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: 5cc55404a1b73
Sample: 5cc55404a1b73

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Summary
ID: 5cc55404a1b73
Date: Sun Apr 28 08:20:49 2019
Strain: lineage2;lineage4.3.3;lineage4.1.1.1
Drug-resistance: Sensitive

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
Streptomycin
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage2East-AsianBeijingRD105
lineage4.3.3Euro-American (LAM)LAM;TRD115
lineage4.1.1.1Euro-American (X-type)X2RD183

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6100c.861G>C0.615
gyrB6109c.870G>T0.688
gyrB6115c.876A>G1.000
gyrB6124c.885C>G0.312
gyrB6127c.888G>C0.688
gyrB6130c.891T>C0.706
gyrB6133c.894G>C1.000
gyrB6142c.903G>A0.263
gyrB6154c.915C>G0.250
gyrB6160c.921C>G1.000
gyrB6169c.930C>T0.250
gyrB6178c.939C>T0.250
gyrB6190c.951A>G1.000
gyrB6196c.957C>T1.000
gyrB6700c.1461T>C0.636
gyrB6703c.1464G>C1.000
gyrB6706c.1467G>A0.364
gyrB6709c.1470A>G0.364
gyrB6712c.1473G>C1.000
gyrB6715c.1476C>T1.000
gyrB6727c.1488G>T0.444
gyrB6728c.1489C>T0.526
gyrB6745c.1506T>G0.481
gyrB6751c.1512G>C1.000
gyrB6760c.1521G>C1.000
gyrB6763c.1524G>C1.000
gyrB6769c.1530C>T1.000
gyrB6775c.1536G>C1.000
gyrB6793c.1554T>C1.000
gyrB6797p.Gly520Ser1.000
gyrB6808c.1569C>G1.000
gyrB6811c.1572C>T0.500
gyrB6838c.1599C>T0.200
gyrA7422c.121C>T1.000
gyrA7427c.126G>C1.000
gyrA7436c.135C>G1.000
gyrA7442c.141G>C1.000
gyrA7457c.156T>C1.000
gyrA7463c.162G>C1.000
gyrA7469c.168C>G1.000
gyrA7472c.171T>C1.000
gyrA7475c.174A>G1.000
gyrA7480p.Phe60Tyr1.000
gyrA7484c.183T>C1.000
gyrA7490c.189C>G1.000
gyrA7499c.198G>C1.000
gyrA7520c.219G>C0.950
gyrA7523c.222C>G0.947
gyrA7526c.225G>C0.947
gyrA7532c.231T>G0.947
gyrA7541c.240C>G0.941
gyrA7547c.246C>T0.941
gyrA7565c.264C>T0.952
gyrA7571c.270G>C0.952
gyrA7585p.Ser95Thr1.000
gyrA7592c.291G>C1.000
gyrA7595c.294C>T1.000
gyrA7607c.306C>G1.000
gyrA7613c.312G>A1.000
gyrA7631c.330G>C1.000
gyrA7658c.357A>C1.000
gyrA7661c.360C>T1.000
gyrA7664c.363T>C1.000
gyrA7667c.366C>T1.000
gyrA7670c.369A>C1.000
gyrA7671p.Pro124Ala1.000
gyrA7676c.375G>C1.000
gyrA7694c.393A>G1.000
gyrA7697c.396C>T1.000
gyrA7706c.405C>G1.000
gyrA7710c.409T>C1.000
gyrA7715c.414G>C1.000
gyrA7728c.427A>C1.000
gyrA7760c.459C>T1.000
gyrA7763c.462T>G1.000
gyrA8129c.828T>C1.000
gyrA8156c.855T>C1.000
gyrA8168c.867A>G1.000
gyrA8177c.876A>G1.000
gyrA8198c.897T>C1.000
gyrA8207c.906T>C1.000
gyrA8219c.918T>C1.000
gyrA8915c.1614A>G1.000
