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: 5cc540d744a63
Sample: 5cc540d744a63

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Summary
ID: 5cc540d744a63
Date: Sun Apr 28 07:01:14 2019
Strain: lineage4.3
Drug-resistance: Drug-resistant

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

Lineage2FamilyMain SpoligotypeRDS
lineage4.3Euro-American (LAM)mainly-LAMNone

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6319c.1080G>C1.000
gyrB6346c.1107C>T1.000
gyrB6982c.1743A>C1.000
gyrB7007c.1768C>T1.000
gyrB7010c.1771C>T1.000
gyrB7023p.Leu595Gln1.000
gyrB7033c.1794G>C1.000
gyrB7051p.Glu604Asp1.000
gyrB7066c.1827G>C0.923
gyrB7078c.1839A>C0.900
gyrB7084c.1845A>G0.900
gyrB7165c.1926C>G1.000
gyrB7178c.1939T>C1.000
gyrB7186c.1947C>G1.000
gyrB7216c.1977G>C1.000
gyrB7228c.1989C>T1.000
gyrB7234c.1995C>T1.000
gyrA7391c.90C>T1.000
gyrA7394c.93T>C1.000
gyrA7406c.105G>C1.000
gyrA7427c.126G>C1.000
gyrA7442c.141G>C0.882
gyrA7451c.150C>G0.875
gyrA7457c.156T>C0.875
gyrA7475c.174A>G0.818
gyrA7480p.Phe60Tyr0.818
gyrA7484c.183T>C0.818
gyrA7514c.213C>G0.833
gyrA7523c.222C>A0.818
gyrA7532c.231T>C0.900
gyrA7763c.462T>C1.000
gyrA7784c.483A>G1.000
gyrA8531c.1230G>C1.000
gyrA8543c.1242C>G1.000
gyrA8546c.1245T>C1.000
gyrA8553c.1252C>A1.000
gyrA8561c.1260A>C1.000
gyrA8588c.1287G>A1.000
gyrA8603c.1302A>G1.000
gyrA8619c.1318T>C1.000
gyrA8624c.1323G>C1.000
gyrA9200c.1899A>G0.917
gyrA9204p.Ser635Thr0.917
gyrA9218c.1917C>T0.917
gyrA9224c.1923C>T0.923
gyrA9230c.1929T>C0.923
gyrA9233c.1932C>G0.933
gyrA9239c.1938C>T1.000
gyrA9252p.Val651Ile1.000
gyrA9284c.1983T>C1.000
gyrA9291c.1990C>T1.000
gyrA9296c.1995T>C1.000
rpoB759606c.-201T>C1.000
rpoB759629c.-178T>C1.000
rpoB760112c.306T>C0.909
rpoB760118c.312T>G0.909
rpoB760121c.315T>C0.909
rpoB760130p.Asp108Glu0.941
rpoB760139c.333A>G0.947
rpoB760142c.336C>G0.947
rpoB760181c.375T>C1.000
rpoB760184c.378A>G1.000
rpoB760196c.390C>G1.000
rpoB760223c.417T>C1.000
rpoB760235c.429T>C1.000
rpoB760283c.477G>C1.000
rpoB760298c.492G>C1.000
rpoB760307c.501T>C1.000
rpoB760310c.504G>C1.000
rpoB760328c.522G>C1.000
rpoB760331c.525G>C1.000
rpoB760340c.534G>T1.000
rpoB760361c.555T>C1.000
rpoB760370c.564C>G1.000
rpoB760376p.Asp190Glu0.929
rpoB760380p.Thr192Leu0.923
rpoB760406c.600G>C0.846
rpoB760412c.606C>G0.846
rpoB760424c.618C>G0.833
rpoB760430c.624T>C0.833
rpoB760522p.Ser239Asn0.917
rpoB760541c.735G>C1.000
rpoB760547c.741G>C1.000
rpoB760563p.Arg253Met1.000
rpoB760591p.Val262Ala0.933
rpoB760611c.805T>C0.938
rpoB760634c.828T>C0.833
rpoB760646c.840C>G0.833
rpoB760655c.849A>G0.846
rpoB760661c.855A>C0.846
rpoB760670c.864G>C0.846
rpoB760674c.868T>C0.833
