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: 5dde9424898fe
Sample: 5dde9424898fe

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Summary
ID: 5dde9424898fe
Date: Wed Nov 27 15:27:15 2019
Strain: lineage4.1.2.1
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
StreptomycinRrrs r.462c>t (0.47)
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
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA9304p.Gly668Asp1.000
rpoB760115c.309C>T1.000
rpoC765150p.Gly594Glu1.000
rpsL781395c.-165T>C1.000
embR1416222p.Phe376Leu0.179
embR1416234p.Cys372Gly0.222
rrs1472193r.348a>t0.398
rrs1472197r.352a>t0.278
rrs1472225r.380c>g0.277
rrs1472240r.395g>c0.473
rrs1472242r.397c>t0.402
rrs1472251r.406g>t0.660
rrs1472252r.407g>a0.369
rrs1472253r.408g>t0.405
rrs1472256r.411t>a0.393
rrs1472259r.414c>a0.429
rrs1472278r.433c>t0.226
rrs1472279r.434t>g0.317
rrs1472285r.440a>g0.431
rrs1472286r.441c>g0.396
rrs1472287r.442c>t0.340
rrs1472288r.443a>t0.204
rrs1472289r.444t>g0.837
rrs1472290r.445c>g0.795
rrs1472293r.448c>a0.143
rrs1472304r.459g>c0.182
rrs1472309r.464c>t0.333
rrs1472311r.466c>t0.176
rrs1472313r.468g>a0.436
rrs1472315r.470t>g0.778
rrs1472324r.479g>c0.816
rrs1472325r.480g>c0.816
rrs1472326r.481t>g0.208
rrs1472328r.483g>c0.388
rrs1472344r.499c>t0.951
rrs1472349r.504a>c0.398
rrs1472374r.529t>g0.406
rrs1472382r.537g>a0.550
rrs1472389r.544g>a0.604
rrs1472390r.545t>a0.485
rrs1472391r.546c>t0.639
rrs1472412r.567a>c0.482
rrs1472415r.570t>g0.250
rrs1472418r.573t>c0.224
rrs1472422r.577t>c0.535
rrs1472431r.586g>a0.373
rrs1472435r.590t>c0.816
rrs1472438r.593t>c0.592
rrs1472439r.594c>t0.816
rrs1472443r.598a>t0.220
rrs1472446r.601t>g0.163
rrs1472448r.603t>c0.742
rrs1472449r.604c>t0.452
rrs1472450r.605a>g0.323
rrs1472451r.606c>g0.516
rrs1472452r.607g>a0.258
rrs1472460r.615t>c0.419
rrs1472461r.616g>c0.516
rrs1472462r.617t>c0.323
rrs1472464r.619a>g0.742
rrs1472465r.620g>a0.433
rrs1472466r.621c>a0.233
rrs1472467r.622g>c0.241
rrs1472471r.626g>a0.793
rrs1472484r.639a>t0.342
rrs1472485r.640g>a0.256
rrs1472489r.644a>t0.590
rrs1472494r.649a>g0.436
rrs1472496r.651t>a0.231
rrs1472497r.652g>a0.333
rrs1472498r.653c>t0.487
rrs1472507r.662c>a0.224
rrs1472515r.670c>t0.173
rrs1472517r.672t>a0.288
rrs1472530r.685g>a0.358
rrs1472536r.691g>a0.160
rrs1472537r.692c>t0.321
rrs1472541r.696t>g0.225
rrs1472544r.699c>a0.173
rrs1472545r.700a>t0.325
rrs1472549r.704g>a0.237
rrs1472557r.712g>a0.377
rrs1472558r.713g>a0.423
rrs1472569r.724g>a0.429
rrs1472570r.725g>a0.167
rrs1472571r.726g>c0.463
rrs1472573r.728c>t0.203
rrs1472579r.734g>t0.203
rrs1472580r.735c>t0.171
rrs1472581r.736a>t0.426
rrs1472582r.737g>t0.181
rrs1472584r.739a>t0.225
rrs1472594r.749g>c0.150
rrs1472598r.753a>c0.458
rrs1472599r.754g>a0.263
rrs1472607r.762g>a0.374
rrs1472612r.767g>t0.422
rrs1472614r.769g>t0.233
rrs1472616r.771g>a0.302
rrs1472634r.789t>g0.259
rrs1472635r.790g>t0.262
katG2155957p.Pro52Gln0.200
kasA2518256p.Asp48Tyr0.200
ald3086788c.-32T>C1.000
alr3841662c.-242A>G0.369
alr3841663c.-243G>A0.188
embC4242643c.2781C>T1.000
embC4242803p.Val981Leu1.000
embB4246633p.Leu40Phe0.200

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;