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: 5cc54bcc42ea3
Sample: 5cc54bcc42ea3

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Summary
ID: 5cc54bcc42ea3
Date: Sun Apr 28 07:45:49 2019
Strain: lineage4.6;lineage4.7;lineage4.6.2.2
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
EthambutolRembB p.Tyr384Asn (1.00), embB p.Asn399Asp (1.00)
Pyrazinamide
StreptomycinRrrs r.462c>t (1.00)
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage4.6Euro-AmericanT;LAMNone
lineage4.7Euro-American (mainly T)T1;T5None
lineage4.6.2.2Euro-American (Cameroon)LAM10-CAMRD726

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6193c.954G>A0.917
gyrB6196c.957C>G1.000
gyrB6208c.969G>A1.000
gyrB6214c.975G>A1.000
gyrB6898c.1659G>C1.000
gyrA7361c.60C>T1.000
gyrA7362p.Glu21Gln1.000
gyrA7370c.69G>A1.000
gyrA7391c.90C>T1.000
gyrA7394c.93T>C1.000
gyrA7415c.114C>G1.000
gyrA7427c.126G>T1.000
gyrA7430c.129G>A1.000
gyrA7451c.150C>G1.000
gyrA7457c.156T>C1.000
gyrA7469c.168C>G1.000
gyrA7475c.174A>C1.000
gyrA7480p.Phe60Tyr1.000
gyrA7484c.183T>C1.000
gyrA7490c.189C>G1.000
gyrA8090c.789C>G1.000
gyrA8096c.795T>C1.000
gyrA8099c.798T>C1.000
gyrA8121c.820T>C1.000
gyrA8138c.837C>T1.000
gyrA8156c.855T>C1.000
gyrA8162c.861C>T1.000
gyrA8168c.867A>G1.000
gyrA8174c.873C>T1.000
gyrA8177c.876A>C1.000
gyrA8207c.906T>C1.000
gyrA8213c.912C>T1.000
gyrA8219c.918T>C1.000
gyrA8225c.924T>C1.000
gyrA8228c.927G>A1.000
gyrA8234c.933T>C1.000
gyrA8237c.936A>G1.000
gyrA8711c.1410A>C1.000
gyrA8717c.1416C>G1.000
gyrA8723c.1422G>C1.000
gyrA8729c.1428T>A1.000
gyrA8730p.Gly477Lys1.000
gyrA8756c.1455A>G1.000
gyrA8762c.1461G>C1.000
gyrA8765p.Asp488Glu1.000
gyrA8767p.Arg489Lys1.000
gyrA8783c.1482G>T1.000
gyrA8810c.1509A>C1.000
gyrA8813c.1512C>T1.000
gyrA8819c.1518C>T1.000
gyrA9197c.1896G>C1.000
gyrA9200c.1899A>G1.000
gyrA9230c.1929T>C1.000
gyrA9248c.1947G>C1.000
gyrA9252p.Val651Ile1.000
gyrA9265p.Asp655Gly1.000
gyrA9267p.Asn656Glu1.000
gyrA9281c.1980C>G1.000
gyrA9284c.1983T>C1.000
gyrA9317c.2016G>A1.000
gyrA9332c.2031C>T1.000
gyrA9365p.Glu688Asp0.900
rpoB760223c.417T>C1.000
rpoB760235c.429T>C1.000
rpoB760253c.447T>C1.000
rpoB760343c.537G>C1.000
rpoB760361c.555T>C1.000
rpoB760376p.Asp190Glu1.000
rpoB760381p.Thr192Met1.000
rpoB760424c.618C>G1.000
rpoB760430c.624T>C1.000
rpoB760454c.648C>T1.000
rpoB760457c.651C>T1.000
rpoB760463c.657C>T1.000
rpoB760938c.1132C>T1.000
rpoB760943c.1137C>T1.000
rpoB760946c.1140A>G1.000
rpoB760970c.1164G>C1.000
rpoB760982c.1176G>C1.000
rpoB760985c.1179G>C1.000
rpoB760988c.1182C>G1.000
rpoB760991c.1185G>C1.000
rpoB761015c.1209G>C1.000