rpoB760679c.873A>G0.800
rpoB760683c.877T>C0.800
rpoB760886c.1080A>G1.000
rpoB760934c.1128C>T1.000
rpoB760946c.1140A>G1.000
rpoB761057c.1251G>C1.000
rpoB761102c.1296A>G1.000
rpoB761180c.1374A>C1.000
rpoB761189c.1383T>C1.000
rpoB761195c.1389G>C1.000
rpoB761207c.1401C>T1.000
rpoB761213c.1407G>C1.000
rpoB761219c.1413G>C1.000
rpoB761249c.1443A>G1.000
rpoB761255c.1449T>G1.000
rpoB761261c.1455G>T1.000
rpoB761306c.1500C>G1.000
rpoB761312c.1506G>C1.000
rpoB761327c.1521A>G1.000
rpoB761330c.1524G>C1.000
rpoB761354c.1548C>T1.000
rpoB761360c.1554T>C1.000
rpoB761362p.Ser519Thr1.000
rpoB761510c.1704T>C1.000
rpoB761537c.1731C>G1.000
rpoB761570c.1764T>C1.000
rpoB761573c.1767C>G1.000
rpoB761579c.1773G>C1.000
rpoB761588c.1782C>T1.000
rpoB761606c.1800C>G1.000
rpoB761612c.1806G>C1.000
rpoB761615c.1809A>C1.000
rpoB761636c.1830G>T1.000
rpoB761645c.1839C>G1.000
rpoB761648c.1842T>C1.000
rpoB761657c.1851C>G1.000
rpoB761675c.1869G>C1.000
rpoB761948c.2142G>C0.947
rpoB761954c.2148C>G0.950
rpoB762008c.2202C>T1.000
rpoB762014c.2208C>T1.000
rpoB762017c.2211A>G1.000
rpoB762053c.2247T>C1.000
rpoB762062c.2256T>C1.000
rpoB762065c.2259T>C1.000
rpoB762083c.2277T>C1.000
rpoB762086c.2280G>C1.000
rpoB762101c.2295C>G1.000
rpoB762114p.Ile770Val1.000
rpoB762131c.2325C>G1.000
rpoB762140c.2334G>C1.000
rpoB762143c.2337T>C1.000
rpoB762149c.2343G>C1.000
rpoB762167c.2361T>C1.000
rpoB762176c.2370T>C1.000
rpoB762185c.2379G>C1.000
rpoB762206c.2400C>G1.000
rpoB762233c.2427G>C1.000
rpoB762246c.2440C>T0.917
rpoB762254c.2448T>G0.923
rpoB762257c.2451C>G0.929
rpoB762266c.2460T>C0.929
rpoB762284c.2478G>C0.933
rpoB762293c.2487T>C0.929
rpoB762314c.2508C>T1.000
rpoB762317c.2511A>G1.000
rpoB762329c.2523G>C0.917
rpoB762338c.2532T>C1.000
rpoB762347c.2541T>C1.000
rpoB762827c.3021G>C1.000
rpoB762857c.3051C>G1.000
rpoB762860c.3054G>C1.000
rpoB762863c.3057T>C1.000
rpoB762929c.3123G>C0.963
rpoB762989c.3183G>C0.960
rpoB762995c.3189G>T0.920
rpoB763013c.3207C>G0.955
rpoB763028c.3222T>C0.889
rpoB763031c.3225T>G1.000
rpoB763034c.3228C>G0.895
rpoB763040c.3234C>G0.905
rpoB763070c.3264T>C0.923
rpoB763085c.3279C>G0.958
rpoB763115c.3309T>C0.958
rpoB763136c.3330C>T0.944
rpoB763148c.3342G>C0.944
rpoB763158c.3352C>T0.929
rpoB763166c.3360A>G0.933
rpoB763190c.3384C>T0.900
rpoC763402c.33C>G1.000
rpoC763411c.42T>G1.000
rpoC763414c.45T>C1.000
rpoC763441c.72C>T1.000
rpoC763444c.75T>C1.000
rpoC763456c.87A>G1.000
rpoC763486c.117T>G1.000
rpoC763528c.159G>A1.000
rpoC763546c.177A>G1.000
rpoC763570c.201G>C1.000
rpoC763573c.204G>C1.000
rpoC763594c.225C>T1.000
rpoC763603c.234C>T1.000
rpoC763636c.267T>C1.000
rpoC763660c.291T>G1.000
rpoC763675c.306C>G1.000
rpoC763696c.327T>C1.000
