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: 5cc55b05efbeb
Sample: 5cc55b05efbeb

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Summary
ID: 5cc55b05efbeb
Date: Sun Apr 28 08:51:34 2019
Strain: lineage4.2.1;lineage1.2.1
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
EthambutolRembB p.His312Arg (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
gyrB5449c.210T>C1.000
gyrB5455c.216T>C1.000
gyrB6178c.939C>T1.000
gyrB6181c.942C>G1.000
gyrB6196c.957C>G1.000
gyrB6214c.975G>C1.000
gyrB6247c.1008G>A1.000
gyrB6250c.1011A>G1.000
gyrB6253c.1014G>C1.000
gyrB6259p.Asp340Glu1.000
gyrB6280c.1041T>C1.000
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
gyrA7664c.363T>C1.000
gyrA7667c.366C>T1.000
gyrA7728c.427A>C1.000
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
gyrA7859c.558A>C1.000
gyrA7886c.585T>C1.000
gyrA7889c.588G>A1.000
gyrA7892c.591G>C1.000
gyrA7919p.Glu206Asp1.000
gyrA7923p.His208Tyr1.000
gyrA8294c.993T>C1.000
gyrA8315c.1014G>A1.000
gyrA8318c.1017C>G1.000
gyrA8324c.1023T>C1.000
gyrA8339c.1038A>G1.000
gyrA8340p.Ala347Ser1.000
gyrA8375c.1074G>C1.000
gyrA8382p.Leu361Met1.000
gyrA8393c.1092T>C1.000
gyrA8399c.1098T>C1.000
gyrA8402p.Asp367Glu1.000
gyrA8420c.1119T>C1.000
gyrA8421p.Val374Ile1.000
gyrA8433p.Thr378Arg1.000
gyrA8447c.1146C>A1.000
gyrA8450c.1149G>A1.000
gyrA8453c.1152A>C1.000
gyrA8462c.1161A>G1.000
gyrA8471c.1170T>C1.000
gyrA8486c.1185T>C1.000
gyrA8510c.1209G>A1.000
gyrA8513c.1212C>G1.000
gyrA8516c.1215T>C1.000
gyrA8519c.1218A>C1.000
gyrA8531c.1230G>A1.000
gyrA8546c.1245T>C1.000
gyrA8561c.1260A>G1.000
gyrA8562c.1261C>T1.000
gyrA8571c.1270C>T1.000
gyrA8603c.1302A>G1.000
gyrA8609c.1308G>C1.000
gyrA8619c.1318T>C1.000
gyrA8627c.1326C>T1.000
gyrA8633c.1332C>G1.000
gyrA8645c.1344C>T1.000
gyrA8655p.Ile452Val1.000
gyrA8666c.1365G>C1.000
gyrA8897c.1596T>C1.000
gyrA8903c.1602T>C1.000
gyrA8915c.1614A>G1.000
gyrA8924c.1623C>G1.000
gyrA8933c.1632G>A1.000
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
gyrA9230c.1929T>C1.000
gyrA9236c.1935G>C1.000
gyrA9242c.1941A>C1.000
gyrA9252p.Val651Ile1.000
gyrA9257c.1956C>T1.000
gyrA9284c.1983T>G1.000
gyrA9296c.1995T>C1.000
gyrA9304p.Gly668Glu1.000
gyrA9315c.2014C>T1.000
gyrA9323c.2022C>T1.000
gyrA9341c.2040C>G1.000
gyrA9345c.2044A>C1.000
gyrA9395c.2094G>C1.000
gyrA9398c.2097T>G1.000
gyrA9401c.2100G>A1.000
gyrA9413c.2112G>A1.000
gyrA9452c.2151G>C1.000
rpoB760142c.336C>G1.000
rpoB760172c.366G>C1.000
rpoB760181c.375T>C1.000
rpoB760184c.378A>G1.000
rpoB760193c.387C>G1.000
rpoB760196c.390C>G1.000
rpoB760202c.396G>A1.000
rpoB760223c.417T>C1.000
rpoB760235c.429T>C1.000
rpoB760256c.450C>T1.000
rpoB760361c.555T>C1.000
rpoB760424c.618C>G1.000
rpoB760430c.624T>C1.000
rpoB760591p.Val262Ala1.000
rpoB760604c.798G>A1.000
rpoB760607c.801G>C1.000
rpoB760611c.805T>C1.000
rpoB760625c.819C>A1.000
