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: 5db5092eda261
Sample: 5db5092eda261

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Summary
ID: 5db5092eda261
Date: Sun Oct 27 03:10:55 2019
Strain: lineage4.6.1.1
Drug-resistance: Sensitive

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

Lineage2FamilyMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.6Euro-AmericanT;LAMNone
lineage4.6.1Euro-American (Uganda)T2RD724
lineage4.6.1.1Euro-AmericanT2-UgandaRD724

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6170p.His311Ala0.135
gyrA7362p.Glu21Gln1.000
gyrA7539p.Thr80Ala0.897
gyrA7585p.Ser95Thr1.000
gyrA7703c.402G>C0.136
gyrA7710c.409T>C0.138
gyrA7728c.427A>C0.191
gyrA7763c.462T>G0.247
gyrA7775c.474C>T0.244
gyrA7784c.483A>G0.183
gyrA7787c.486G>A0.165
gyrA7793c.492G>C0.158
gyrA8294c.993T>C0.129
gyrA8324c.1023T>C0.196
gyrA8327c.1026C>T0.191
gyrA8339c.1038A>G0.209
gyrA8366c.1065G>C0.200
gyrA9304p.Gly668Asp0.986
rpoB760196c.390C>G0.157
rpoB760208p.Ile134Met0.167
rpoB760223c.417T>C0.170
rpoB760235c.429T>C0.173
rpoB760265p.Met153Ile0.162
rpoB760283c.477G>C0.138
rpoB760406c.600G>C0.171
rpoB760415c.609C>T0.234
rpoB760424c.618C>G0.241
rpoB760430c.624T>C0.247
rpoB760457c.651C>G0.278
rpoB760475c.669A>G0.253
rpoB760481c.675G>C0.233
rpoB760484c.678A>G0.215
rpoB760485p.Pro227Ser0.215
rpoB760928c.1122G>C0.158
rpoB760934c.1128C>T0.183
rpoB760946c.1140A>G0.235
rpoB760964c.1158C>G0.288
rpoB760965p.Met387Leu0.276
rpoB760970c.1164G>C0.287
rpoB760985c.1179G>T0.265
rpoB760991c.1185G>C0.247
rpoB761015c.1209G>C0.284
rpoB761027c.1221A>G0.289
rpoB761036c.1230G>C0.244
rpoB761037c.1231T>C0.247
rpoB761051c.1245G>C0.227
rpoB761097c.1291A>T0.157
rpoB761102c.1296A>G0.167
rpoB761129c.1323G>C0.194
rpoB761133c.1327T>C0.196
rpoB761150c.1344A>G0.170
rpoB761282c.1476C>G0.180
rpoB761300c.1494G>C0.205
rpoB761327c.1521A>G0.168
rpoB761333c.1527G>C0.173
rpoB761345c.1539G>C0.172
rpoB762053c.2247T>C0.126
rpoB762083c.2277T>C0.127
rpoB762086c.2280G>C0.128
rpoB762170c.2364C>G0.147
rpoB762176c.2370T>C0.130
rpoB762185c.2379G>C0.121
rpoB762293c.2487T>C0.156
rpoB762314c.2508C>G0.134
rpoB762317c.2511A>G0.135
rpoB762857c.3051C>G0.160
rpoB762860c.3054G>C0.158
rpoB762863c.3057T>C0.167
rpoB762929c.3123G>C0.291
rpoB762983c.3177C>T0.184
rpoB762995c.3189G>T0.157
rpoB763166c.3360A>G0.154
rpoB763169c.3363A>G0.155
rpoC763468c.99G>C0.161
rpoC763486c.117T>C0.170
rpoC763489c.120G>A0.179
rpoC763492c.123G>C0.194
rpoC763546c.177A>G0.265
rpoC763696c.327T>C0.190
rpoC763702c.333C>G0.181
rpoC763717c.348T>C0.159
rpoC763732c.363C>G0.198
rpoC763744c.375G>C0.184
rpoC763765c.396T>C0.150
rpoC764060p.Pro231Thr0.124
rpoC764083c.714A>G0.156
rpoC764098c.729A>G0.188
rpoC764102p.Val245Ile0.182
rpoC764134c.765C>G0.203
rpoC764140c.771C>T0.173
rpoC764143c.774G>C0.164
rpoC764147p.Ser260Ala0.145
rpoC764194p.Glu275Asp0.128
rpoC764236c.867G>A0.141
rpoC764257c.888G>C0.164
rpoC764266c.897T>C0.162
rpoC764278c.909A>G0.167