rpoC763702c.333C>G1.000
rpoC763717c.348T>C1.000
rpoC763723c.354G>C1.000
rpoC763732c.363C>G1.000
rpoC763741c.372C>T1.000
rpoC763744c.375G>C1.000
rpoC763765c.396T>C1.000
rpoC763774c.405G>C1.000
rpoC763807c.438T>C1.000
rpoC763816c.447C>G1.000
rpoC763835p.Ala156Met1.000
rpoC763853p.Val162Ile1.000
rpoC763858c.489A>G1.000
rpoC763872p.Gly168Ala1.000
rpoC763876p.Glu169Asp1.000
rpoC763879c.510A>G1.000
rpoC763900c.531G>C1.000
rpoC763945c.576T>C1.000
rpoC763948c.579G>A1.000
rpoC763949c.580C>A1.000
rpoC763954c.585C>G1.000
rpoC763963c.594C>T1.000
rpoC764083c.714A>G1.000
rpoC764098c.729A>G1.000
rpoC764101c.732C>G1.000
rpoC764102p.Val245Ile1.000
rpoC764112p.Tyr248Phe1.000
rpoC764116c.747C>T1.000
rpoC764131c.762T>C1.000
rpoC764140c.771C>T1.000
rpoC764236c.867G>A1.000
rpoC764248c.879C>G1.000
rpoC764257c.888G>C1.000
rpoC764266c.897T>C1.000
rpoC764269c.900G>C1.000
rpoC764272c.903G>C1.000
rpoC764278c.909A>G1.000
rpoC764338c.969G>A1.000
rpoC764353c.984G>C1.000
rpoC764365c.996C>T1.000
rpoC764380c.1011G>C1.000
rpoC764497c.1128A>G1.000
rpoC764539c.1170C>G1.000
rpoC764554c.1185C>T1.000
rpoC764566c.1197C>G1.000
rpoC764575c.1206T>G1.000
rpoC764581c.1212T>C1.000
rpoC764593c.1224C>T1.000
rpoC764611c.1242G>T0.944
rpoC764650c.1281G>C0.938
rpoC764651c.1282T>A0.938
rpoC764752c.1383G>C0.962
rpoC764764c.1395T>C0.964
rpoC764809c.1440C>T0.957
rpoC764815c.1446A>G0.958
rpoC764827c.1458G>C0.889
rpoC764858c.1489T>C0.893
rpoC764872c.1503A>G0.909
rpoC764888c.1519T>C0.955
rpoC764911c.1542A>G1.000
rpoC764932c.1563C>A1.000
rpoC764935c.1566T>C1.000
rpoC764948c.1579T>C1.000
rpoC764968c.1599T>C1.000
rpoC764995c.1626C>G1.000
rpoC765019c.1650A>G1.000
rpoC765034c.1665T>C0.960
rpoC765040c.1671T>C1.000
rpoC765041c.1672T>C1.000
rpoC765047c.1678T>C1.000
rpoC765053c.1684T>A1.000
rpoC765073c.1704G>C1.000
rpoC765076c.1707A>G1.000
rpoC765079c.1710T>G1.000
rpoC765082c.1713G>C1.000
rpoC765089c.1720T>C1.000
rpoC765103c.1734G>T1.000
rpoC765298c.1929G>C0.900
rpoC765300p.Val644Ala0.900
rpoC765319c.1950A>G0.909
rpoC765346c.1977C>G0.917
rpoC765349c.1980T>C0.917
rpoC765352c.1983G>C0.917
rpoC765383p.Met672Leu1.000
rpoC765404p.Leu679Val1.000
rpoC765409c.2040T>C1.000
rpoC765421c.2052C>G1.000
rpoC765478c.2109T>C1.000
rpoC765499c.2130C>G1.000
rpoC765529c.2160C>T1.000
rpoC765541c.2172C>G1.000
rpoC765553c.2184C>T1.000
rpoC765556c.2187G>C1.000
rpoC765559c.2190G>C1.000
rpoC765580c.2211G>C1.000
rpoC765613p.His748Gln1.000
rpoC765625c.2256C>G1.000
rpoC765631p.Asp754Glu1.000
rpoC765700c.2331T>C1.000
rpoC765883c.2514C>G1.000
rpoC765886c.2517C>G1.000
rpoC765892c.2523T>C1.000
rpoC765937c.2568T>C1.000
rpoC765967c.2598C>T1.000
rpoC765982c.2613C>G1.000
