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: 5dc6cc8971730
Sample: 5dc6cc8971730

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Summary
ID: 5dc6cc8971730
Date: Sat Nov 9 14:27:47 2019
Strain: lineage4.4;lineage4.8
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
StreptomycinRrrs r.888g>a (0.33)
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.4Euro-AmericanS;TNone
lineage4.8Euro-American (mainly T)T1;T2;T3;T5RD219

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
rpsL781395c.-165T>C1.000
embR1416222p.Phe376Leu0.149
rrs1471878r.33c>t0.146
rrs1471896r.51t>c0.238
rrs1471900r.55c>t0.233
rrs1472112r.267c>t0.353
rrs1472122r.277g>a0.245
rrs1472127r.282c>t0.259
rrs1472129r.284g>c0.257
rrs1472137r.292g>a0.339
rrs1472150r.305t>a0.504
rrs1472151r.306c>t0.364
rrs1472164r.319g>a0.288
rrs1472172r.327t>c0.484
rrs1472177r.332c>t0.312
rrs1472203r.358g>a0.347
rrs1472210r.365a>c0.279
rrs1472213r.368g>c0.274
rrs1472215r.370a>g0.284
rrs1472225r.380c>a0.324
rrs1472234r.389t>c0.283
rrs1472236r.391c>g0.286
rrs1472240r.395g>a0.289
rrs1472251r.406g>a0.333
rrs1472338r.493a>g0.122
rrs1472344r.499c>t0.344
rrs1472378r.533g>t0.374
rrs1472379r.534t>g0.387
rrs1472380r.535g>c0.140
rrs1472382r.537g>a0.255
rrs1472389r.544g>a0.286
rrs1472396r.551a>t0.171
rrs1472400r.555c>t0.431
rrs1472412r.567a>c0.219
rrs1472415r.570t>g0.216
rrs1472416r.571c>t0.143
rrs1472422r.577t>c0.342
rrs1472494r.649a>g0.167
rrs1472496r.651t>a0.143
rrs1472498r.653c>t0.187
rrs1472517r.672t>a0.206
rrs1472518r.673g>t0.221
rrs1472530r.685g>a0.279
rrs1472541r.696t>g0.176
rrs1472544r.699c>a0.248
rrs1472545r.700a>t0.233
rrs1472557r.712g>a0.248
rrs1472570r.725g>a0.190
rrs1472571r.726g>c0.304
rrs1472573r.728c>t0.232
rrs1472579r.734g>t0.271
rrs1472581r.736a>t0.440
rrs1472596r.751g>t0.229
rrs1472598r.753a>t0.270
rrs1472614r.769g>t0.212
rrs1472616r.771g>a0.296
rrs1472655r.810g>a0.267
rrs1472658r.813g>a0.204
rrs1472660r.815t>c0.173
rrs1472661r.816a>g0.198
rrs1472675r.830t>c0.157
rrs1472679r.834t>c0.149
rrs1472690r.845c>a0.220
rrs1472692r.847t>c0.131
rrs1472697r.852t>c0.210
rrs1472713r.868t>c0.327
rrs1472714r.869a>g0.156
rrs1472716r.871c>t0.333
rrs1472742r.897c>t0.338
rrs1472744r.899a>g0.344
rrs1472767r.922g>a0.248
rrs1472781r.936c>t0.351
rrs1472790r.945t>c0.128
rrs1472793r.948a>t0.338
rrs1472803r.958t>a0.331
rrs1472824r.979t>a0.182
rrs1472825r.980g>a0.126
rrs1472828r.983t>c0.161
rrs1472870r.1025t>g0.136
rrs1472875r.1030t>a0.108
rrs1472895r.1050c>t0.446
rrs1472956r.1111t>c0.156
rrs1472957r.1112c>t0.130
rrs1472973r.1128a>t0.156
rrs1472987r.1142g>a0.117
rrs1472989r.1144g>a0.111
rrs1472990r.1145a>g0.183
rrs1473035r.1190g>a0.360
rrs1473053r.1208t>a0.129
rrs1473055r.1210c>t0.211
rrs1473056r.1211a>t0.289
rrs1473062r.1217t>a0.135
rrs1473066r.1221a>g0.182
rrs1473068r.1223a>g0.124
rrs1473088r.1243a>g0.182
rrs1473093r.1248c>t0.241