rpoB760646c.840C>G1.000
rpoB760655c.849A>G1.000
rpoB760661c.855A>C1.000
rpoB760664c.858G>C1.000
rpoB760859c.1053T>G1.000
rpoB760868c.1062C>G1.000
rpoB760919c.1113C>G1.000
rpoB760920c.1114C>T1.000
rpoB760946c.1140A>G1.000
rpoB760971c.1165C>A1.000
rpoB760994c.1188G>A1.000
rpoB761006c.1200C>T1.000
rpoB761015c.1209G>C1.000
rpoB761036c.1230G>A1.000
rpoB761037c.1231T>C1.000
rpoB761051c.1245G>C1.000
rpoB761066c.1260G>C1.000
rpoB761201c.1395G>A1.000
rpoB761204c.1398C>G1.000
rpoB761207c.1401C>T1.000
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
rpoB761346p.Val514Ile1.000
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
rpoB761537c.1731C>G1.000
rpoB761561c.1755C>G1.000
rpoB761564c.1758G>C1.000
rpoB761573c.1767C>G1.000
rpoB761579c.1773G>C1.000
rpoB761600c.1794T>G1.000
rpoB761603c.1797C>T1.000
rpoB761606c.1800C>G1.000
rpoB761612c.1806G>T1.000
rpoB761615c.1809A>C1.000
rpoB761636c.1830G>T1.000
rpoB761645c.1839C>G1.000
rpoB761648c.1842T>C1.000
rpoB761657c.1851C>G1.000
rpoB761675c.1869G>C1.000
rpoB761682c.1876C>T1.000
rpoB761687c.1881C>T1.000
rpoB761693c.1887G>C1.000
rpoB761708c.1902C>T1.000
rpoB761885c.2079T>C1.000
rpoB761891c.2085G>C1.000
rpoB761954c.2148C>G1.000
rpoB762053c.2247T>C1.000
rpoB762062c.2256T>C1.000
rpoB762065c.2259T>C1.000
rpoB762071c.2265C>T1.000
rpoB762083c.2277T>C1.000
rpoB762086c.2280G>C1.000
rpoB762119c.2313C>T1.000
rpoB762131c.2325C>G1.000
rpoB762134c.2328C>G1.000
rpoB762470c.2664G>C1.000
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>G1.000
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>T0.824
rpoB763127c.3321G>C1.000
rpoB763169c.3363A>G1.000
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
rpoC764044c.675T>C1.000
rpoC764083c.714A>G1.000
rpoC764161c.792G>C1.000
rpoC764203c.834G>C1.000
rpoC764206p.Asp279Glu1.000
rpoC764217p.Asn283Ser1.000
rpoC764254c.885G>C1.000
rpoC764266c.897T>C1.000
rpoC764269c.900G>C1.000
rpoC764272c.903G>T1.000
rpoC764278c.909A>G1.000
rpoC764284c.915G>C1.000
rpoC764344c.975C>T0.900
rpoC764347c.978G>C1.000
rpoC764419c.1050C>G1.000
rpoC764648c.1279C>A1.000
rpoC764653c.1284G>C1.000
rpoC764656c.1287C>T1.000
rpoC764668c.1299C>T1.000
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
rpoC764872c.1503A>G1.000
rpoC764875c.1506C>A1.000
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
rpoC765562c.2193G>C1.000
rpoC765583c.2214G>T1.000
rpoC765610c.2241C>T1.000
rpoC765612p.His748Arg1.000
rpoC765622p.Glu751Asp1.000
rpoC765628c.2259G>C1.000
rpoC765676c.2307G>A1.000
rpoC765688c.2319G>C1.000
rpoC765689c.2320C>T1.000
rpoC765694c.2325G>C1.000
rpoC765700c.2331T>C1.000
rpoC765724c.2355C>G1.000
rpoC765727c.2358T>C1.000
rpoC765734c.2365T>C1.000
rpoC765748c.2379C>T1.000
rpoC765784c.2415C>G1.000
rpoC765787c.2418C>T1.000
rpoC765790c.2421C>T1.000
rpoC765793c.2424C>G1.000
rpoC765796c.2427C>T1.000