rpoC764284c.915G>C0.179
rpoC764338c.969G>A0.156
rpoC764347c.978G>C0.122
rpoC764500c.1131C>G0.116
rpoC764503c.1134G>C0.116
rpoC764575c.1206T>G0.158
rpoC764581c.1212T>C0.179
rpoC764626c.1257C>T0.206
rpoC764644c.1275G>C0.196
rpoC764650c.1281G>T0.198
rpoC764656c.1287C>G0.206
rpoC764695c.1326T>C0.198
rpoC764701c.1332C>G0.191
rpoC764713c.1344G>A0.144
rpoC764716c.1347G>C0.135
rpoC764746c.1377G>C0.190
rpoC764752c.1383G>C0.183
rpoC764758c.1389C>G0.187
rpoC764764c.1395T>C0.177
rpoC765409c.2040T>C0.136
rpoC765412c.2043T>C0.139
rpoC765421c.2052C>G0.148
rpoC765435p.His689Pro0.828
rpoC765454c.2085C>G0.202
rpoC765466c.2097C>T0.200
rpoC765478c.2109T>C0.214
rpoC765493c.2124G>C0.239
rpoC765586c.2217G>C0.170
rpoC765728p.Gln787Glu0.160
rpoC765734c.2365T>C0.131
rpoC765739c.2370G>C0.143
rpoC765742p.Glu791Asp0.138
rpoC765781p.Asp804Glu0.132
rpoC765796c.2427C>T0.142
rpoC765850c.2481G>C0.181
rpoC765875p.Val836Ile0.200
rpoC765886c.2517C>G0.184
rpoC765892c.2523T>C0.184
rpoC765898c.2529C>T0.179
rpoC766348c.2979A>G0.128
rpoC766381c.3012C>T0.131
rpoC766384c.3015A>G0.143
rpoC766390c.3021C>T0.155
rpoC766426c.3057C>T0.186
rpoC766447c.3078T>C0.168
rpoC766456c.3087C>G0.176
rpoC766714c.3345G>C0.144
rpoC766726c.3357T>C0.143
rpoC766738c.3369G>C0.163
rpoC766765c.3396A>C0.197
rpoC766774c.3405T>C0.165
rpoC766775p.Arg1136Lys0.165
rpoC766804c.3435A>G0.209
rpoC766813c.3444G>C0.200
rpoC766843c.3474T>C0.141
rpoC766846c.3477C>G0.137
rpoC766996c.3627C>G0.222
rpoC767002c.3633G>C0.247
rpoC767011c.3642G>C0.280
rpoC767035c.3666G>C0.244
rpoC767044c.3675G>C0.232
rpoC767059c.3690T>C0.184
rpoC767062c.3693C>G0.170
rpoC767068c.3699G>C0.156
rpoC767074c.3705T>C0.140
rpoC767206c.3837C>G0.155
rpoC767209c.3840T>C0.165
rpoC767221c.3852C>G0.144
rpsL781395c.-165T>C1.000
rpsL781808c.249C>G0.176
rpsL781832c.273T>C0.160
rrs1471923r.78t>c0.224
rrs1471925r.80t>c0.220
rrs1471932r.87a>g0.211
rrs1471934r.89a>g0.219
rrs1471936r.91a>g0.220
rrs1472061r.216a>t0.165
rrs1472075r.230a>g0.218
rrs1472106r.261g>t0.305
rrs1472108r.263c>t0.327
rrs1472225r.380c>g0.347
rrs1472435r.590t>c0.293
rrs1472438r.593t>c0.287
rrs1472448r.603t>c0.274
rrs1472451r.606c>t0.279
rrs1472464r.619a>g0.298
rrs1472489r.644a>g0.285
rrs1472858r.1013g>t0.130
rrs1472859r.1014g>c0.131
rrs1472860r.1015c>g0.131
rrs1472880r.1035g>a0.303
rrs1472952r.1107t>c0.390
rrs1472955r.1110c>t0.350
rrs1472956r.1111t>c0.349
rrs1472969r.1124a>g0.342
rrs1472973r.1128a>g0.322
rrs1472978r.1133t>c0.280
rrs1472987r.1142g>a0.262
rrs1472990r.1145a>g0.262
rrs1473104r.1259c>t0.318
rrs1473110r.1265t>g0.288
rrs1473111r.1266a>g0.288
rrs1473123r.1278a>c0.263
rrs1473289r.1444t>a0.248
rrs1473290r.1445c>a0.242
rrs1473294r.1449a>g0.250
rrl1473668r.11c>t0.240
rrl1473677r.20c>t0.265
rrl1473698r.41g>a0.316
rrl1473699r.42a>g0.316
rrl1473758r.101g>a0.274
rrl1473806r.149c>t0.143
rrl1473871r.214t>c0.178
rrl1473876r.219g>a0.188
rrl1473898r.241c>t0.180
rrl1473899r.242a>t0.178
rrl1474016r.359c>g0.217