rrs1473100r.1255g>a0.221
rrs1473102r.1257c>t0.115
rrs1473104r.1259c>t0.182
rrs1473110r.1265t>g0.178
rrs1473111r.1266a>g0.167
rrs1473115r.1270g>t0.133
rrs1473121r.1276t>c0.250
rrs1473123r.1278a>t0.139
rrs1473145r.1300c>t0.287
rrs1473166r.1321g>a0.299
rrs1473173r.1328c>t0.121
rrs1473177r.1332g>a0.210
rrs1473191r.1346c>t0.164
rrs1473192r.1347a>g0.155
rrs1473202r.1357c>t0.158
rrs1473205r.1360t>c0.142
rrs1473206r.1361g>a0.163
rrs1473226r.1381c>t0.226
rrs1473248r.1403g>a0.151
rrs1473249r.1404t>c0.151
rrs1473252r.1407t>c0.330
rrs1473255r.1410a>g0.147
rrs1473259r.1414c>t0.319
rrs1473260r.1415g>t0.146
rrs1473276r.1431a>g0.230
rrs1473281r.1436c>a0.122
rrs1473282r.1437c>g0.152
rrs1473288r.1443c>a0.136
rrs1473290r.1445c>t0.198
rrs1473291r.1446g>t0.146
rrs1473296r.1451g>c0.165
rrs1473297r.1452g>t0.126
rrs1473301r.1456t>c0.221
rrs1473316r.1471c>t0.123
rrs1473327r.1482a>g0.170
rrs1473328r.1483c>t0.176
rrs1473352r.1507c>t0.391
rrl1473698r.41g>a0.132
rrl1473871r.214t>c0.147
rrl1473876r.219g>a0.156
rrl1474001r.344c>t1.000
rrl1474151r.494c>t0.122
rrl1474155r.498g>a0.125
rrl1474164r.507c>t0.159
rrl1474181r.524c>t0.119
rrl1474184r.527c>t0.149
rrl1474185r.528g>a0.143
rrl1474197r.540c>t0.170
rrl1474218r.561t>a0.338
rrl1474228r.571t>c0.271
rrl1474249r.592g>t0.384
rrl1474252r.595t>a0.300
rrl1474269r.612c>t0.130
rrl1474330r.673a>t0.145
rrl1474476r.819c>t0.140
rrl1474488r.831g>t0.195
rrl1474496r.839c>a0.150
rrl1474497r.840g>c0.150
rrl1474506r.849c>g0.214
rrl1474507r.850g>t0.220
rrl1474516r.859c>a0.250
rrl1474529r.872a>c0.256
rrl1474530r.873g>a0.256
rrl1474537r.880g>a0.256
rrl1474539r.882c>t0.262
rrl1474540r.883t>g0.262
rrl1474558r.901g>a0.204
rrl1474584r.927c>t0.256
rrl1474627r.970g>a0.140
rrl1474632r.975g>t0.140
rrl1474636r.979a>t0.143
rrl1474637r.980c>t0.163
rrl1474638r.981c>g0.178
rrl1474639r.982g>c0.133
rrl1474672r.1015c>t0.220
rrl1474674r.1017a>c0.184
rrl1474675r.1018c>a0.184
rrl1474676r.1019t>c0.184
rrl1474677r.1020a>g0.229
rrl1474694r.1037c>t0.220
rrl1474723r.1066g>a0.222
rrl1474734r.1077g>a0.233
rrl1474736r.1079c>t0.227
rrl1474749r.1092c>t0.195
rrl1474751r.1094g>a0.190
rrl1474754r.1097c>t0.195
rrl1474760r.1103a>g0.138
rrl1474777r.1120t>c0.238
rrl1474779r.1122g>a0.220
rrl1474782r.1125g>a0.220
rrl1474783r.1126g>a0.190
rrl1474794r.1137c>t0.195
rrl1474823r.1166c>g0.189
rrl1474827r.1170c>t0.184
rrl1474830r.1173a>t0.184
rrl1474831r.1174a>t0.184
rrl1474839r.1182c>t0.400
rrl1474844r.1187g>t0.394
rrl1474864r.1207c>t0.537
rrl1474866r.1209c>a0.394
rrl1474869r.1212g>t0.377
rrl1474892r.1235g>a0.500
rrl1474896r.1239a>g0.508
rrl1474902r.1245t>c0.493
rrl1474903r.1246t>a0.397
rrl1474904r.1247g>c0.559
rrl1474913r.1256t>a0.508
rrl1474920r.1263g>c0.492
rrl1475124r.1467a>t0.250
rrl1475129r.1472g>t0.278
rrl1475137r.1480a>t0.357
rrl1475144r.1487g>c0.227
rrl1475145r.1488c>t0.244
rrl1475163r.1506t>g0.292
