800c.1431G>A1.000
rpoC764803c.1434C>T1.000
rpoC764809c.1440C>T1.000
rpoC764815c.1446A>G1.000
rpoC764830c.1461C>G1.000
rpoC764833c.1464A>G1.000
rpoC764888c.1519T>C1.000
rpoC764902c.1533C>G1.000
rpoC764911c.1542A>G1.000
rpoC764918p.Val517Ile1.000
rpoC764923c.1554A>G1.000
rpoC764932c.1563C>G1.000
rpoC764948c.1579T>C1.000
rpoC764968c.1599T>C1.000
rpoC765430c.2061G>A1.000
rpoC765445c.2076G>T1.000
rpoC765451c.2082C>G1.000
rpoC765452p.Ala695Ser1.000
rpoC765478c.2109T>C1.000
rpoC765496c.2127C>G1.000
rpoC765499c.2130C>G1.000
rpoC765676c.2307G>A1.000
rpoC765826c.2457T>A1.000
rpoC765835c.2466C>T1.000
rpoC765850c.2481G>C1.000
rpoC765883c.2514C>G1.000
rpoC765886c.2517C>G1.000
rpoC765892c.2523T>C1.000
rpoC765910c.2541G>C1.000
rpoC765934c.2565C>T1.000
rpoC765952c.2583G>C1.000
rpoC765967c.2598C>T1.000
rpoC765979c.2610C>G1.000
rpoC765994c.2625A>T1.000
rpoC765997c.2628T>C1.000
rpoC766021c.2652G>C1.000
rpoC766312c.2943T>C1.000
rpoC766315c.2946C>G1.000
rpoC766324c.2955C>T1.000
rpoC766351c.2982C>G1.000
rpoC766360c.2991C>T1.000
rpoC766381c.3012C>T1.000
rpoC766384c.3015A>G1.000
rpoC766387c.3018C>G1.000
rpoC766393c.3024C>G1.000
rpoC766397c.3028C>T1.000
rpoC766408c.3039C>T1.000
rpoC766417c.3048C>T1.000
rpoC766426c.3057C>T1.000
rpoC766483c.3114G>C1.000
rpoC766486c.3117A>G1.000
rpoC766492c.3123T>C1.000
rpoC766495c.3126C>T1.000
rpoC766657c.3288A>G1.000
rpoC766672c.3303T>C1.000
rpoC766681c.3312C>T1.000
rpoC766684c.3315C>G1.000
rpoC766700c.3331C>T1.000
rpoC766714c.3345G>C1.000
rpoC766726c.3357T>C1.000
rpoC766747c.3378C>T1.000
rpoC766765c.3396A>C1.000
rpoC766774c.3405T>C1.000
rpoC766792c.3423C>G1.000
rpoC766795c.3426C>T1.000
rpoC766801c.3432C>T1.000
rpoC766804c.3435A>G1.000
rpoC766843c.3474T>G1.000
rpoC766864c.3495G>C1.000
rpoC766894c.3525T>C1.000
rpoC766895c.3526T>C1.000
rpoC766900c.3531T>C1.000
rpoC766903c.3534C>T1.000
rpoC766907c.3538C>T1.000
rpoC766918c.3549C>T1.000
rpoC766921c.3552G>C1.000
rpoC766933c.3564A>G1.000
rpoC766945c.3576A>G1.000
rpoC766963c.3594T>C1.000
rpoC767059c.3690T>G1.000
rpoC767062c.3693C>A1.000
rpoC767098c.3729T>C1.000
rpoC767119c.3750A>G1.000
rpoC767167c.3798C>T1.000
rpoC767180p.Ala1271Gln1.000
rpoC767185c.3816G>T1.000
rpoC767191c.3822C>G1.000
rpoC767200c.3831G>A1.000
rpoC767206c.3837C>A1.000
rpoC767209c.3840T>G1.000
rpoC767212c.3843G>C1.000
rpoC767221c.3852C>G1.000
rpoC767233c.3864T>C1.000
rpsL781709c.150G>C1.000
rpsL781715c.156T>C1.000
rpsL781718c.159C>G1.000
rpsL781721c.162C>G1.000
rpsL781728c.169T>C1.000
rpsL781742c.183C>T1.000
rpsL781760c.201T>C1.000
rpsL781808c.249C>T1.000
rpsL781832c.273T>C1.000
rpsL781841c.282C>G1.000
rpsL781847c.288G>A1.000
rpsL781916c.357T>C1.000
