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: 5d726613393d4
Sample: 5d726613393d4

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Summary
ID: 5d726613393d4
Date: Fri Sep 6 15:03:03 2019
Strain: lineage4.2.2
Drug-resistance: MDR

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRkatG p.Ser315Thr (1.00)
RifampicinRrpoB p.Ser450Leu (0.95)
EthambutolRembB p.Gly406Ala (1.00)
PyrazinamideRpncA p.Asp136Gly (0.99)
StreptomycinRrpsL p.Lys88Thr (1.00)
EthionamideRethA p.Met1Arg (1.00)
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.2Euro-AmericanH;T;LAMNone
lineage4.2.2Euro-American (Ural)T;LAM7-TURNone

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA8688p.Ala463Ser1.000
gyrA9304p.Gly668Asp1.000
rpoB761489c.1683G>A1.000
rpoC764405c.1036A>C0.172
rpoC764701c.1332C>G0.196
rpoC764705p.Leu446Glu0.193
rpoC764719c.1350G>A0.226
rpsL781395c.-165T>C1.000
embR1416222p.Phe376Leu0.202
embR1416234p.Cys372Gly0.211
rrs1471896r.51t>c0.259
rrs1471900r.55c>t0.252
rrs1472127r.282c>t0.233
rrs1472129r.284g>c0.242
rrs1472137r.292g>a0.260
rrs1472150r.305t>a0.300
rrs1472172r.327t>c0.403
rrs1472203r.358g>a0.490
rrs1472210r.365a>t0.467
rrs1472213r.368g>c0.465
rrs1472225r.380c>a0.511
rrs1472236r.391c>g0.490
rrs1472240r.395g>a0.464
rrs1472344r.499c>t0.357
rrs1472379r.534t>g0.435
rrs1472382r.537g>a0.430
rrs1472400r.555c>t0.417
rrs1472530r.685g>a0.246
rrs1472537r.692c>t0.233
rrs1472541r.696t>g0.226
rrs1472544r.699c>g0.230
rrs1472545r.700a>t0.239
rrs1472557r.712g>a0.270
rrs1472571r.726g>c0.277
rrs1472573r.728c>t0.274
rrs1472579r.734g>t0.304
rrs1472581r.736a>t0.321
rrs1472598r.753a>c0.424
rrs1472616r.771g>a0.488
rrs1472655r.810g>a0.288
rrs1472658r.813g>a0.252
rrs1472661r.816a>g0.238
rrs1472697r.852t>c0.439
rrs1472708r.863t>a0.445
rrs1472713r.868t>c0.449
rrs1472716r.871c>t0.466
rrs1472733r.888g>c0.500
rrs1472734r.889c>t0.502
rrs1472741r.896g>a0.490
rrs1472742r.897c>g0.492
rrs1472744r.899a>g0.494
rrs1472781r.936c>t0.536
rrs1472793r.948a>t0.516
rrs1472803r.958t>a0.530
rrs1472895r.1050c>t0.360
rrs1473020r.1175t>c0.490
rrs1473035r.1190g>a0.546
rrs1473053r.1208t>a0.520
rrs1473056r.1211a>t0.517
rrs1473062r.1217t>a0.516
rrs1473068r.1223a>g0.496
rrs1473081r.1236c>t0.496
rrs1473145r.1300c>t0.178
rrs1473148r.1303g>a0.169
rrs1473150r.1305t>g0.164
rrs1473161r.1316a>c0.244
rrs1473163r.1318c>t0.238
rrs1473164r.1319c>g0.237
rrs1473166r.1321g>a0.256
rrs1473177r.1332g>a0.324
rrs1473192r.1347a>g0.402
rrs1473202r.1357c>t0.381
rrs1473205r.1360t>c0.420
rrs1473346r.1501g>t0.424
rrs1473365r.1520c>a0.462
rrl1473384c.-274A>C0.385
rrl1473862r.205c>a0.311
rrl1473867r.210c>g0.311
rrl1473871r.214t>g0.324
rrl1473876r.219g>a0.360
rrl1473887r.230t>c0.377
rrl1473888r.231t>a0.377
rrl1473898r.241c>t0.407
rrl1473899r.242a>c0.414
rrl1473923r.266c>g0.413
rrl1473926r.269g>c0.402
rrl1474218r.561t>a0.360
rrl1474228r.571t>c0.407
rrl1474252r.595t>a0.469
rrl1474269r.612c>t0.373
rrl1474406r.749t>c0.324
rrl1474527r.870t>g0.440
rrl1474528r.871t>c0.438