rpoC765994c.2625A>T1.000
rpoC766010c.2641T>A1.000
rpoC766021c.2652G>C1.000
rpoC766027c.2658G>C1.000
rpoC766030c.2661C>G1.000
rpoC766036c.2667C>T1.000
rpoC766043p.Gln892Glu1.000
rpoC766054c.2685C>G1.000
rpoC766082p.Ala905Gln1.000
rpoC766096c.2727G>C1.000
rpoC766357c.2988C>T1.000
rpoC766363c.2994G>C1.000
rpoC766381c.3012C>T0.929
rpoC766384c.3015A>G1.000
rpoC766408c.3039C>G1.000
rpoC766411c.3042C>G1.000
rpoC766426c.3057C>T1.000
rpoC766447c.3078T>C1.000
rpoC766462c.3093G>C1.000
rpoC766468c.3099G>A1.000
rpoC766483c.3114G>C1.000
rpoC766484p.Val1039Ile1.000
rpoC766492c.3123T>C1.000
rpoC766657c.3288A>G1.000
rpoC766660c.3291G>C1.000
rpoC766672c.3303T>C1.000
rpoC766673p.Gly1102Asn1.000
rpoC766726c.3357T>C0.962
rpoC766738c.3369G>C0.923
rpoC766765c.3396A>C0.962
rpoC766774c.3405T>C1.000
rpoC766801c.3432C>G1.000
rpoC766804c.3435A>G1.000
rpoC766861c.3492G>T1.000
rpoC766864c.3495G>C1.000
rpoC766876c.3507C>T1.000
rpoC766882c.3513C>T1.000
rpoC766894c.3525T>C1.000
rpoC766900c.3531T>C1.000
rpoC766933c.3564A>G1.000
rpoC766945c.3576A>G1.000
rpoC766963c.3594T>C1.000
rpoC766972c.3603G>C1.000
rpoC767059c.3690T>G0.917
rpoC767062c.3693C>A0.917
rpoC767098c.3729T>C0.812
rpoC767119c.3750A>G0.800
rpoC767134c.3765C>A0.769
rpoC767158c.3789T>G0.800
rpoC767180p.Ala1271Gln0.769
rpoC767191c.3822C>G0.786
rpoC767206c.3837C>G0.846
rpoC767209c.3840T>C0.833
rpoC767212c.3843G>C0.857
rpoC767221c.3852C>G0.857
rpoC767230c.3861G>C1.000
rpoC767233c.3864T>C1.000
rpsL781595c.36T>C1.000
rpsL781605p.Ile16Val1.000
rpsL781608p.Ser17Ala1.000
rpsL781628c.69T>C1.000
rpsL781631c.72G>C0.941
rpsL781649c.90T>C0.938
rpsL781655c.96T>C0.952
rpsL781700c.141G>C0.920
rpsL781703c.144G>T0.917
rpsL781715c.156T>C0.920
rpsL781728c.169T>C0.923
rpsL781736c.177T>C0.917
rpsL781742c.183C>T0.917
rpsL781748c.189C>G0.909
rpsL781754c.195G>C0.917
rpsL781760c.201T>C0.913
rpsL781772c.213C>A0.905
rpsL781808c.249C>T0.938
rpsL781811c.252C>T0.938
rpsL781832c.273T>C1.000
rpsL781838c.279G>C1.000
rpsL781841c.282C>G1.000
rpsL781865c.306G>C1.000
rpsL781868c.309T>C1.000
rpsL781871c.312G>C1.000
rpsL781877c.318T>C1.000
rpsL781892c.333A>G1.000
rpsL781898c.339A>T1.000
rpsL781916c.357T>C1.000
rpsL781929p.Gly124Ser1.000
rplC800794c.-15A>G1.000
rplC801168c.360C>G1.000
rplC801171c.363A>G1.000
rplC801174c.366T>C1.000
rplC801195c.387G>C1.000
rplC801207c.399C>T1.000
rplC801246c.438C>T0.938
rplC801249c.441T>C0.909
rplC801255c.447C>T0.909
rrs1471923r.78t>c1.000
rrs1471925r.80t>c1.000
rrs1471932r.87a>g0.960
rrs1471934r.89a>g0.960
rrs1471969r.124t>c0.976
rrs1471970r.125g>a0.976
rrs1472044r.199g>t0.818
rrs1472045r.200t>a0.818
rrs1472061r.216a>t0.857
rrs1472075r.230a>g0.882