rpoC765811c.2442T>C1.000
rpoC765814c.2445A>G1.000
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
rpoC766300c.2931C>G1.000
rpoC766303c.2934C>T1.000
rpoC766306c.2937C>T1.000
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>C0.923
rpoC766486c.3117A>G1.000
rpoC766492c.3123T>C1.000
rpoC766495c.3126C>T1.000
rpoC766519c.3150C>A1.000
rpoC766528c.3159T>C1.000
rpoC766534c.3165C>G1.000
rpoC766537c.3168G>A1.000
rpoC766543c.3174C>T1.000
rpoC766549c.3180G>T1.000
rpoC766645c.3276A>G1.000
rpoC766651c.3282T>C1.000
rpoC766654c.3285C>G1.000
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
rpoC766907c.3538C>T1.000
rpoC766918c.3549C>T1.000
rpoC766921c.3552G>C1.000
rpoC766933c.3564A>G1.000
rpoC766945c.3576A>G1.000
rpoC766963c.3594T>C1.000
rpoC766972c.3603G>C1.000
rpoC766975c.3606C>T1.000
rpoC766996c.3627C>T1.000
rpoC767002c.3633G>C1.000
rpoC767033c.3664T>A1.000
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
rpsL781571c.12C>T1.000
rpsL781586c.27C>A1.000
rpsL781608p.Ser17Ala1.000
rpsL781628c.69T>C1.000
rpsL781631c.72G>C1.000
rpsL781649c.90T>C1.000
rpsL781655c.96T>C1.000
rpsL781658c.99A>G1.000
rpsL781664c.105C>T1.000
rpsL781667c.108C>G1.000
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>C0.962
rpsL781808c.249C>T1.000
rpsL781832c.273T>C1.000
rpsL781841c.282C>G1.000
rpsL781847c.288G>A1.000
rpsL781865c.306G>C1.000
rpsL781868c.309T>C1.000
rpsL781871c.312G>C1.000
rpsL781877c.318T>A1.000
rpsL781880c.321C>G1.000
rpsL781892c.333A>G1.000
rpsL781898c.339A>T1.000
rpsL781916c.357T>C1.000
rpsL781929p.Gly124Ser1.000
rplC800797c.-12T>G1.000
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
rplC801246c.438C>G1.000
rplC801252c.444G>C1.000
rplC801267c.459A>T1.000
rplC801276c.468G>C1.000
rplC801297c.489C>T1.000
rplC801312c.504G>C1.000
rplC801339c.531T>G1.000
rplC801341p.Leu178Gln1.000
rplC801348c.540T>G1.000
rplC801357c.549T>C1.000
rplC801372c.564G>A1.000
rrs1471935r.90t>c1.000
rrs1471969r.124t>c1.000
rrs1471970r.125g>a1.000
rrs1471984r.139t>a1.000
rrs1471985r.140t>c1.000
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
rrs1472969r.1124a>g1.000
rrs1472970r.1125c>g1.000
rrs1472977r.1132g>c1.000
rrs1472978r.1133t>c1.000
rrs1473120r.1275c>ct0.923
rrs1473123r.1278a>t1.000
rrl1473541c.-117G>A1.000
rrl1473542c.-116C>T1.000
rrl1473571c.-87C>T1.000
rrl1473648c.-10TTTG>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
rrl1473980r.323a>at0.625
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
rrl1474362r.705a>g1.000
rrl1474376r.719t>c1.000
rrl1474419r.762a>t1.000
rrl1474427r.770a>g1.000
rrl1474430r.773c>a1.000
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
rrl1474961r.1304t>g1.000
rrl1474962r.1305t>c1.000
rrl1474963r.1306g>a1.000
rrl1474964r.1307t>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>c1.000