rrl1474026r.369c>t0.228
rrl1474083r.426c>t0.341
rrl1474093r.436g>a0.299
rrl1474103r.446a>t0.200
rrl1474105r.448t>c0.185
rrl1474106r.449a>g0.183
rrl1474107r.450t>g0.183
rrl1474109r.452a>g0.179
rrl1474110r.453a>t0.176
rrl1474151r.494c>t0.330
rrl1474174r.517a>g0.333
rrl1474181r.524c>t0.296
rrl1474183r.526t>c0.287
rrl1474184r.527c>t0.293
rrl1474201r.544t>c0.360
rrl1474202r.545t>g0.366
rrl1474249r.592g>t0.330
rrl1474263r.606g>a0.250
rrl1474266r.609t>c0.239
rrl1474282r.625g>a0.163
rrl1474356r.699t>c0.278
rrl1474362r.705a>g0.269
rrl1474381r.724t>g0.173
rrl1474387r.730c>t0.168
rrl1474495r.838g>a0.273
rrl1474496r.839c>g0.273
rrl1474497r.840g>c0.269
rrl1474498r.841g>a0.263
rrl1474505r.848c>t0.266
rrl1474506r.849c>g0.280
rrl1474507r.850g>c0.280
rrl1474508r.851c>t0.276
rrl1474632r.975g>c0.134
rrl1474710r.1053t>c0.177
rrl1474712r.1055g>t0.163
rrl1474753r.1096a>g0.380
rrl1474760r.1103a>g0.400
rrl1474794r.1137c>t0.427
rrl1474812r.1155g>a0.408
rrl1474830r.1173a>g0.353
rrl1475061r.1404c>t0.404
rrl1475202r.1545g>c0.309
rrl1475209r.1552g>a0.272
rrl1475217r.1560t>a0.261
rrl1475291r.1634a>c0.247
rrl1475315r.1658a>t0.312
rrl1475355r.1698c>t0.248
rrl1475369r.1712g>c0.146
rrl1475429r.1772g>t0.133
rrl1475430r.1773t>a0.131
rrl1475453r.1796t>a0.226
rrl1475460r.1803a>g0.255
rrl1475480r.1823a>t0.324
rrl1475505r.1848g>a0.450
rrl1475526r.1869c>a0.447
rrl1475544r.1887a>t0.416
rrl1475545r.1888t>g0.425
rrl1475586r.1929c>a0.333
rrl1475659r.2002g>a0.316
rrl1475775r.2118g>t0.192
rrl1475995r.2338g>a0.444
rrl1475997r.2340a>g0.433
rrl1476033r.2376t>c0.210
rrl1476034r.2377c>g0.217
rrl1476035r.2378g>c0.217
rrl1476044r.2387t>g0.217
rrl1476045r.2388g>t0.217
rrl1476049r.2392c>t0.250
rrl1476076r.2419a>g0.311
rrl1476085r.2428g>a0.224
rrl1476086r.2429g>a0.217
rrl1476088r.2431a>c0.225
rrl1476103r.2446c>g0.227
rrl1476105r.2448g>c0.242
rrl1476106r.2449a>t0.242
rrl1476110r.2453g>c0.254
rrl1476115r.2458t>c0.306
rrl1476165r.2508t>a0.380
rrl1476214r.2557g>t0.353
rrl1476215r.2558c>t0.343
rrl1476224r.2567a>g0.372
rrl1476245r.2588c>t0.393
rrl1476252r.2595t>g0.333
rrl1476256r.2599a>c0.337
rrl1476262r.2605g>a0.364
rrl1476281r.2624t>c0.337
rrl1476540r.2883c>a0.360
rrl1476583r.2926g>a0.343
rrl1476597r.2940g>a0.333
rrl1476628r.2971t>a0.413
rrl1476664r.3007t>c0.256
rrl1476665r.3008t>c0.244
rrl1476666r.3009c>t0.244
rrl1476674r.3017t>c0.238
rrl1476690r.3033c>t0.203
rrl1476691r.3034t>c0.211
rrl1476692r.3035t>a0.211
rrl1476693r.3036g>a0.208
rpsA1834411c.870T>C0.128
tlyA1917972c.33A>G1.000
kasA2519137c.1023T>G0.178
kasA2519143c.1029G>C0.194
kasA2519152c.1038G>C0.197
kasA2519158c.1044C>T0.219
kasA2519194c.1080G>C0.151
kasA2519197c.1083G>C0.137
kasA2519202p.Arg363His0.148
eis2715188p.Arg49Cys1.000
ahpC2726669c.477T>C0.133
ahpC2726681c.489A>G0.122
alr3841652c.-232A>T0.988
alr3841654c.-234A>C0.990
alr3841662c.-242A>G0.990
alr3841663c.-243G>A0.989
embC4242643c.2781C>T1.000

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;