gyrA9044c.1743C>T1.000
gyrA9051c.1750T>C1.000
gyrA9065c.1764C>G1.000
gyrA9068c.1767G>C1.000
gyrA9071c.1770G>C1.000
gyrA9080c.1779G>A1.000
gyrA9099c.1798T>C1.000
gyrA9104c.1803C>G1.000
gyrA9119c.1818A>G1.000
rpoB760181c.375T>C1.000
rpoB760184c.378A>G1.000
rpoB760196c.390C>G1.000
rpoB760235c.429T>C1.000
rpoB760244c.438G>C1.000
rpoB760283c.477G>C1.000
rpoB760298c.492G>C1.000
rpoB760310c.504G>C1.000
rpoB760316c.510C>G1.000
rpoB760325c.519G>C1.000
rpoB760331c.525G>T1.000
rpoB760340c.534G>T1.000
rpoB760357p.Thr184Ser1.000
rpoB760361c.555T>C1.000
rpoB760376p.Asp190Glu1.000
rpoB760406c.600G>C1.000
rpoB760407p.Ser201Gly1.000
rpoB760415c.609C>T1.000
rpoB760424c.618C>G1.000
rpoB760430c.624T>C1.000
rpoB760460c.654G>C1.000
rpoB760475c.669A>G1.000
rpoB760481c.675G>C1.000
rpoB760484c.678A>G1.000
rpoB760585p.Asn260Ser1.000
rpoB760591p.Val262Ala1.000
rpoB760595c.789C>T1.000
rpoB760596p.Thr264Pro1.000
rpoB760611c.805T>C1.000
rpoB760646c.840C>G1.000
rpoB760655c.849A>G1.000
rpoB760661c.855A>C1.000
rpoB760670c.864G>C1.000
rpoB760674c.868T>C1.000
rpoB760679c.873A>G1.000
rpoB760683c.877T>C1.000
rpoB760724c.918T>C1.000
rpoB760730c.924T>C1.000
rpoB760817c.1011A>G1.000
rpoB760820c.1014T>C1.000
rpoB760826c.1020C>G1.000
rpoB760830c.1024T>C1.000
rpoB760841c.1035T>C1.000
rpoB760859c.1053T>C1.000
rpoB760862c.1056G>C1.000
rpoB760877c.1071G>C1.000
rpoB760883c.1077G>C1.000
rpoB760886c.1080A>G1.000
rpoB760887p.Thr361Val1.000
rpoB760946c.1140A>G1.000
rpoB761147c.1341C>T1.000
rpoB761165c.1359G>C1.000
rpoB761180c.1374A>C1.000
rpoB761234c.1428G>C1.000
rpoB761249c.1443A>G1.000
rpoB761261c.1455G>T1.000
rpoB761264c.1458C>G1.000
rpoB761300c.1494G>C1.000
rpoB761318c.1512G>C1.000
rpoB761327c.1521A>G1.000
rpoB761345c.1539G>C1.000
rpoB761346p.Val514Ile1.000
rpoB761354c.1548C>T1.000
rpoB761360c.1554T>C1.000
rpoB761367p.Glu521Gln1.000
rpoB761374p.Val523Asp1.000
rpoB761408c.1602G>C1.000
rpoB761414c.1608A>G1.000
rpoB761537c.1731C>G1.000
rpoB761555c.1749G>C1.000
rpoB761558c.1752C>G1.000
rpoB761564c.1758G>C1.000
rpoB761570c.1764T>C1.000
rpoB761573c.1767C>G1.000
rpoB761579c.1773G>C1.000
rpoB761606c.1800C>G1.000
rpoB761612c.1806G>T1.000
rpoB761615c.1809A>C1.000
rpoB761930c.2124G>C1.000
rpoB761933c.2127G>C1.000
rpoB761948c.2142G>C1.000
rpoB761954c.2148C>G1.000
rpoB761969c.2163G>A1.000
rpoB761999c.2193G>C1.000
rpoB762002c.2196C>G1.000
rpoB762008c.2202C>T1.000
rpoB762038c.2232C>T1.000
rpoB762047c.2241G>A1.000
rpoB762053c.2247T>C1.000