rpoB761027c.1221A>G1.000
rpoB761036c.1230G>C1.000
rpoB761037c.1231T>C1.000
rpoB761054c.1248G>T1.000
rpoB761057c.1251G>C1.000
rpoB761168c.1362C>G1.000
rpoB761180c.1374A>C1.000
rpoB761189c.1383T>G1.000
rpoB761207c.1401C>T1.000
rpoB761249c.1443A>G1.000
rpoB761255c.1449T>G1.000
rpoB761261c.1455G>T1.000
rpoB761264c.1458C>G1.000
rpoB761267c.1461C>T1.000
rpoB761270c.1464C>T1.000
rpoB761282c.1476C>G1.000
rpoB761300c.1494G>A1.000
rpoB761327c.1521A>G1.000
rpoB761531c.1725C>G1.000
rpoB761537c.1731C>G1.000
rpoB761573c.1767C>G1.000
rpoB761579c.1773G>C1.000
rpoB761669c.1863C>T0.900
rpoB761675c.1869G>T0.900
rpoB761682c.1876C>T0.900
rpoB761768c.1962G>C1.000
rpoB761778p.Asn658Ala1.000
rpoB761792c.1986T>C1.000
rpoB761813c.2007T>C1.000
rpoB761885c.2079T>C1.000
rpoB761969c.2163G>A1.000
rpoB761990c.2184G>C1.000
rpoB761999c.2193G>C1.000
rpoB762008c.2202C>G1.000
rpoB762014c.2208C>T1.000
rpoB762047c.2241G>A1.000
rpoB762062c.2256T>C1.000
rpoB762065c.2259T>C1.000
rpoB762233c.2427G>C1.000
rpoB762246c.2440C>T1.000
rpoB762284c.2478G>C1.000
rpoB762293c.2487T>C1.000
rpoB762296c.2490G>A1.000
rpoB762314c.2508C>T1.000
rpoB762341c.2535G>C1.000
rpoB762347c.2541T>C1.000
rpoB762362p.Glu852Asp1.000
rpoB762368c.2562G>A1.000
rpoB762369c.2563T>C1.000
rpoB762374c.2568G>T1.000
rpoB762380c.2574T>C1.000
rpoB762395c.2589G>C1.000
rpoB762398c.2592T>C1.000
rpoB762401c.2595G>C1.000
rpoB762404c.2598T>C1.000
rpoB762410c.2604T>C1.000
rpoB762416c.2610A>G1.000
rpoB762458c.2652C>T1.000
rpoB762470c.2664G>T1.000
rpoB762483c.2677C>T1.000
rpoB762857c.3051C>G0.900
rpoB762917c.3111C>T1.000
rpoB762923c.3117C>G1.000
rpoB762929c.3123G>T1.000
rpoB762957c.3151C>T1.000
rpoB762962c.3156C>T1.000
rpoB762971c.3165G>C1.000
rpoB762995c.3189G>T0.947
rpoB762998c.3192G>A1.000
rpoB763028c.3222T>C1.000
rpoB763031c.3225T>C1.000
rpoB763034c.3228C>G1.000
rpoB763040c.3234C>G1.000
rpoB763053c.3247T>C1.000
rpoB763070c.3264T>C1.000
rpoB763085c.3279C>G1.000
rpoB763094c.3288G>C1.000
rpoB763115c.3309T>C1.000
rpoB763139c.3333C>T1.000
rpoB763142c.3336C>G1.000
rpoB763166c.3360A>G1.000
rpoB763169c.3363A>G1.000
rpoB763175c.3369G>A1.000
rpoC763375c.6C>A1.000
rpoC763402c.33C>T1.000
rpoC763417c.48C>T1.000
rpoC763444c.75T>C1.000
rpoC763456c.87A>G1.000
rpoC763468c.99G>C1.000
rpoC763486c.117T>C1.000
rpoC763492c.123G>A1.000
rpoC763528c.159G>A1.000
rpoC763531c.162G>T1.000
rpoC763546c.177A>G1.000
rpoC763573c.204G>T1.000
rpoC763576c.207C>T1.000
rpoC763594c.225C>T1.000
rpoC763603c.234C>T1.000
rpoC763660c.291T>G1.000
rpoC763666c.297G>A1.000
rpoC763669c.300C>G1.000
rpoC763702c.333C>G1.000
rpoC763714c.345G>A1.000
