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: 5d323a0c6930f
Sample: 5d323a0c6930f

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Summary
ID: 5d323a0c6930f
Date: Fri Jul 19 22:47:29 2019
Strain: lineage2.2.1
Drug-resistance: XDR

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRkatG p.Ser315Thr (1.00)
RifampicinRrpoB p.Ser450Leu (1.00), rpoC p.Ile491Thr (1.00)
EthambutolRembB p.Met306Val (0.99)
PyrazinamideRpncA c.99 100insG (0.97)
StreptomycinRrpsL p.Lys43Arg (1.00), rrs r.888g>a (0.49)
EthionamideRethA c.1010 1010del (1.00)
FluoroquinolonesRgyrA p.Asp94Gly (1.00)
Amikacin
Capreomycin
KanamycinReis c.-10G>A (1.00)

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>c0.245
rrs1471900r.55c>t0.240
rrs1472137r.292g>a0.213
rrs1472150r.305t>a0.231
rrs1472151r.306c>t0.231
rrs1472172r.327t>c0.258
rrs1472203r.358g>a0.232
rrs1472530r.685g>a0.128
rrs1472537r.692c>t0.171
rrs1472544r.699c>a0.173
rrs1472545r.700a>t0.175
rrs1472566r.721g>a0.184
rrs1472570r.725g>a0.139
rrs1472571r.726g>c0.333
rrs1472579r.734g>t0.365
rrs1472581r.736a>t0.381
rrs1472598r.753a>c0.398
rrs1472599r.754g>t0.388
rrs1472612r.767g>t0.162
rrs1472616r.771g>a0.400
rrs1472697r.852t>c0.160
rrs1472713r.868t>c0.370
rrs1472716r.871c>t0.395
rrs1472742r.897c>t0.483
rrs1472744r.899a>g0.484
rrs1472767r.922g>a0.244
rrs1472781r.936c>t0.519
rrs1472793r.948a>t0.497
rrs1472803r.958t>a0.462
rrs1472895r.1050c>t0.463
rrs1473177r.1332g>a0.158
rrs1473192r.1347a>g0.163
rrs1473205r.1360t>c0.185
rrs1473327r.1482a>g0.125
rrs1473328r.1483c>t0.125
rrs1473352r.1507c>t0.477
rrl1474218r.561t>a0.412
rrl1474228r.571t>a0.277
rrl1474249r.592g>t0.192
rrl1474252r.595t>a0.202
rrl1474269r.612c>t0.227
rrl1475129r.1472g>t0.228
rrl1475154r.1497c>t0.221
rrl1475175r.1518g>a0.245
rrl1475783r.2126t>g0.367
rrl1475803r.2146t>c0.434
rrl1475804r.2147g>c0.451
rrl1475816r.2159c>g0.466
rrl1475817r.2160a>g0.458
rrl1475858r.2201t>c0.397
rrl1475866r.2209t>a0.368
rrl1476225r.2568t>g0.130
rrl1476229r.2572c>g0.126
rrl1476251r.2594t>c0.131
rrl1476260r.2603a>g0.129
rrl1476280r.2623a>c0.131
rrl1476332r.2675g>c0.259
rrl1476338r.2681c>t0.278
rrl1476353r.2696g>t0.351
rrl1476358r.2701t>c0.366
rrl1476369r.2712c>t0.378
rrl1476372r.2715t>c0.372
rrl1476382r.2725a>g0.392
rrl1476383r.2726t>a0.394
rrl1476408r.2751g>a0.236
rrl1476425r.2768g>a0.264
rrl1476428r.2771c>t0.413
rrl1476429r.2772a>c0.416
rrl1476466r.2809c>t0.267
rrl1476481r.2824t>c0.392
rrl1476506r.2849t>c0.308
rrl1476514r.2857c>t0.121
rpsA1834177c.636A>C1.000
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
ald3086788c.-32T>C1.000
ald3087293c.475 476insC0.985
embC4242643c.2781C>T1.000
embA4243346c.114A>G1.000
embA4243460c.228C>T1.000
gid4407588c.615T>C1.000
gid4407927p.Glu92Asp1.000

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;