rpoB762065c.2259T>C1.000
rpoB762083c.2277T>C1.000
rpoB762086c.2280G>C1.000
rpoB762233c.2427G>C1.000
rpoB762245c.2439G>C1.000
rpoB762284c.2478G>T1.000
rpoB762293c.2487T>G1.000
rpoB762314c.2508C>T1.000
rpoB762317c.2511A>G1.000
rpoB762329c.2523G>C1.000
rpoB762338c.2532T>C1.000
rpoB762341c.2535G>C1.000
rpoB762347c.2541T>C1.000
rpoB762857c.3051C>G1.000
rpoB762863c.3057T>C1.000
rpoB762878p.Ile1024Met1.000
rpoB762879p.Met1025Leu1.000
rpoB762929c.3123G>C1.000
rpoB762989c.3183G>A1.000
rpoB762995c.3189G>T1.000
rpoB763004c.3198G>A1.000
rpoB763007c.3201C>T1.000
rpoB763028c.3222T>C1.000
rpoB763031c.3225T>C1.000
rpoB763053c.3247T>C1.000
rpoB763070c.3264T>C1.000
rpoB763076c.3270C>T1.000
rpoB763085c.3279C>G1.000
rpoB763115c.3309T>C1.000
rpoB763127c.3321G>C1.000
rpoB763130c.3324G>A1.000
rpoB763133c.3327G>C1.000
rpoB763136c.3330C>T1.000
rpoB763142c.3336C>G1.000
rpoB763158c.3352C>T1.000
rpoB763166c.3360A>G1.000
rpoB763169c.3363A>G1.000
rpoC763375c.6C>A1.000
rpoC763468c.99G>C1.000
rpoC763483c.114G>C1.000
rpoC763484c.115C>T1.000
rpoC763528c.159G>A1.000
rpoC763546c.177A>G1.000
rpoC763570c.201G>C1.000
rpoC763573c.204G>C1.000
rpoC763576c.207C>G1.000
rpoC763594c.225C>T1.000
rpoC763621c.252C>T1.000
rpoC763633c.264T>C1.000
rpoC763660c.291T>G1.000
rpoC763666c.297G>A1.000
rpoC763675c.306C>G1.000
rpoC763699c.330G>T1.000
rpoC763702c.333C>G1.000
rpoC763705c.336G>C1.000
rpoC763709c.340C>T1.000
rpoC763714c.345G>T1.000
rpoC763717c.348T>C1.000
rpoC763723c.354G>C1.000
rpoC763741c.372C>T1.000
rpoC763747c.378G>A1.000
rpoC763765c.396T>G1.000
rpoC763792p.Glu141Asp1.000
rpoC763807c.438T>C1.000
rpoC763813c.444C>G1.000
rpoC763816c.447C>G1.000
rpoC763831c.462A>G1.000
rpoC763837c.468G>C1.000
rpoC763840c.471G>C1.000
rpoC763855c.486C>T1.000
rpoC763858c.489A>G1.000
rpoC763861c.492C>T1.000
rpoC763871p.Gly168Ser1.000
rpoC763876p.Glu169Asp1.000
rpoC763879c.510A>G1.000
rpoC763891c.522G>C1.000
rpoC763894c.525A>G1.000
rpoC763900c.531G>C1.000
rpoC763921c.552G>C1.000
rpoC763924c.555G>A1.000
rpoC763940p.Ala191Ser1.000
rpoC763945c.576T>C1.000
rpoC763947p.Ala193Val1.000
rpoC763951c.582G>C1.000
rpoC763960c.591T>G1.000
rpoC764153p.Gln262Lys1.000
rpoC764161c.792G>C1.000
rpoC764182p.Asp271Glu1.000
rpoC764188c.819A>G1.000
rpoC764215c.846A>C1.000
rpoC764217p.Asn283Ser1.000
rpoC764344c.975C>T1.000
rpoC764353c.984G>T1.000
rpoC764365c.996C>T1.000
rpoC764371c.1002G>T1.000
rpoC764380c.1011G>C1.000
rpoC764383c.1014C>G1.000
rpoC764387c.1018T>C1.000