rpsL781929p.Gly124Ser1.000
rplC800817c.9A>C1.000
rplC800844c.36T>C1.000
rplC800865c.57A>G1.000
rplC800867p.Ser20Asn1.000
rplC800877c.69A>C1.000
rplC800907c.99C>G1.000
rplC800913c.105G>C1.000
rplC800916c.108A>T1.000
rplC800922c.114C>G1.000
rplC800934c.126C>G1.000
rplC800937c.129A>G1.000
rplC800946c.138T>G1.000
rplC800949c.141T>C1.000
rplC800955c.147C>G1.000
rplC800958c.150G>A1.000
rplC800970c.162T>C1.000
rrs1471935r.90t>c1.000
rrs1471969r.124t>c1.000
rrs1471970r.125g>a1.000
rrs1471984r.139t>a1.000
rrs1471985r.140t>c1.000
rrs1472040r.195t>c1.000
rrs1472053r.208agc>a1.000
rrs1472061r.216a>t1.000
rrs1472075r.230a>g1.000
rrs1472969r.1124a>g1.000
rrs1472970r.1125c>g1.000
rrs1472977r.1132g>c1.000
rrs1472978r.1133t>c1.000
rrs1473120r.1275c>ct1.000
rrs1473123r.1278a>t1.000
rrl1473731r.74t>a1.000
rrl1473806r.149c>t1.000
rrl1473877r.220g>a1.000
rrl1473887r.230t>a1.000
rrl1473888r.231t>a1.000
rrl1473898r.241c>t1.000
rrl1473924r.267a>at1.000
rrl1473981r.324g>c1.000
rrl1473986r.329t>c1.000
rrl1473995r.338g>t1.000
rrl1474009r.352a>g1.000
rrl1474034r.377g>a1.000
rrl1474083r.426c>t1.000
rrl1474103r.446a>t1.000
rrl1474140r.483c>t1.000
rrl1474151r.494c>t1.000
rrl1474201r.544t>a1.000
rrl1474285r.628cct>c1.000
rrl1474292r.635ttcctctccggagg>t1.000
rrl1474306r.649a>c1.000
rrl1474308r.651g>t1.000
rrl1474310r.653t>g0.917
rrl1474362r.705a>g1.000
rrl1474376r.719t>c1.000
rrl1474632r.975g>t1.000
rrl1474639r.982g>a1.000
rrl1474673r.1016t>c1.000
rrl1474717r.1060a>t1.000
rrl1474794r.1137c>a1.000
rrl1474831r.1174a>g1.000
rrl1474950r.1293g>a1.000
rrl1475005r.1348c>t1.000
rrl1475006r.1349a>g1.000
rrl1475028r.1371g>a1.000
rrl1475061r.1404c>t1.000
rrl1475213r.1556c>t1.000
rrl1475266r.1609t>c1.000
rrl1475273r.1616t>g1.000
rrl1475289r.1632g>a1.000
rrl1475290r.1633a>g1.000
rrl1475291r.1634a>c0.941
rrl1475315r.1658a>t1.000
rrl1475333r.1676t>c1.000
rrl1475355r.1698c>t1.000
rrl1475369r.1712g>a1.000
rrl1475403r.1746t>a1.000
rrl1475429r.1772g>a1.000
rrl1475526r.1869c>a1.000
rrl1475608r.1951t>c1.000
rrl1475638r.1981c>t1.000
rrl1475659r.2002g>a1.000
rrl1475988r.2331a>g1.000
rrl1476035r.2378g>a1.000
rrl1476049r.2392c>t1.000
rrl1476086r.2429g>a1.000
rrl1476089r.2432t>c1.000
rrl1476095r.2438c>g1.000
rrl1476115r.2458t>c1.000
rrl1476117r.2460g>c1.000
rrl1476224r.2567a>g1.000
rrl1476251r.2594t>c1.000
rrl1476281r.2624t>c1.000
rrl1476297r.2640c>t1.000
rrl1476299r.2642c>t1.000
rrl1476529r.2872a>g1.000
rrl1476580r.2923g>a1.000
rrl1476597r.2940g>a1.000
rrl1476619r.2962c>t1.000
rrl1476628r.2971t>a1.000
rrl1476679r.3022t>c1.000
rrl1476726r.3069a>g1.000
rrl1476732r.3075t>c1.000
rrl1476755r.3098g>a1.000
fabG11673568c.129C>G1.000
