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: 5dca5b5a5ce25
Sample: 5dca5b5a5ce25

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Summary
ID: 5dca5b5a5ce25
Date: Tue Nov 12 07:16:08 2019
Strain: lineage2.2.1
Drug-resistance: MDR

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRkatG p.Ser315Thr (0.99)
RifampicinRrpoB p.His445Arg (1.00)
EthambutolRembB p.Met306Ile (0.23), embB p.Gly406Ser (0.73)
PyrazinamideRpncA c.-11A>G (0.71)
Streptomycin
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage2East-AsianBeijingRD105
lineage2.2East-Asian (Beijing)Beijing-RD207RD105;RD207
lineage2.2.1East-Asian (Beijing)Beijing-RD181RD105;RD207;RD181

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA9304p.Gly668Asp1.000
rpoB763031c.3225T>C1.000
rpsL781395c.-165T>C1.000
rrs1471896r.51t>c0.472
rrs1471900r.55c>t0.459
rrs1472106r.261g>a0.222
rrs1472112r.267c>t0.205
rrs1472113r.268t>c0.200
rrs1472127r.282c>t0.383
rrs1472129r.284g>c0.383
rrs1472137r.292g>a0.435
rrs1472150r.305t>a0.438
rrs1472151r.306c>a0.422
rrs1472172r.327t>c0.478
rrs1472203r.358g>a0.432
rrs1472210r.365a>c0.419
rrs1472213r.368g>c0.392
rrs1472215r.370a>g0.392
rrs1472225r.380c>a0.319
rrs1472234r.389t>c0.254
rrs1472236r.391c>g0.242
rrs1472240r.395g>a0.246
rrs1472344r.499c>t0.462
rrs1472379r.534t>g0.439
rrs1472382r.537g>a0.439
rrs1472400r.555c>t0.354
rrs1472507r.662c>g0.256
rrs1472517r.672t>a0.256
rrs1472518r.673g>c0.262
rrs1472530r.685g>a0.392
rrs1472537r.692c>t0.436
rrs1472544r.699c>g0.436
rrs1472545r.700a>t0.436
rrs1472557r.712g>a0.464
rrs1472570r.725g>a0.433
rrs1472571r.726g>c0.433
rrs1472581r.736a>t0.424
rrs1472598r.753a>c0.433
rrs1472616r.771g>a0.431
rrs1472734r.889c>t0.469
rrs1472741r.896g>a0.493
rrs1472744r.899a>g0.479
rrs1472767r.922g>a0.500
rrs1472779r.934g>a0.500
rrs1472781r.936c>t0.515
rrs1472786r.941c>t0.485
rrs1472793r.948a>t0.493
rrs1472803r.958t>a0.493
rrs1472895r.1050c>t0.500
rrs1473020r.1175t>c0.333
rrs1473035r.1190g>a0.366
rrs1473053r.1208t>a0.298
rrs1473055r.1210c>t0.298
rrs1473056r.1211a>t0.293
rrs1473062r.1217t>a0.298
rrs1473068r.1223a>g0.321
rrs1473070r.1225g>a0.327
rrs1473081r.1236c>t0.365
rrs1473089r.1244a>c0.279
rrs1473093r.1248c>a0.268
rrs1473094r.1249t>a0.268
rrs1473099r.1254t>a0.237
rrs1473130r.1285g>a0.176
rrs1473177r.1332g>a0.275
rrs1473179r.1334c>t0.288
rrs1473192r.1347a>g0.291
rrs1473202r.1357c>t0.242
rrs1473205r.1360t>c0.250
rrs1473226r.1381c>t0.408
rrs1473352r.1507c>t0.394
rrl1474218r.561t>a0.324
rrl1474228r.571t>c0.171
rrl1474527r.870t>g0.143
rrl1474530r.873g>t0.147
rrl1474537r.880g>a0.152
rrl1474539r.882c>a0.152
rrl1474542r.885a>c0.200
rrl1474552r.895c>g0.226
rrl1474555r.898t>g0.226
rrl1474562r.905g>c0.212
rrl1474565r.908t>a0.219
rrl1474570r.913g>t0.235
rrl1474571r.914g>t0.222
rrl1474578r.921a>g0.237
rrl1474584r.927c>g0.270
rrl1474586r.929t>a0.263
rrl1474777r.1120t>c0.200
rrl1474779r.1122g>a0.200
rrl1474780r.1123c>t0.200
rrl1474782r.1125g>a0.205
rrl1474790r.1133c>t0.244
rrl1474798r.1141c>t0.310
rrl1474804r.1147c>t0.317
rrl1474823r.1166c>g0.326
rrl1474827r.1170c>t0.333
rrl1474831r.1174a>c0.348
rrl1474844r.1187g>t0.354
rrl1474866r.1209c>a0.463
rrl1474869r.1212g>t0.442
rrl1474896r.1239a>g0.341
rrl1474902r.1245t>c0.349
rrl1474904r.1247g>c0.349
rrl1474913r.1256t>a0.317
rrl1474920r.1263g>a0.250
rrl1475574r.1917c>a0.360
rrl1475672r.2015c>g0.147
rrl1475673r.2016t>c0.147
rrl1475687r.2030c>t0.282
rrl1475696r.2039t>c0.282
rrl1475699r.2042c>t0.282
rrl1475703r.2046a>g0.275
rrl1475707r.2050t>a0.275
rrl1475716r.2059a>g0.302
rrl1475803r.2146t>c0.377
rrl1475804r.2147g>c0.385
rrl1475816r.2159c>g0.423
rrl1475817r.2160a>g0.431
rrl1475843r.2186g>a0.412
rrl1475849r.2192g>a0.408
rrl1475853r.2196c>t0.396
rrl1475858r.2201t>c0.404
rrl1476126r.2469c>t0.358
rrl1476128r.2471t>a0.358
rrl1476135r.2478t>c0.302
rrl1476141r.2484a>g0.312
rrl1476153r.2496t>c0.362
rrl1476164r.2507a>g0.345
rrl1476165r.2508t>a0.345
rrl1476181r.2524a>c0.291
rrl1476251r.2594t>c0.420
rrl1476260r.2603a>g0.421
rrl1476280r.2623a>c0.377
rrl1476332r.2675g>c0.276
rrl1476338r.2681c>t0.267
rrl1476353r.2696g>t0.298
rrl1476358r.2701t>c0.321
rrl1476372r.2715t>c0.321
rrl1476382r.2725a>g0.327
rrl1476383r.2726t>a0.327
rrl1476408r.2751g>a0.283
rrl1476425r.2768g>a0.309
rrl1476428r.2771c>t0.265
rrl1476466r.2809c>t0.286
rrl1476481r.2824t>c0.299
rrl1476506r.2849t>c0.250
rrl1476547r.2890c>t0.167
rrl1476567r.2910c>t0.203
rrl1476573r.2916a>t0.210
rrl1476577r.2920t>g0.219
rrl1476594r.2937c>t0.217
rrl1476637r.2980c>g0.261
rpsA1834177c.636A>C1.000
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
ald3086788c.-32T>C1.000
embC4240372c.510A>G1.000
embC4242643c.2781C>T1.000
embA4243460c.228C>T1.000
embB4246584p.Arg24Pro0.429
gid4407588c.615T>C1.000
gid4407927p.Glu92Asp1.000
gid4407980p.Pro75Thr1.000

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;