rrl1474530r.873g>c0.437
rrl1474537r.880g>a0.455
rrl1474539r.882c>g0.455
rrl1474542r.885a>c0.470
rrl1474552r.895c>g0.496
rrl1474558r.901g>c0.510
rrl1474562r.905g>c0.533
rrl1474570r.913g>t0.563
rrl1474571r.914g>t0.566
rrl1474578r.921a>g0.568
rrl1474584r.927c>g0.605
rrl1474586r.929t>a0.606
rrl1474798r.1141c>t0.145
rrl1474801r.1144g>a0.147
rrl1474804r.1147c>t0.174
rrl1474816r.1159g>c0.265
rrl1474823r.1166c>g0.291
rrl1474827r.1170c>t0.297
rrl1474830r.1173a>c0.301
rrl1474831r.1174a>c0.307
rrl1474844r.1187g>t0.428
rrl1474866r.1209c>a0.488
rrl1474869r.1212g>t0.506
rrl1474896r.1239a>g0.516
rrl1474902r.1245t>c0.522
rrl1474904r.1247g>c0.520
rrl1474910r.1253c>g0.513
rrl1474913r.1256t>a0.478
rrl1474920r.1263g>a0.466
rrl1475574r.1917c>g0.407
rrl1475672r.2015c>g0.389
rrl1475673r.2016t>c0.406
rrl1475687r.2030c>t0.450
rrl1475688r.2031g>c0.444
rrl1475696r.2039t>c0.477
rrl1475703r.2046a>g0.506
rrl1475707r.2050t>a0.494
rrl1475713r.2056c>g0.490
rrl1475716r.2059a>g0.488
rrl1475803r.2146t>c0.537
rrl1475804r.2147g>c0.546
rrl1475816r.2159c>g0.572
rrl1475817r.2160a>g0.585
rrl1475858r.2201t>c0.621
rrl1475866r.2209t>a0.548
rrl1476141r.2484a>g0.209
rrl1476153r.2496t>c0.246
rrl1476165r.2508t>g0.266
rrl1476194r.2537a>g0.204
rrl1476195r.2538c>a0.203
rrl1476196r.2539c>a0.206
rrl1476200r.2543a>t0.204
rrl1476204r.2547c>a0.200
rrl1476210r.2553g>t0.199
rrl1476211r.2554g>t0.198
rrl1476212r.2555t>c0.209
rrl1476214r.2557g>c0.211
rrl1476215r.2558c>a0.224
rrl1476225r.2568t>g0.403
rrl1476229r.2572c>g0.431
rrl1476251r.2594t>c0.530
rrl1476260r.2603a>g0.543
rrl1476280r.2623a>c0.551
rrl1476293r.2636c>t0.233
rrl1476294r.2637a>g0.228
rrl1476295r.2638c>g0.224
rrl1476296r.2639c>t0.227
rrl1476297r.2640c>t0.219
rrl1476301r.2644a>c0.218
rrl1476302r.2645g>a0.210
rrl1476311r.2654g>c0.281
rrl1476312r.2655t>c0.281
rrl1476313r.2656g>a0.288
rrl1476332r.2675g>c0.465
rrl1476338r.2681c>t0.498
rrl1476353r.2696g>t0.576
rrl1476358r.2701t>c0.593
rrl1476372r.2715t>c0.620
rrl1476382r.2725a>g0.653
rrl1476383r.2726t>a0.657
rrl1476408r.2751g>a0.691
rrl1476425r.2768g>a0.693
rrl1476428r.2771c>t0.698
rrl1476466r.2809c>t0.815
rrl1476481r.2824t>c0.820
rrl1476506r.2849t>c0.751
rrl1476512r.2855c>t0.588
rrl1476514r.2857c>t0.580
rrl1476519r.2862c>g0.570
rrl1476523r.2866t>c0.481
rrl1476524r.2867c>a0.528
rrl1476525r.2868a>g0.528
rrl1476529r.2872a>g0.519
rrl1476530r.2873c>t0.530
rrl1476538r.2881a>g0.522
rrl1476540r.2883c>g0.556
rrl1476547r.2890c>t0.660
rrl1476567r.2910c>t0.674
rrl1476573r.2916a>c0.668
rrl1476577r.2920t>g0.683
rrl1476594r.2937c>t0.639
rrl1476603r.2946g>a0.614
rrl1476608r.2951c>a0.579
rrl1476614r.2957a>g0.466
rrl1476619r.2962c>t0.446
rrl1476621r.2964c>t0.431
rrl1476624r.2967t>g0.431
rrl1476628r.2971t>a0.399
rrl1476630r.2973a>g0.414
rrl1476637r.2980c>g0.504
tlyA1917972c.33A>G1.000
ahpC2726146c.-47G>GT0.994
ald3086788c.-32T>C1.000
alr3841662c.-242A>G0.256
alr3841663c.-243G>A0.216
embC4242643c.2781C>T1.000
gid4407997p.Gly69Asp1.000

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;