fabG11673574c.135C>G1.000
rpsA1833661c.120A>G1.000
rpsA1833694c.153G>T1.000
rpsA1833718c.177C>T1.000
rpsA1833724c.183C>G1.000
rpsA1833727c.186G>C1.000
rpsA1833802c.261A>G1.000
rpsA1833928c.387G>C1.000
rpsA1833949c.408T>C1.000
rpsA1833979c.438T>C1.000
rpsA1834000c.459G>C1.000
rpsA1834015c.474G>C1.000
rpsA1834024c.483G>A1.000
rpsA1834030c.489C>G1.000
rpsA1834051c.510G>A1.000
rpsA1834102c.561T>G1.000
rpsA1834105c.564C>G1.000
rpsA1834135c.594G>C1.000
rpsA1834495c.954G>A1.000
rpsA1834528c.987T>C1.000
rpsA1834546c.1005T>C1.000
rpsA1834609c.1068T>C1.000
rpsA1834615c.1074C>T1.000
rpsA1834618c.1077G>C1.000
rpsA1834633c.1092A>G1.000
rpsA1834639c.1098T>C1.000
rpsA1834690c.1149T>C1.000
kasA2518162c.48G>A1.000
kasA2518187p.Ile25Val1.000
kasA2518248p.Ala45Val1.000
kasA2518252c.138C>T1.000
kasA2518279c.165T>C1.000
kasA2518283p.Ala57Pro1.000
kasA2518561c.447T>C1.000
kasA2518756c.642G>C1.000
kasA2518783c.669T>C1.000
kasA2518789c.675G>T1.000
kasA2518795c.681C>G1.000
kasA2518798c.684G>C1.000
kasA2518816c.702C>T1.000
kasA2518822c.708C>T1.000
kasA2518825c.711T>C0.917
kasA2518855c.741C>G1.000
kasA2518856p.Ile248Leu1.000
kasA2518864c.750G>C1.000
kasA2518885c.771T>C1.000
kasA2518903c.789C>T1.000
kasA2518906c.792A>G1.000
kasA2518910c.796C>T1.000
kasA2518939c.825T>C1.000
kasA2518942c.828T>C1.000
folC2747071c.528G>A1.000
folC2747086c.513T>G1.000
folC2747089c.510C>G1.000
folC2747107c.492C>G1.000
folC2747110c.489A>G1.000
folC2747113c.486G>C1.000
folC2747116c.483C>G1.000
thyA3073977c.495T>C1.000
thyA3073989c.483A>G1.000
thyA3073997c.475G>A1.000
thyA3074004c.468A>G1.000
thyA3074031c.441A>G1.000
thyA3074037c.435G>C1.000
thyA3074045c.427G>A1.000
thyA3074053p.Arg140Gln1.000
thyA3074057p.Glu139Pro1.000
thyA3074061p.Glu137Asp1.000
thyA3074091c.381G>C1.000
thyA3074123p.Asp117Asn1.000
thyA3074391c.81G>C1.000
thyA3074397c.75T>G1.000
thyA3074409c.63G>A1.000
fbiA3640298c.-245A>G1.000
fbiA3640318c.-225A>T1.000
fbiA3640365c.-178C>G1.000
fbiA3641286c.744C>A1.000
fbiA3641288p.Glu249Gly1.000
fbiA3641292c.750G>A1.000
fbiA3641314p.Thr258Ala1.000
fbiA3641319c.777C>T1.000
fbiA3641322c.780T>C1.000
fbiA3641328c.786T>A1.000
embC4240777c.915G>A1.000
embC4240780c.918T>C1.000
embC4240783c.921G>C1.000
embC4240795c.933C>G1.000
embC4240801c.939C>T1.000
embC4240831c.969T>C1.000
embC4241095c.1233C>T1.000
embC4241107c.1245G>C1.000
embC4241140c.1278A>G1.000
embC4241153p.Ile431Leu1.000
embC4241161c.1299C>G1.000
embC4241162c.1300T>C1.000
embC4241167c.1305C>G0.957
embC4241185c.1323G>C1.000
embC4241197c.1335G>C1.000
embC4241230c.1368A>G1.000
embA4243228c.-5G>C1.000
embA4243240p.His3Leu1.000
embA4243271c.39A>C1.000
embA4243279p.Ala16Val1.000