rrs1472108r.263c>t0.917
rrs1472969r.1124a>g0.935
rrs1472970r.1125c>g0.935
rrs1472977r.1132g>c0.967
rrs1472978r.1133t>c0.967
rrs1473105r.1260g>a1.000
rrs1473120r.1275c>ct0.889
rrs1473123r.1278a>t1.000
rrs1473145r.1300c>t1.000
rrs1473166r.1321g>a1.000
rrs1473290r.1445c>t1.000
rrl1473668r.11c>t1.000
rrl1473756r.99g>a1.000
rrl1473758r.101g>t1.000
rrl1473806r.149c>t1.000
rrl1473877r.220g>a1.000
rrl1473898r.241c>t1.000
rrl1473943r.286g>t1.000
rrl1473945r.288t>a1.000
rrl1473946r.289a>t1.000
rrl1473986r.329t>c0.909
rrl1473987r.330g>a0.909
rrl1473995r.338g>t0.929
rrl1474001r.344c>t0.929
rrl1474009r.352a>g0.923
rrl1474012r.355c>t0.923
rrl1474093r.436g>t0.958
rrl1474099r.442g>a0.962
rrl1474103r.446a>t0.958
rrl1474140r.483c>t0.960
rrl1474151r.494c>t0.966
rrl1474181r.524c>t0.960
rrl1474249r.592g>t0.955
rrl1474291r.634tttcctctccggagga>t0.857
rrl1474308r.651g>t0.800
rrl1474310r.653t>g0.800
rrl1474356r.699t>c0.944
rrl1474362r.705a>g0.941
rrl1474376r.719t>c0.889
rrl1474639r.982g>a0.966
rrl1474794r.1137c>t0.969
rrl1474812r.1155g>a0.971
rrl1474823r.1166c>t1.000
rrl1474831r.1174a>g1.000
rrl1474904r.1247g>a1.000
rrl1474956r.1299c>t1.000
rrl1474960r.1303c>g1.000
rrl1474963r.1306g>t1.000
rrl1474964r.1307t>a1.000
rrl1474965r.1308g>c1.000
rrl1474970r.1313g>a1.000
rrl1475006r.1349a>t1.000
rrl1475061r.1404c>t1.000
rrl1475088r.1431a>t1.000
rrl1475199r.1542g>a1.000
rrl1475209r.1552g>c1.000
rrl1475213r.1556c>t1.000
rrl1475252r.1595c>t1.000
rrl1475266r.1609t>c1.000
rrl1475267r.1610g>a1.000
rrl1475275r.1618c>t1.000
rrl1475276r.1619t>c1.000
rrl1475291r.1634a>c1.000
rrl1475313r.1656g>a1.000
rrl1475315r.1658a>t1.000
rrl1475355r.1698c>t1.000
rrl1475369r.1712g>t0.962
rrl1475402r.1745c>t0.950
rrl1475419r.1762c>t0.917
rrl1475436r.1779c>t0.913
rrl1475483r.1826c>t0.962
rrl1475505r.1848g>a1.000
rrl1475526r.1869c>a1.000
rrl1475599r.1942a>g1.000
rrl1475608r.1951t>c1.000
rrl1475642r.1985t>c1.000
rrl1475657r.2000a>g1.000
rrl1475659r.2002g>t1.000
rrl1475758r.2101ac>a0.947
rrl1475763r.2106c>t0.938
rrl1475765r.2108ag>a0.938
rrl1475881r.2224t>c1.000
rrl1475988r.2331a>g1.000
rrl1476086r.2429g>a1.000
rrl1476089r.2432t>c1.000
rrl1476095r.2438c>g1.000
rrl1476106r.2449a>t1.000
rrl1476115r.2458t>c1.000
rrl1476117r.2460g>c1.000
rrl1476224r.2567a>g1.000
rrl1476281r.2624t>c0.938
rrl1476583r.2926g>a0.929
rrl1476584r.2927c>t0.923
rrl1476594r.2937c>t0.941
rrl1476597r.2940g>a0.941
rrl1476603r.2946g>a0.941
rrl1476608r.2951c>g0.944
rrl1476628r.2971t>a0.944
rrl1476689r.3032a>t0.917
rrl1476690r.3033c>t0.909
rrl1476693r.3036g>a0.909
rrl1476695r.3038t>a0.909
rrl1476716r.3059a>c0.933
rrl1476726r.3069a>g0.929
rrl1476732r.3075t>c0.929