rpoC763723c.354G>C1.000
rpoC763732c.363C>G1.000
rpoC763735c.366G>C1.000
rpoC763747c.378G>A1.000
rpoC764040p.Ser224Thr1.000
rpoC764044c.675T>C1.000
rpoC764077c.708C>G1.000
rpoC764083c.714A>G1.000
rpoC764131c.762T>C1.000
rpoC764134c.765C>A1.000
rpoC764140c.771C>T1.000
rpoC764152c.783C>T1.000
rpoC764623c.1254C>A1.000
rpoC764626c.1257C>T1.000
rpoC764632c.1263T>C1.000
rpoC764650c.1281G>T1.000
rpoC764752c.1383G>T1.000
rpoC764764c.1395T>C1.000
rpoC764791c.1422C>G1.000
rpoC764803c.1434C>T1.000
rpoC764809c.1440C>T1.000
rpoC764812c.1443C>G1.000
rpoC764815c.1446A>G1.000
rpoC764824c.1455T>C1.000
rpoC764833c.1464A>G1.000
rpoC764858c.1489T>C1.000
rpoC764869c.1500C>G1.000
rpoC764888c.1519T>C1.000
rpoC764893c.1524T>C1.000
rpoC764902c.1533C>T1.000
rpoC764932c.1563C>A1.000
rpoC764968c.1599T>C1.000
rpoC764995c.1626C>T1.000
rpoC765007c.1638T>G0.900
rpoC765008c.1639T>C1.000
rpoC765011c.1642A>T0.900
rpoC765019c.1650A>G1.000
rpoC765040c.1671T>C1.000
rpoC765047c.1678T>C1.000
rpoC765052c.1683C>G1.000
rpoC765055c.1686C>T1.000
rpoC765079c.1710T>C1.000
rpoC765082c.1713G>C1.000
rpoC765085c.1716T>G1.000
rpoC765089c.1720T>C1.000
rpoC765100c.1731G>C1.000
rpoC765103c.1734G>A1.000
rpoC765129p.Tyr587Phe1.000
rpoC765352c.1983G>C1.000
rpoC765356p.Met663Val1.000
rpoC765383p.Met672Leu1.000
rpoC765409c.2040T>C1.000
rpoC765421c.2052C>G1.000
rpoC765454c.2085C>G1.000
rpoC765478c.2109T>C1.000
rpoC765493c.2124G>C1.000
rpoC765499c.2130C>A1.000
rpoC765589c.2220G>T1.000
rpoC765592c.2223C>T1.000
rpoC765625c.2256C>G1.000
rpoC765628c.2259G>C1.000
rpoC765640c.2271A>G1.000
rpoC765670c.2301C>T1.000
rpoC765688c.2319G>A1.000
rpoC765700c.2331T>C1.000
rpoC765734c.2365T>C1.000
rpoC765850c.2481G>C1.000
rpoC765934c.2565C>T1.000
rpoC765937c.2568T>A1.000
rpoC765958c.2589C>G1.000
rpoC765961c.2592G>A1.000
rpoC765967c.2598C>T1.000
rpoC765973c.2604C>A1.000
rpoC765979c.2610C>G1.000
rpoC765994c.2625A>T1.000
rpoC766082p.Ala905Gln1.000
rpoC766087c.2718C>G1.000
rpoC766096c.2727G>T1.000
rpoC766129c.2760C>G1.000
rpoC766135c.2766G>A1.000
rpoC766280p.Ser971Gly1.000
rpoC766291c.2922G>C1.000
rpoC766312c.2943T>G1.000
rpoC766315c.2946C>G1.000
rpoC766345c.2976T>C1.000
rpoC766348c.2979A>G1.000
rpoC766363c.2994G>C1.000
rpoC766366c.2997C>A1.000
rpoC766657c.3288A>G1.000
rpoC766660c.3291G>A1.000
rpoC766666c.3297C>G1.000
rpoC766693c.3324C>T1.000
rpoC766741c.3372G>C1.000
rpoC766769c.3400C>T1.000
rpoC766774c.3405T>C1.000
rpoC766798c.3429C>G1.000
rpoC766801c.3432C>T1.000
rpoC766804c.3435A>G1.000
rpoC766843c.3474T>G1.000
rpoC766861c.3492G>C1.000
rpoC766864c.3495G>C1.000
rpoC766882c.3513C>T1.000