embA4245083c.1851A>C1.000
embA4245101c.1869G>C1.000
embA4245110c.1878C>T1.000
embA4245137c.1905T>C1.000
embA4245149c.1917C>G1.000
embA4245182c.1950T>C1.000
embA4245186p.Thr652Ala1.000
embA4245662c.2430G>C1.000
embA4245674c.2442A>T1.000
embA4245677c.2445G>C1.000
embA4245683c.2451C>T1.000
embA4245693p.Ile821Val1.000
embA4245714c.2482C>T1.000
embA4245725c.2493A>G1.000
embA4245726c.2494T>C1.000
embA4245734c.2502G>C1.000
embA4245737c.2505A>T1.000
embA4245764c.2532G>C1.000
embA4245772p.Asn847Thr1.000
embA4246359p.Ala1043Ser1.000
embA4246373c.3141T>C1.000
embA4246376c.3144G>C1.000
embA4246398p.Ser1056Thr1.000
embA4246413p.His1061Tyr1.000
embB4246828c.315A>G1.000
embB4246843c.330T>C1.000
embB4247398c.885G>C1.000
embB4247401c.888T>C1.000
embB4247404c.891G>C1.000
embB4247407c.894G>C1.000
embB4247440c.927C>G1.000
embB4247470c.957T>C1.000
embB4247497c.984T>C1.000
embB4247500c.987C>G1.000
embB4247512c.999T>C1.000
embB4247554c.1041T>C1.000
embB4247555p.Leu348Ile1.000
embB4247566c.1053C>G1.000
embB4247579p.Ala356Phe1.000
embB4247590c.1077A>G1.000
embB4247608c.1095G>C1.000
embB4247611c.1098G>C1.000
embB4247632c.1119C>G1.000
embB4247657p.Pro382Ala1.000
embB4247671c.1158G>A1.000
embB4247684c.1171T>C1.000
embB4247899p.Met462Ile1.000
embB4247932c.1419C>G1.000
embB4247948p.Val479Leu1.000
embB4247975p.Val488Ile1.000
embB4247989c.1476G>C1.000
embB4248001c.1488C>T1.000
embB4248007c.1494C>G1.000
embB4248042p.Ala510Gly1.000
embB4248052c.1539G>T1.000
embB4248055c.1542G>C1.000
embB4248058c.1545C>T1.000
embB4248061c.1548G>A1.000
embB4248064c.1551G>C1.000
embB4248070c.1557T>C1.000
embB4248094c.1581C>T1.000
embB4248178c.1665C>T1.000
embB4248206p.Ser565Gly1.000
embB4248214c.1701C>G1.000
embB4248217c.1704C>G1.000
embB4248220c.1707A>G1.000
embB4248233c.1720C>T1.000
embB4248252p.Gly580Ala1.000
embB4248266c.1753C>T1.000
embB4248277c.1764G>C1.000
embB4248280c.1767C>G1.000
embB4248316c.1803C>G1.000
embB4248319c.1806A>G1.000
embB4248334c.1821C>G1.000
embB4248349c.1836G>A1.000
embB4248358c.1845C>G1.000
embB4248361c.1848A>G1.000
embB4248379c.1866G>A1.000
embB4248407p.Leu632Val1.000
embB4248412p.Phe633Leu1.000
embB4248416p.Leu635Met1.000
embB4248424c.1911G>A1.000
embB4248430c.1917T>C1.000
embB4248448c.1935C>T1.000
embB4248457c.1944T>C1.000
embB4248472c.1959T>C1.000
embB4248496c.1983G>C1.000
embB4248504p.Asp664Ala1.000
embB4248508c.1995G>A1.000
embB4248514c.2001A>G1.000
embB4248535c.2022C>G1.000
ethA4326556c.918A>G1.000
ethA4326563p.Ala304Gly1.000
ethA4326565c.909C>A1.000
ethA4326591c.883A>G1.000
ethA4326598c.876T>C1.000
ethA4326610c.864G>C1.000
ethA4326613c.861G>A1.000

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;