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>a0.952
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
fabG11673871c.432C>T1.000
fabG11673916c.477A>T1.000
fabG11673919c.480G>C1.000
fabG11673922c.483T>C1.000
fabG11673925c.486C>G1.000
fabG11673946c.507C>A1.000
fabG11673955c.516G>C1.000
fabG11673960p.Ala174Val1.000
fabG11673970c.531C>G1.000
fabG11673976c.537T>C1.000
fabG11673982c.543G>C1.000
fabG11673988c.549G>C1.000
fabG11673991c.552C>G1.000
rpsA1833512c.-30AC>A1.000
rpsA1833554p.Thr5Ala1.000
rpsA1833589c.48A>T1.000
rpsA1833593p.Ser18Thr1.000
rpsA1833604c.63C>T1.000
rpsA1833610c.69C>A1.000
rpsA1833802c.261A>G1.000
rpsA1833841c.300C>G1.000
rpsA1833847c.306C>G1.000
rpsA1833850c.309C>G1.000
rpsA1833856c.315A>G1.000
rpsA1833874c.333T>C1.000
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
rpsA1834177c.636A>C1.000
rpsA1834186c.645C>G1.000
rpsA1834189c.648G>C1.000
rpsA1834195c.654G>C1.000
rpsA1834213c.672G>C1.000
rpsA1834222c.681T>C1.000
rpsA1834225c.684C>G1.000
rpsA1834249c.708T>C1.000
rpsA1834261c.720A>G1.000
rpsA1834264c.723G>C1.000
rpsA1834297c.756C>T1.000
rpsA1834303c.762T>G1.000
rpsA1834306c.765T>C1.000
rpsA1834336c.795C>G1.000
rpsA1834339c.798C>T1.000
rpsA1834348c.807T>C1.000
rpsA1834366c.825A>G1.000
rpsA1834369c.828C>G1.000
rpsA1834375c.834G>A1.000
rpsA1834396c.855G>C1.000
rpsA1834411c.870T>C1.000
rpsA1834417c.876G>C1.000
rpsA1834423c.882G>C1.000
rpsA1834451c.910T>C1.000
rpsA1834456c.915T>G1.000
rpsA1834468c.927A>G1.000
rpsA1834489c.948T>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
rpsA1834732c.1191T>C1.000
rpsA1834810c.1269C>G1.000
katG2155632c.480T>G1.000
katG2155637p.Leu159Ile1.000
katG2155641p.Lys157Asn1.000
katG2155649p.Tyr155His1.000
katG2155680c.432C>G1.000
katG2155691c.421A>G1.000
katG2155704c.408G>C1.000
kasA2518756c.642G>C1.000
kasA2518783c.669T>C1.000
kasA2518789c.675G>T1.000
kasA2518795c.681C>G1.000
kasA2518798c.684G>C1.000
kasA2518864c.750G>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
thyX3067832c.114G>A1.000
thyX3067838c.108G>C1.000
thyA3073929c.543A>G1.000
thyA3073932c.540G>A1.000
thyA3073947c.525C>G1.000
thyA3073953c.519A>G1.000
thyA3073956c.516C>G1.000
thyA3073962c.510C>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
thyA3074262c.210A>G1.000
thyA3074268c.204A>G1.000
thyA3074274c.198A>G1.000
thyA3074283c.189C>T1.000
thyA3074286c.186A>G1.000
thyA3074297c.175G>A1.000
thyA3074307c.165T>C1.000
thyA3074313c.159T>C1.000
thyA3074334c.138A>G1.000
thyA3074349c.123A>G1.000
thyA3074355c.117C>G1.000
thyA3074360c.112A>G1.000
thyA3074361c.111A>G1.000
thyA3074369c.103G>C1.000
thyA3074370p.Met34Ile1.000
thyA3074391c.81G>C1.000
thyA3074397c.75T>G1.000
thyA3074409c.63G>A1.000
fbiA3640269c.-274A>C1.000
fbiA3640282c.-261C>G1.000
fbiA3640298c.-245A>G1.000
fbiA3640318c.-225A>T1.000
fbiA3640365c.-178C>G1.000
alr3840248c.1173G>T1.000