rpoC766996c.3627C>T1.000
rpoC767002c.3633G>C1.000
rpoC767098c.3729T>C1.000
rpoC767119c.3750A>G1.000
rpoC767167c.3798C>T1.000
rpoC767180p.Ala1271Gln1.000
rpoC767185c.3816G>T1.000
rpoC767209c.3840T>C1.000
rpoC767221c.3852C>G1.000
rpoC767230c.3861G>C1.000
rpoC767233c.3864T>C1.000
rpsL781571c.12C>T1.000
rpsL781608p.Ser17Gly1.000
rpsL781631c.72G>T1.000
rpsL781649c.90T>C1.000
rpsL781655c.96T>C1.000
rpsL781682c.123T>C1.000
rpsL781694c.135G>C1.000
rpsL781715c.156T>C1.000
rpsL781718c.159C>T1.000
rpsL781721c.162C>T1.000
rpsL781728c.169T>C1.000
rpsL781742c.183C>T1.000
rpsL781751c.192G>C1.000
rpsL781754c.195G>C1.000
rpsL781760c.201T>C1.000
rpsL781763c.204C>G1.000
rpsL781766c.207C>T1.000
rpsL781787c.228G>A1.000
rpsL781808c.249C>T1.000
rpsL781811c.252C>T1.000
rpsL781827c.268C>T1.000
rpsL781832c.273T>C1.000
rpsL781865c.306G>C1.000
rpsL781868c.309T>C1.000
rpsL781871c.312G>C1.000
rpsL781880c.321C>G1.000
rplC801222c.414T>C1.000
rplC801255c.447C>T1.000
rplC801258c.450C>G1.000
rplC801267c.459A>C1.000
rplC801270c.462T>C1.000
rplC801276c.468G>T1.000
rplC801282c.474G>C1.000
rplC801307p.Ala167Ser1.000
rplC801312c.504G>C1.000
rplC801324c.516T>C1.000
rrs1471923r.78t>c1.000
rrs1471925r.80t>c1.000
rrs1471932r.87a>g1.000
rrs1471934r.89a>g1.000
rrs1471970r.125g>a1.000
rrs1472028r.183a>c1.000
rrs1472031r.186g>a1.000
rrs1472033r.188a>g1.000
rrs1472034r.189t>c1.000
rrs1472040r.195t>c1.000
rrs1472045r.200t>g1.000
rrs1472053r.208agc>a1.000
rrs1472061r.216a>t1.000
rrs1472075r.230a>g1.000
rrs1472489r.644a>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
rrs1473290r.1445c>t1.000
rrl1473571c.-87C>T1.000
rrl1473594c.-64A>AT0.800
rrl1473600c.-58A>G1.000
rrl1473612c.-46A>C1.000
rrl1473614c.-44C>T1.000
rrl1473797r.140g>c1.000
rrl1473806r.149c>t1.000
rrl1473813r.156c>t1.000
rrl1473876r.219g>a1.000
rrl1473877r.220g>a1.000
rrl1473887r.230t>a1.000
rrl1473888r.231t>a1.000
rrl1473899r.242a>t1.000
rrl1473923r.266c>t1.000
rrl1473924r.267a>at1.000
rrl1473938r.281g>a1.000
rrl1473943r.286g>t1.000
rrl1473974r.317t>c1.000
rrl1473986r.329t>c1.000
rrl1473987r.330g>a1.000
rrl1473995r.338g>t1.000
rrl1474001r.344c>t1.000
rrl1474009r.352a>g1.000
rrl1474018r.361g>a1.000
rrl1474056r.399t>c1.000
rrl1474083r.426c>t1.000
rrl1474084r.427g>t1.000
rrl1474093r.436g>t1.000
rrl1474103r.446a>t1.000
rrl1474127r.470g>a1.000
rrl1474139r.482c>t1.000
rrl1474140r.483c>t1.000
rrl1474151r.494c>t1.000
rrl1474181r.524c>t1.000
rrl1474289r.632cttttcctctccggag>c0.810
rrl1474291r.634tttcctctccggagga>t1.000
rrl1474308r.651g>t1.000
rrl1474310r.653t>g1.000
rrl1474447r.790g>a1.000
rrl1474627r.970g>a1.000