rpoC764405c.1036A>C1.000
rpoC764485c.1116G>C1.000
rpoC764491c.1122G>T1.000
rpoC764497c.1128A>G1.000
rpoC764500c.1131C>G1.000
rpoC764521c.1152T>C1.000
rpoC764527c.1158C>T1.000
rpoC764536c.1167G>T1.000
rpoC764539c.1170C>G1.000
rpoC764575c.1206T>G1.000
rpoC764605c.1236G>C1.000
rpoC764611c.1242G>T1.000
rpoC764626c.1257C>T1.000
rpoC764632c.1263T>C1.000
rpoC764650c.1281G>T1.000
rpoC764701c.1332C>G1.000
rpoC764713c.1344G>T1.000
rpoC764746c.1377G>T1.000
rpoC764752c.1383G>C1.000
rpoC764755c.1386C>T1.000
rpoC764758c.1389C>G1.000
rpoC764764c.1395T>C1.000
rpoC764803c.1434C>T1.000
rpoC764809c.1440C>T1.000
rpoC764815c.1446A>G1.000
rpoC764911c.1542A>G1.000
rpoC764912p.Met515Gln1.000
rpoC764935c.1566T>C1.000
rpoC764948c.1579T>C1.000
rpoC764968c.1599T>C1.000
rpoC765403c.2034G>C1.000
rpoC765404p.Leu679Lys1.000
rpoC765409c.2040T>C1.000
rpoC765425p.Lys686Glu1.000
rpoC765445c.2076G>C1.000
rpoC765452p.Ala695Arg1.000
rpoC765466c.2097C>T1.000
rpoC765478c.2109T>C1.000
rpoC765480p.Tyr704Phe1.000
rpoC765496c.2127C>G1.000
rpoC765499c.2130C>G1.000
rpoC765533p.Tyr722His1.000
rpoC765826c.2457T>C1.000
rpoC765835c.2466C>T1.000
rpoC765871c.2502T>C1.000
rpoC765875p.Val836Ile1.000
rpoC765886c.2517C>G1.000
rpoC765904c.2535C>G1.000
rpoC765908c.2539C>T1.000
rpoC765934c.2565C>T1.000
rpoC765940c.2571A>T1.000
rpoC765946c.2577C>T1.000
rpoC765947c.2578T>C1.000
rpoC765952c.2583G>C1.000
rpoC765962c.2593T>C1.000
rpoC765967c.2598C>T1.000
rpoC765979c.2610C>G1.000
rpoC765982c.2613C>T1.000
rpoC765994c.2625A>T1.000
rpoC766798c.3429C>G1.000
rpoC766804c.3435A>G1.000
rpoC767068c.3699G>C1.000
rpoC767098c.3729T>C1.000
rpoC767104c.3735C>G1.000
rpoC767105p.Asn1246Gln1.000
rpoC767119c.3750A>G1.000
rpoC767158c.3789T>C1.000
rpoC767162p.Asn1265Ala1.000
rpoC767167c.3798C>T1.000
rpoC767174p.Asn1269Asp1.000
rpoC767180p.Ala1271Gln1.000
rpoC767191c.3822C>G1.000
rpoC767197c.3828G>A1.000
rpoC767221c.3852C>G1.000
rpoC767230c.3861G>C1.000
rpoC767233c.3864T>C1.000
rpsL781631c.72G>C1.000
rpsL781649c.90T>C1.000
rpsL781658c.99A>G1.000
rpsL781664c.105C>G1.000
rpsL781682c.123T>C1.000
rpsL781709c.150G>C1.000
rpsL781715c.156T>C1.000
rpsL781718c.159C>G1.000
rpsL781721c.162C>T1.000
rpsL781728c.169T>C1.000
rpsL781733c.174G>C1.000
rpsL781737p.Gln60Gly1.000
rpsL781742c.183C>T1.000
rpsL781751c.192G>C1.000
rpsL781754c.195G>C1.000
rpsL781760c.201T>C1.000
rpsL781766c.207C>T1.000
rpsL781772c.213C>T1.000
rpsL781814c.255C>T1.000
rpsL781817c.258G>T1.000
