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: 5d7b82a5534c3
Sample: 5d7b82a5534c3

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Summary
ID: 5d7b82a5534c3
Date: Fri Sep 13 12:52:25 2019
Strain: lineage4.1.2.1
Drug-resistance: Sensitive

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

Lineage2FamilyMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.1Euro-AmericanT;X;HNone
lineage4.1.2Euro-American (X-type)T;HNone
lineage4.1.2.1Euro-American (X-type)T1;H1RD182

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
rrs1472193r.348a>t0.463
rrs1472197r.352a>t0.333
rrs1472225r.380c>g0.324
rrs1472240r.395g>c0.516
rrs1472242r.397c>t0.429
rrs1472251r.406g>a0.306
rrs1472252r.407g>a0.408
rrs1472253r.408g>t0.434
rrs1472256r.411t>a0.434
rrs1472259r.414c>a0.461
rrs1472278r.433c>t0.267
rrs1472279r.434t>g0.394
rrs1472285r.440a>g0.512
rrs1472286r.441c>g0.463
rrs1472287r.442c>t0.400
rrs1472288r.443a>t0.244
rrs1472289r.444t>g1.000
rrs1472290r.445c>t0.244
rrs1472293r.448c>a0.171
rrs1472298r.453g>c0.156
rrs1472307r.462c>a0.182
rrs1472312r.467g>a0.182
rrs1472313r.468g>a0.548
rrs1472315r.470t>g0.946
rrs1472324r.479g>a0.244
rrs1472325r.480g>t0.244
rrs1472326r.481t>g0.244
rrs1472328r.483g>c0.452
rrs1472344r.499c>t1.000
rrs1472349r.504a>c0.418
rrs1472374r.529t>g0.441
rrs1472382r.537g>a0.589
rrs1472389r.544g>a0.619
rrs1472390r.545t>a0.541
rrs1472391r.546c>t0.700
rrs1472412r.567a>c0.500
rrs1472415r.570t>g0.224
rrs1472418r.573t>c0.252
rrs1472422r.577t>c0.575
rrs1472431r.586g>a0.440
rrs1472435r.590t>c1.000
rrs1472438r.593t>c0.725
rrs1472439r.594c>t1.000
rrs1472443r.598a>t0.268
rrs1472446r.601t>g0.194
rrs1472448r.603t>c0.958
rrs1472449r.604c>t0.583
rrs1472450r.605a>g0.417
rrs1472451r.606c>g0.667
rrs1472452r.607g>a0.333
rrs1472460r.615t>c0.542
rrs1472461r.616g>c0.667
rrs1472462r.617t>c0.417
rrs1472464r.619a>g0.958
rrs1472465r.620g>a0.565
rrs1472466r.621c>a0.304
rrs1472467r.622g>c0.304
rrs1472471r.626g>a1.000
rrs1472484r.639a>t0.406
rrs1472485r.640g>a0.312
rrs1472489r.644a>t0.719
rrs1472494r.649a>g0.531
rrs1472496r.651t>a0.281
rrs1472497r.652g>a0.406
rrs1472498r.653c>t0.594
rrs1472507r.662c>a0.250
rrs1472515r.670c>t0.224
rrs1472517r.672t>a0.196
rrs1472522r.677t>g0.183
rrs1472530r.685g>a0.250
rrs1472536r.691g>a0.217
rrs1472537r.692c>t0.233
rrs1472544r.699c>a0.121
rrs1472545r.700a>t0.207
rrs1472549r.704g>a0.267
rrs1472557r.712g>a0.333
rrs1472558r.713g>a0.550
rrs1472569r.724g>a0.559
rrs1472570r.725g>a0.117
rrs1472571r.726g>c0.327
rrs1472573r.728c>t0.138
rrs1472580r.735c>t0.222
rrs1472581r.736a>t0.360
rrs1472582r.737g>t0.197
rrs1472584r.739a>t0.257
rrs1472594r.749g>c0.119
rrs1472598r.753a>c0.403
rrs1472599r.754g>a0.270
rrs1472607r.762g>a0.440
rrs1472612r.767g>t0.484
rrs1472614r.769g>t0.242
rrs1472616r.771g>a0.218
rrs1472634r.789t>g0.273
rrs1472635r.790g>t0.268

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;