alr3840272c.1149G>C1.000
alr3840275c.1146A>C1.000
alr3840293c.1128A>C1.000
alr3840296c.1125C>G1.000
embC4240087c.225T>C1.000
embC4240093c.231C>T1.000
embC4240105p.Asp81Glu1.000
embC4240106c.244T>C1.000
embC4240123c.261C>G1.000
embC4240128p.Gln89Arg1.000
embC4240150c.288A>G1.000
embC4240151p.Ser97Pro1.000
embC4240171c.309G>C1.000
embC4240175c.313T>C1.000
embC4240183c.321A>G1.000
embC4240201c.339G>C1.000
embC4240204c.342T>C1.000
embC4240207p.Lys115Asn1.000
embC4240801c.939C>T1.000
embC4240831c.969T>C1.000
embC4241741p.Val627Ile1.000
embC4241750p.Leu630Met1.000
embC4241755c.1893C>G1.000
embC4241761c.1899G>C1.000
embC4241788c.1926C>T1.000
embC4241791c.1929G>C1.000
embC4241797c.1935C>T1.000
embC4241809c.1947A>G1.000
embC4241818c.1956C>T1.000
embC4241821c.1959G>A1.000
embC4241824c.1962T>C1.000
embC4241836c.1974A>C1.000
embC4241845c.1983T>C1.000
embA4243271c.39A>C1.000
embA4243279p.Ala16Val1.000
embA4243301c.69G>C1.000
embA4243304c.72T>A1.000
embA4243311c.79C>T1.000
embA4244822c.1590G>A1.000
embA4244823p.Val531Met1.000
embA4244856p.Ala542Pro1.000
embA4244885c.1653A>G1.000
embA4244897c.1665T>G1.000
embA4244903c.1671G>C1.000
embA4244919c.1687C>T1.000
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
embA4245215c.1983A>C1.000
embA4245224c.1992T>C1.000
embA4245248c.2016G>A1.000
embA4245257c.2025A>G1.000
embA4245263c.2031A>G1.000
embA4245281c.2049C>G1.000
embA4245285c.2053T>C1.000
embA4245620c.2388T>C1.000
embA4245623c.2391G>A1.000
embA4245662c.2430G>C1.000
embA4245674c.2442A>T1.000
embA4245677c.2445G>C1.000
embA4245683c.2451C>T1.000
embA4245693p.Ile821Val1.000
embA4245714c.2482C>T1.000
embA4245737c.2505A>T1.000
embA4246268c.3036G>A1.000
embA4246279p.Ala1016Val1.000
embA4246292c.3060A>G1.000
embA4246307c.3075G>C1.000
embA4246316c.3084T>C1.000
embA4246346c.3114C>G1.000
embA4246359p.Ala1043Ser1.000
embA4246373c.3141T>C1.000
embA4246376c.3144G>C1.000
embA4246398p.Ser1056Thr1.000
embA4246413p.His1061Tyr1.000
embB4247440c.927C>G1.000
embB4247470c.957T>C1.000
embB4247497c.984T>C1.000
embB4247500c.987C>G1.000
embB4247512c.999T>C1.000
embB4247858c.1345C>T1.000
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
embB4248130c.1617G>C1.000
embB4248142c.1629T>C1.000
embB4248143c.1630T>C1.000
embB4248154c.1641G>T0.929
embB4248157c.1644A>T1.000
embB4248163c.1650G>A1.000
embB4248169c.1656C>T1.000
embB4248175c.1662G>A1.000
embB4248178c.1665C>T1.000
embB4248206p.Ser565Gly1.000
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
ethA4326298c.1176C>T1.000
ethA4326304c.1170G>C1.000
ethA4326322c.1152A>G0.917
ethA4326331c.1143G>C0.917
ethA4326337c.1137G>A0.917
ethA4326343c.1131G>A0.917
ethA4326346c.1128G>C0.917
ethA4326352c.1122A>C0.917
ethA4326556c.918A>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.

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