rrl1474632r.975g>t1.000
rrl1474639r.982g>a1.000
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
rrl1475007r.1350c>t1.000
rrl1475013r.1356g>a1.000
rrl1475061r.1404c>t1.000
rrl1475315r.1658a>t1.000
rrl1475333r.1676t>c1.000
rrl1475355r.1698c>t1.000
rrl1475369r.1712g>c1.000
rrl1475402r.1745c>t1.000
rrl1475429r.1772g>a1.000
rrl1475479r.1822c>t1.000
rrl1475480r.1823a>t1.000
rrl1475505r.1848g>a1.000
rrl1475526r.1869c>a1.000
rrl1475604r.1947a>c1.000
rrl1475607r.1950a>g1.000
rrl1475608r.1951t>c1.000
rrl1475619r.1962c>t1.000
rrl1475622r.1965g>t1.000
rrl1475635r.1978g>a1.000
rrl1475637r.1980t>a1.000
rrl1475659r.2002g>a1.000
rrl1475760r.2103c>t1.000
rrl1475763r.2106c>t1.000
rrl1475975r.2318c>t1.000
rrl1475977r.2320a>g1.000
rrl1475988r.2331a>t1.000
rrl1476032r.2375c>t1.000
rrl1476033r.2376t>c1.000
rrl1476035r.2378g>a1.000
rrl1476040r.2383c>t1.000
rrl1476086r.2429g>a1.000
rrl1476089r.2432t>c1.000
rrl1476095r.2438c>g1.000
rrl1476131r.2474c>t1.000
rrl1476214r.2557g>t1.000
rrl1476215r.2558c>t1.000
rrl1476529r.2872a>g1.000
rrl1476580r.2923g>a1.000
rrl1476594r.2937c>t1.000
rrl1476597r.2940g>a1.000
rrl1476603r.2946g>a1.000
rrl1476608r.2951c>t1.000
rrl1476619r.2962c>t1.000
rrl1476628r.2971t>a1.000
fabG11673916c.477A>T1.000
fabG11673922c.483T>C1.000
inhA1674703c.502T>C1.000
rpsA1833568c.27G>C1.000
rpsA1833595c.54T>C1.000
rpsA1833709c.168C>T1.000
rpsA1833724c.183C>G1.000
rpsA1833727c.186G>C1.000
rpsA1833742c.201A>G1.000
rpsA1833745c.204G>C1.000
rpsA1833748c.207C>G1.000
rpsA1833754c.213G>A1.000
rpsA1833772c.231C>T1.000
rpsA1833790c.249T>C1.000
rpsA1833802c.261A>G1.000
rpsA1833808c.267G>C1.000
rpsA1833811c.270G>C1.000
rpsA1833856c.315A>G1.000
rpsA1833874c.333T>C1.000
rpsA1833877c.336C>G1.000
rpsA1833916c.375C>A1.000
rpsA1833940c.399C>G1.000
rpsA1833970c.429G>C1.000
rpsA1833979c.438T>C1.000
rpsA1834000c.459G>C1.000
rpsA1834021c.480C>T1.000
rpsA1834030c.489C>G1.000
rpsA1834099c.558C>G1.000
rpsA1834102c.561T>G1.000
rpsA1834144c.603G>A1.000
rpsA1834177c.636A>C1.000
rpsA1834186c.645C>G1.000
rpsA1834189c.648G>C1.000
rpsA1834213c.672G>A1.000
rpsA1834231c.690T>G1.000
rpsA1834249c.708T>C1.000
rpsA1834252c.711C>G1.000
rpsA1834261c.720A>G1.000
rpsA1834264c.723G>C1.000
rpsA1834297c.756C>T1.000
rpsA1834303c.762T>G1.000
rpsA1834306c.765T>C1.000
rpsA1834330c.789C>T1.000
rpsA1834348c.807T>C1.000
rpsA1834366c.825A>G1.000
rpsA1834369c.828C>G1.000
rpsA1834396c.855G>T1.000
rpsA1834411c.870T>C1.000
rpsA1834417c.876G>C1.000
rpsA1834423c.882G>C1.000
rpsA1834435c.894G>C1.000
rpsA1834438c.897C>A1.000
rpsA1834451c.910T>C1.000
rpsA1834546c.1005T>C1.000