rpsL781829c.270G>C1.000
rpsL781832c.273T>C1.000
rpsL781838c.279G>C1.000
rpsL781841c.282C>T1.000
rpsL781859c.300T>G1.000
rpsL781865c.306G>C1.000
rpsL781868c.309T>C1.000
rpsL781871c.312G>C1.000
rpsL781892c.333A>G1.000
rpsL781898c.339A>C1.000
rpsL781901c.342C>T1.000
rpsL781916c.357T>G1.000
rpsL781929p.Gly124Ser1.000
rrs1471986r.141c>t1.000
rrs1472019r.174g>a1.000
rrs1472061r.216a>t1.000
rrs1472075r.230a>g1.000
rrs1472106r.261g>a1.000
rrs1472108r.263c>t1.000
rrs1472150r.305t>a1.000
rrs1472251r.406g>a1.000
rrs1472337r.492c>g1.000
rrs1472380r.535g>c1.000
rrs1472446r.601t>a1.000
rrs1472452r.607g>a1.000
rrs1472464r.619a>g1.000
rrs1472847r.1002g>c1.000
rrs1472848r.1003t>g1.000
rrs1472849r.1004c>g1.000
rrs1472850r.1005t>c1.000
rrs1472857r.1012a>g1.000
rrs1472858r.1013g>t1.000
rrs1472859r.1014g>c1.000
rrs1472860r.1015c>g1.000
rrs1472973r.1128a>t1.000
rrs1473104r.1259c>t1.000
rrs1473110r.1265t>g1.000
rrs1473111r.1266a>g1.000
rrs1473120r.1275c>ct0.906
rrs1473123r.1278a>c1.000
rrs1473276r.1431a>g1.000
rrs1473290r.1445c>cgt1.000
rrs1473301r.1456t>c1.000
rrl1473668r.11c>t1.000
rrl1473696r.39t>c1.000
rrl1473697r.40c>t1.000
rrl1473699r.42a>g1.000
rrl1473717r.60g>t0.970
rrl1473746r.89t>c1.000
rrl1473758r.101g>t1.000
rrl1473770r.113t>g1.000
rrl1473788r.131a>g1.000
rrl1473876r.219g>a1.000
rrl1473884r.227c>ca1.000
rrl1473887r.230t>a1.000
rrl1473898r.241c>t1.000
rrl1473899r.242a>g1.000
rrl1473916r.259c>a1.000
rrl1473922r.265a>g1.000
rrl1473923r.266c>g1.000
rrl1473924r.267a>at1.000
rrl1473935r.278c>t1.000
rrl1473937r.280c>t1.000
rrl1473943r.286g>t1.000
rrl1473945r.288t>a1.000
rrl1473946r.289a>t1.000
rrl1474083r.426c>t1.000
rrl1474091r.434c>t1.000
rrl1474093r.436g>a1.000
rrl1474096r.439c>t1.000
rrl1474102r.445t>ttgaac1.000
rrl1474105r.448tatca>t1.000
rrl1474110r.453a>g1.000
rrl1474135r.478g>a1.000
rrl1474140r.483c>t1.000
rrl1474151r.494c>t1.000
rrl1474174r.517a>g1.000
rrl1474181r.524c>t1.000
rrl1474183r.526t>c1.000
rrl1474185r.528g>a1.000
rrl1474186r.529a>g1.000
rrl1474249r.592g>t1.000
rrl1474266r.609t>c1.000
rrl1474269r.612c>t1.000
rrl1474301r.644g>c1.000
rrl1474303r.646a>t1.000
rrl1474306r.649a>t1.000
rrl1474362r.705a>g1.000
rrl1474374r.717t>g1.000
rrl1474446r.789c>t1.000
rrl1474626r.969t>c1.000
rrl1474627r.970g>a1.000
rrl1474629r.972g>a1.000
rrl1474632r.975g>t1.000
rrl1474636r.979a>t1.000
rrl1474637r.980c>t1.000
rrl1474638r.981c>g1.000
rrl1474639r.982g>t1.000
rrl1474640r.983c>t1.000
rrl1474673r.1016t>c1.000