rrl1475171r.1514c>t0.370
rrl1475175r.1518g>a0.439
rrl1475188r.1531c>t0.273
rrl1475498r.1841c>g0.172
rrl1475499r.1842c>t0.164
rrl1475539r.1882a>t0.171
rrl1475545r.1888t>g0.163
rrl1475548r.1891c>t0.152
rrl1475549r.1892t>c0.156
rrl1475574r.1917c>a0.526
rrl1475699r.2042c>t0.111
rrl1475775r.2118g>t0.143
rrl1475783r.2126t>g0.210
rrl1475803r.2146t>c0.542
rrl1475804r.2147g>c0.537
rrl1475816r.2159c>g0.596
rrl1475817r.2160a>g0.589
rrl1475858r.2201t>c0.546
rrl1475866r.2209t>a0.551
rrl1475881r.2224t>c0.122
rrl1475883r.2226a>t0.125
rrl1475898r.2241a>g0.140
rrl1475899r.2242g>a0.140
rrl1475916r.2259c>g0.140
rrl1475937r.2280a>t0.189
rrl1475943r.2286g>a0.179
rrl1475952r.2295a>g0.132
rrl1476126r.2469c>t0.283
rrl1476130r.2473g>a0.323
rrl1476135r.2478t>c0.431
rrl1476141r.2484a>g0.435
rrl1476153r.2496t>c0.443
rrl1476164r.2507a>g0.127
rrl1476165r.2508t>g0.448
rrl1476179r.2522c>t0.230
rrl1476194r.2537a>g0.326
rrl1476195r.2538c>a0.174
rrl1476196r.2539c>a0.152
rrl1476200r.2543a>t0.326
rrl1476201r.2544c>t0.326
rrl1476204r.2547c>a0.186
rrl1476210r.2553g>t0.152
rrl1476211r.2554g>t0.174
rrl1476212r.2555t>c0.174
rrl1476214r.2557g>t0.225
rrl1476215r.2558c>a0.205
rrl1476225r.2568t>g0.435
rrl1476227r.2570c>t0.141
rrl1476229r.2572c>t0.438
rrl1476250r.2593c>g0.209
rrl1476251r.2594t>c0.424
rrl1476257r.2600g>c0.217
rrl1476260r.2603a>g0.554
rrl1476268r.2611a>t0.256
rrl1476275r.2618t>a0.259
rrl1476279r.2622g>a0.253
rrl1476280r.2623a>c0.458
rrl1476293r.2636c>t0.413
rrl1476294r.2637a>g0.444
rrl1476295r.2638c>g0.431
rrl1476296r.2639c>t0.438
rrl1476297r.2640c>t0.411
rrl1476301r.2644a>c0.271
rrl1476302r.2645g>a0.390
rrl1476311r.2654g>c0.421
rrl1476312r.2655t>c0.423
rrl1476313r.2656g>a0.356
rrl1476332r.2675g>c0.444
rrl1476338r.2681c>t0.205
rrl1476353r.2696g>t0.480
rrl1476358r.2701t>c0.492
rrl1476359r.2702c>g0.129
rrl1476369r.2712c>t0.457
rrl1476372r.2715t>c0.473
rrl1476381r.2724g>c0.147
rrl1476382r.2725a>g0.504
rrl1476383r.2726t>a0.504
rrl1476408r.2751g>a0.248
rrl1476425r.2768g>t0.496
rrl1476428r.2771c>t0.643
rrl1476429r.2772a>c0.640
rrl1476466r.2809c>t0.425
rrl1476481r.2824t>c0.663
rrl1476506r.2849t>c0.638
rrl1476514r.2857c>t0.158
rrl1476515r.2858c>t0.263
rrl1476517r.2860c>t0.193
rrl1476519r.2862c>g0.158
rrl1476524r.2867c>t0.227
rrl1476525r.2868a>g0.382
rrl1476530r.2873c>t0.286
rrl1476536r.2879g>a0.309
rrl1476537r.2880a>g0.155
rrl1476538r.2881a>g0.172
rrl1476539r.2882a>g0.155
rrl1476540r.2883c>g0.293
rrl1476547r.2890c>t0.322
rrl1476567r.2910c>t0.217
rrl1476572r.2915g>a0.167
rrl1476573r.2916a>t0.155
rrl1476584r.2927c>t0.316
rrl1476585r.2928a>g0.143
rrl1476608r.2951c>g0.152
rrl1476614r.2957a>t0.143
rrl1476619r.2962c>t0.146
tlyA1917972c.33A>G1.000
alr3841652c.-232A>T0.228
alr3841654c.-234A>C0.231
alr3841662c.-242A>G0.302
alr3841663c.-243G>A0.260
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;