rpsA1834609c.1068T>C1.000
rpsA1834612c.1071G>A1.000
rpsA1834624c.1083G>A1.000
rpsA1834633c.1092A>G1.000
rpsA1834639c.1098T>C1.000
rpsA1834657c.1116G>A1.000
rpsA1834690c.1149T>C1.000
folC2747065c.534G>A1.000
thyX3067718c.228G>T1.000
thyX3067721c.225A>G1.000
thyX3067727c.219T>C1.000
fbiA3640260c.-283TC>T1.000
fbiA3640262c.-281G>T1.000
fbiA3640268c.-275T>G1.000
fbiA3640303c.-240TA>T1.000
fbiA3640308c.-235C>A1.000
fbiA3640347c.-196A>G1.000
fbiA3640365c.-178C>G1.000
fbiA3640377c.-166G>C1.000
embC4241050c.1188T>G1.000
embC4241053c.1191G>C1.000
embC4241059c.1197G>A1.000
embC4241077c.1215C>A1.000
embC4242877c.3015G>A1.000
embC4242880c.3018A>C1.000
embC4242883c.3021C>G1.000
embC4242892c.3030G>C1.000
embC4242901c.3039G>A1.000
embC4242919c.3057A>G1.000
embA4245077c.1845G>C1.000
embA4245083c.1851A>C1.000
embA4245092c.1860C>G1.000
embA4245125c.1893G>C1.000
embA4245149c.1917C>G1.000
embA4245173c.1941G>C1.000
embA4245182c.1950T>C1.000
embA4245187p.Thr652Met1.000
embA4245198p.Leu656Val1.000
embA4245224c.1992T>C1.000
embB4247434c.921C>G1.000
embB4247437c.924A>C1.000
embB4247440c.927C>A1.000
embB4247452c.939C>G1.000
embB4247491c.978G>C1.000
embB4247494c.981G>A1.000
embB4247497c.984T>C1.000
embB4247500c.987C>G1.000
embB4247512c.999T>C1.000
embB4247683c.1170C>G1.000
embB4247684c.1171T>C1.000
embB4247716c.1203C>G1.000
embB4247722c.1209G>C1.000
embB4247755c.1242C>G1.000
embB4247761c.1248T>C1.000
embB4248025c.1512A>G1.000
embB4248041p.Ala510Ser1.000
embB4248046c.1533A>G1.000
embB4248055c.1542G>C1.000
embB4248064c.1551G>C1.000
embB4248070c.1557T>C1.000
embB4248085c.1572T>C1.000
embB4248106c.1593C>G1.000
embB4248118c.1605T>C1.000
embB4248124c.1611G>C1.000
embB4248130c.1617G>C1.000
embB4248133c.1620C>G1.000
embB4248142c.1629T>C1.000
embB4248143c.1630T>C1.000
embB4248157c.1644A>G1.000
embB4248172c.1659G>C1.000
embB4248175c.1662G>C1.000
embB4248266c.1753C>T1.000
embB4248277c.1764G>C1.000
embB4248316c.1803C>A1.000
embB4248319c.1806A>G1.000
embB4248325c.1812G>C1.000
embB4248349c.1836G>A1.000
embB4248358c.1845C>G1.000
embB4248397c.1884C>T1.000
embB4248398c.1885C>T1.000
embB4248407p.Leu632Val1.000
embB4248416p.Leu635Met1.000
embB4248432p.Trp640Phe1.000
embB4248472c.1959T>C1.000
embB4248478c.1965G>C1.000
embB4249381c.2868A>G1.000
ethA4326469c.1005A>G1.000
ethA4326481c.993G>C1.000
ethA4326484c.990A>C1.000
ethA4326487c.987T>C1.000
ethA4326511c.963G>C1.000
ethA4326520p.Glu318Asp1.000
ethA4326523c.951A>G1.000
ethA4326532c.942G>A1.000
ethA4326535c.939C>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
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;