rrl1474676r.1019t>a1.000
rrl1474677r.1020a>g1.000
rrl1474710r.1053t>a1.000
rrl1474711r.1054g>c1.000
rrl1474712r.1055g>a1.000
rrl1474713r.1056t>a1.000
rrl1474717r.1060a>g1.000
rrl1474720r.1063c>t1.000
rrl1474753r.1096a>g1.000
rrl1474760r.1103a>g1.000
rrl1474794r.1137c>t1.000
rrl1474812r.1155g>a1.000
rrl1474830r.1173a>g1.000
rrl1475031r.1374g>t1.000
rrl1475061r.1404c>a1.000
rrl1475062r.1405a>t1.000
rrl1475120r.1463g>t1.000
rrl1475315r.1658a>t1.000
rrl1475353r.1696a>t1.000
rrl1475354r.1697a>g1.000
rrl1475355r.1698c>t1.000
rrl1475363r.1706c>t1.000
rrl1475379r.1722g>a1.000
rrl1475380r.1723c>a1.000
rrl1475381r.1724g>c1.000
rrl1475382r.1725a>g1.000
rrl1475395r.1738t>c1.000
rrl1475396r.1739c>g1.000
rrl1475397r.1740g>t1.000
rrl1475398r.1741c>t1.000
rrl1475403r.1746t>a1.000
rrl1475404r.1747a>t1.000
rrl1475419r.1762c>t1.000
rrl1475429r.1772g>t1.000
rrl1475452r.1795c>a1.000
rrl1475479r.1822c>g1.000
rrl1475483r.1826c>t1.000
rrl1475505r.1848g>a1.000
rrl1475526r.1869c>a1.000
rrl1475531r.1874c>t1.000
rrl1475544r.1887a>t1.000
rrl1475545r.1888t>g1.000
rrl1475602r.1945g>c1.000
rrl1475603r.1946g>c1.000
rrl1475604r.1947a>c0.909
rrl1475612r.1955g>c1.000
rrl1475615r.1958c>g1.000
rrl1475616r.1959a>g1.000
rrl1475618r.1961c>t1.000
rrl1475626r.1969t>c1.000
rrl1475629r.1972g>c1.000
rrl1475637r.1980t>g1.000
rrl1475638r.1981c>g1.000
rrl1475639r.1982c>g1.000
rrl1475643r.1986c>g1.000
rrl1475647r.1990g>c1.000
rrl1475659r.2002g>a1.000
rrl1475753r.2096c>t1.000
rrl1475762r.2105g>t0.976
rrl1475763r.2106c>t1.000
rrl1475764r.2107a>c1.000
rrl1475765r.2108a>g1.000
rrl1475775r.2118g>a1.000
rrl1475988r.2331a>g1.000
rrl1475991r.2334t>c1.000
rrl1475995r.2338g>a1.000
rrl1476044r.2387t>g1.000
rrl1476045r.2388g>t1.000
rrl1476049r.2392c>t1.000
rrl1476088r.2431a>c1.000
rrl1476099r.2442a>g1.000
rrl1476103r.2446c>g1.000
rrl1476105r.2448g>a1.000
rrl1476106r.2449a>t1.000
rrl1476110r.2453g>c1.000
rrl1476115r.2458t>c1.000
rrl1476131r.2474c>t1.000
rrl1476160r.2503t>c1.000
rrl1476214r.2557g>t1.000
rrl1476215r.2558c>t1.000
rrl1476224r.2567a>g1.000
rrl1476251r.2594t>g1.000
rrl1476256r.2599a>t1.000
rrl1476260r.2603a>g1.000
rrl1476281r.2624t>c1.000
rrl1476297r.2640c>t1.000
rrl1476299r.2642c>t1.000
rrl1476529r.2872a>g1.000
rrl1476540r.2883c>t1.000
rrl1476583r.2926g>a1.000
rrl1476584r.2927c>t1.000
rrl1476594r.2937c>t1.000
rrl1476597r.2940g>a1.000
rrl1476603r.2946g>a1.000
rrl1476628r.2971t>a1.000
rrl1476664r.3007t>c1.000