rrl1476750r.3093t>c1.000
rrl1476755r.3098g>a1.000
rrl1476759r.3102t>c1.000
fabG11673679c.240T>C0.900
fabG11673685c.246C>T0.900
fabG11673710p.Leu91Ile0.833
fabG11673716p.Ala93Lys0.833
fabG11673733p.Met98Ile0.909
fabG11673955c.516G>C1.000
fabG11673961c.522A>C1.000
fabG11673985c.546C>A1.000
inhA1674660c.459G>C1.000
inhA1674672c.471C>G1.000
inhA1674703c.502T>C1.000
inhA1674708c.507G>A1.000
rpsA1833568c.27G>C0.846
rpsA1833589c.48A>T0.875
rpsA1833595c.54T>C0.875
rpsA1833661c.120A>G0.929
rpsA1833667c.126C>G0.923
rpsA1833787c.246C>G0.944
rpsA1833790c.249T>C0.941
rpsA1833802c.261A>G0.941
rpsA1833811c.270G>T0.938
rpsA1833838c.297G>C0.929
rpsA1833841c.300C>G0.929
rpsA1833847c.306C>G0.950
rpsA1833856c.315A>G0.957
rpsA1833874c.333T>C0.960
rpsA1833928c.387G>C0.962
rpsA1833940c.399C>G1.000
rpsA1833971c.430C>T1.000
rpsA1833979c.438T>C1.000
rpsA1834000c.459G>C1.000
rpsA1834021c.480C>T1.000
rpsA1834030c.489C>G1.000
rpsA1834099c.558C>G1.000
rpsA1834102c.561T>C1.000
rpsA1834105c.564C>G1.000
rpsA1834108c.567C>G1.000
rpsA1834123c.582C>G1.000
rpsA1834303c.762T>C1.000
rpsA1834306c.765T>C1.000
rpsA1834333c.792C>T1.000
rpsA1834348c.807T>C1.000
rpsA1834366c.825A>G1.000
rpsA1834396c.855G>C0.950
rpsA1834411c.870T>C0.950
rpsA1834417c.876G>C0.947
rpsA1834423c.882G>C0.947
rpsA1834435c.894G>C0.944
rpsA1834451c.910T>C0.929
rpsA1834465c.924T>C0.909
rpsA1834468c.927A>G0.909
rpsA1834489c.948T>C0.909
rpsA1834528c.987T>C1.000
rpsA1834540c.999G>C1.000
rpsA1834546c.1005T>C1.000
rpsA1834555c.1014T>G1.000
rpsA1834609c.1068T>C1.000
rpsA1834618c.1077G>C0.944
rpsA1834633c.1092A>G0.947
rpsA1834639c.1098T>C0.941
rpsA1834654p.Glu371Asp1.000
rpsA1834690c.1149T>C0.955
rpsA1834732c.1191T>C0.950
rpsA1834733p.Ala398Ser0.950
rpsA1834738c.1197A>G0.952
rpsA1834753c.1212T>C0.955
rpsA1834765p.Glu408Asp1.000
rpsA1834775p.Ala412Thr1.000
rpsA1834780c.1239A>G1.000
rpsA1834786c.1245A>G1.000
rpsA1834789c.1248T>C1.000
rpsA1834792c.1251G>C1.000
katG2155704c.408G>C1.000
katG2155716c.396A>C1.000
katG2155722c.390C>G1.000
katG2155728c.384C>G1.000
kasA2518162c.48G>A0.900
kasA2518174c.60A>G0.900
kasA2518190p.Ser26Ala0.909
kasA2518199p.Ile29Val0.909
kasA2518220c.106C>T1.000
kasA2518248p.Ala45Val0.900
kasA2518825c.711T>C1.000
kasA2518864c.750G>C1.000
kasA2518879c.765A>G1.000
kasA2519116c.1002C>G1.000
kasA2519122c.1008G>C1.000
kasA2519137c.1023T>G1.000
kasA2519158c.1044C>T1.000
ahpC2726601p.Ile137Leu0.900
ahpC2726638p.Ala149Val0.923
ahpC2726645c.453C>G0.909
ahpC2726657c.465A>C0.923
thyX3067652c.294A>G1.000
thyX3067661c.285G>C1.000
thyX3067685c.261T>G1.000
thyX3067693p.Ile85Leu1.000
thyX3067694c.252C>G1.000
thyX3067718c.228G>C1.000
thyX3067721c.225A>G1.000