rrl1476665r.3008t>c1.000
rrl1476674r.3017t>c0.968
rrl1476679r.3022t>c1.000
rrl1476689r.3032a>t1.000
rrl1476690r.3033c>t1.000
rrl1476693r.3036g>a1.000
rrl1476695r.3038t>a1.000
rrl1476716r.3059a>c1.000
rrl1476723r.3066t>a1.000
rrl1476725r.3068c>t1.000
rrl1476726r.3069a>g1.000
rrl1476731r.3074g>a1.000
rrl1476732r.3075t>c1.000
fabG11673724c.285A>G1.000
fabG11673730c.291C>G1.000
fabG11673748c.309A>G1.000
fabG11673749p.Lys104Arg1.000
fabG11673760p.Lys107Asn1.000
fabG11673772c.333C>G1.000
rpsA1833664c.123C>G1.000
rpsA1833676c.135A>G1.000
rpsA1833787c.246C>G1.000
rpsA1833790c.249T>C1.000
rpsA1833793c.252C>T1.000
rpsA1833802c.261A>G1.000
rpsA1833832c.291G>A1.000
rpsA1833838c.297G>C1.000
rpsA1833841c.300C>G1.000
rpsA1833847c.306C>G1.000
rpsA1833856c.315A>G1.000
rpsA1833862c.321G>A1.000
rpsA1833894p.Ala118Glu1.000
rpsA1833901c.360G>A1.000
rpsA1833928c.387G>C1.000
rpsA1833949c.408T>C1.000
rpsA1833970c.429G>C1.000
rpsA1833979c.438T>C1.000
rpsA1833994c.453G>C1.000
rpsA1834000c.459G>C1.000
rpsA1834009c.468C>T1.000
rpsA1834012c.471G>T1.000
rpsA1834015c.474G>C1.000
rpsA1834021c.480C>T1.000
rpsA1834030c.489C>G1.000
rpsA1834097c.556T>A1.000
rpsA1834102c.561T>C1.000
rpsA1834177c.636A>C1.000
rpsA1834189c.648G>C1.000
rpsA1834213c.672G>C1.000
rpsA1834234c.693G>C1.000
rpsA1834261c.720A>G1.000
rpsA1834264c.723G>C1.000
rpsA1834279c.738C>T1.000
rpsA1834297c.756C>T1.000
rpsA1834306c.765T>C1.000
rpsA1834345c.804C>T1.000
rpsA1834348c.807T>C1.000
rpsA1834361c.820T>C1.000
rpsA1834366c.825A>G1.000
rpsA1834387c.846C>T1.000
rpsA1834396c.855G>T1.000
rpsA1834411c.870T>C1.000
rpsA1834423c.882G>C1.000
rpsA1834451c.910T>C1.000
rpsA1834456c.915T>G1.000
rpsA1834465c.924T>C1.000
rpsA1834468c.927A>G1.000
rpsA1834489c.948T>C1.000
rpsA1834513c.972C>G1.000
rpsA1834520p.Ala327Ser1.000
rpsA1834528c.987T>C1.000
rpsA1834540c.999G>C1.000
rpsA1834543c.1002C>G1.000
rpsA1834546c.1005T>C1.000
rpsA1834606c.1065C>T1.000
rpsA1834609c.1068T>C1.000
rpsA1834619c.1078T>C1.000
rpsA1834622c.1081T>A1.000
rpsA1834633c.1092A>G1.000
rpsA1834639c.1098T>C1.000
rpsA1834654c.1113G>A1.000
rpsA1834667p.Ala376Ser1.000
rpsA1834690c.1149T>C1.000
rpsA1834798c.1257C>T1.000
panD4044180p.Asp34Glu1.000
panD4044188c.94A>G1.000
panD4044195c.87A>G1.000
embC4240717c.855T>C1.000
embC4240783c.921G>C1.000
embC4240789c.927T>C1.000
embC4240819c.957A>C1.000
embC4240825c.963G>A1.000
embC4240828c.966G>C1.000
embC4240831c.969T>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;