thyX3067727c.219T>G0.917
thyX3067736c.210G>A0.917
thyX3067739c.207A>G0.917
thyX3067814c.132A>G0.889
thyX3067850c.96T>G0.900
thyX3067898p.Asp16Glu1.000
thyX3067935p.Thr4Ile0.909
fbiA3640347c.-196A>G1.000
fbiA3640349c.-194A>G1.000
fbiA3640350c.-193C>T1.000
fbiA3640365c.-178C>G1.000
embC4240726c.864G>C1.000
embC4240780c.918T>C1.000
embC4240783c.921G>C1.000
embC4240789c.927T>C1.000
embC4241089c.1227C>G1.000
embC4241095c.1233C>T1.000
embC4241107c.1245G>C1.000
embC4241140c.1278A>G1.000
embC4241146c.1284C>G1.000
embC4241158c.1296T>C1.000
embC4241161c.1299C>G1.000
embC4241162c.1300T>C1.000
embC4241170c.1308G>C1.000
embC4241173c.1311C>T1.000
embC4241179c.1317G>A1.000
embC4241203c.1341T>C0.900
embC4241206c.1344G>C0.900
embC4241374c.1512T>G0.923
embC4241380c.1518A>C1.000
embC4241383c.1521G>C1.000
embC4241394p.Lys511Ser1.000
embC4241449c.1587C>G0.905
embC4241453p.Ile531Val0.900
embC4241479c.1617C>G0.857
embC4241480c.1618T>C0.818
embC4241488c.1626G>C0.800
embA4245101c.1869G>C0.900
embA4245137c.1905T>C0.929
embA4245146c.1914G>A1.000
embA4245149c.1917C>G1.000
embA4245153p.Ile641Val1.000
embA4245182c.1950T>C1.000
embA4245189c.1957C>T1.000
embA4245198p.Leu656Ile1.000
embA4245207c.1975T>C1.000
embA4245215c.1983A>C1.000
embA4245222p.Tyr664Gln1.000
embA4245242c.2010C>T1.000
embA4245248c.2016G>C1.000
embB4247512c.999T>C1.000
embB4247539c.1026T>C1.000
embB4247554c.1041T>C1.000
embB4247566c.1053C>A1.000
embB4247797c.1284C>G0.917
embB4247800c.1287A>T0.917
embB4247803c.1290G>C0.917
embB4247815c.1302C>G0.923
embB4247819p.Val436Ile0.923
embB4247830c.1317A>G0.929
embB4247839c.1326G>C0.933
embB4247875c.1362G>C1.000
embB4247876c.1363C>T1.000
embB4247881c.1368G>C1.000
embB4247887c.1374C>T1.000
embB4247899p.Met462Ile1.000
embB4247905c.1392G>C1.000
embB4247909c.1396T>C1.000
embB4247914c.1401G>C1.000
embB4247932c.1419C>G1.000
embB4247940p.Leu476Trp1.000
embB4247945c.1432T>C1.000
embB4247951p.Ser480Ala0.941
embB4247974c.1461C>G0.882
embB4248070c.1557T>C1.000
embB4248085c.1572T>C0.923
embB4248097c.1584C>G0.923
embB4248130c.1617G>C0.923
embB4248142c.1629T>C1.000
embB4248143c.1630T>C1.000
embB4248157c.1644A>G1.000
embB4248457c.1944T>C1.000
embB4248472c.1959T>C1.000
embB4248475c.1962G>C1.000
embB4249369c.2856T>C0.800
embB4249375c.2862G>C0.800
embB4249381c.2868A>G0.800
embB4249469p.Leu986Met1.000
embB4249486c.2973T>G1.000
embB4249498c.2985G>C1.000
ethA4327396c.78A>T0.923
ethA4327399p.Asp25Glu0.923
ethA4327423c.51G>C0.923
ethA4327435c.39T>G0.923
ethA4327438c.36A>G0.923
ethA4327452p.Val8Leu0.900
ethA4327453c.21A>G0.900
ethA4327459c.15G>A0.900

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;