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.
Back to results page.
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: 5d7b8514d9d57
Sample: 5d7b8514d9d57

Download results

Summary
ID: 5d7b8514d9d57
Date: Fri Sep 13 13:03:55 2019
Strain: lineage4.1.2.1
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
StreptomycinRrrs r.462c>t (0.31)
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
rrs1472193r.348a>t0.343
rrs1472214r.369c>g0.241
rrs1472235r.390g>c0.248
rrs1472240r.395g>c0.628
rrs1472242r.397c>t0.591
rrs1472251r.406g>t0.500
rrs1472252r.407g>a0.349
rrs1472253r.408g>t0.516
rrs1472256r.411t>a0.391
rrs1472259r.414c>a0.550
rrs1472277r.432c>g0.190
rrs1472278r.433c>t0.221
rrs1472279r.434t>c0.254
rrs1472285r.440a>g0.391
rrs1472287r.442c>t0.258
rrs1472289r.444t>g0.517
rrs1472290r.445c>g0.429
rrs1472298r.453g>c0.204
rrs1472313r.468g>a0.149
rrs1472315r.470t>g0.483
rrs1472324r.479g>c0.429
rrs1472325r.480g>c0.439
rrs1472330r.485g>t0.171
rrs1472344r.499c>t0.737
rrs1472378r.533g>t0.332
rrs1472379r.534t>g0.388
rrs1472382r.537g>a0.562
rrs1472389r.544g>a0.557
rrs1472391r.546c>t0.420
rrs1472400r.555c>t0.340
rrs1472412r.567a>c0.662
rrs1472415r.570t>g0.573
rrs1472422r.577t>c0.385
rrs1472435r.590t>c0.500
rrs1472438r.593t>c0.420
rrs1472439r.594c>t0.480
rrs1472447r.602c>t0.235
rrs1472448r.603t>c0.343
rrs1472450r.605a>g0.314
rrs1472451r.606c>g0.265
rrs1472461r.616g>c0.265
rrs1472462r.617t>c0.229
rrs1472464r.619a>g0.343
rrs1472471r.626g>a0.333
rrs1472485r.640g>a0.294
rrs1472489r.644a>t0.344
rrs1472494r.649a>g0.226
rrs1472498r.653c>t0.452
rrs1472504r.659a>t0.175
rrs1472505r.660g>a0.175
rrs1472507r.662c>a0.162
rrs1472517r.672t>a0.631
rrs1472518r.673g>t0.429
rrs1472530r.685g>a0.755
rrs1472537r.692c>t0.366
rrs1472541r.696t>g0.582
rrs1472544r.699c>a0.489
rrs1472545r.700a>t0.678
rrs1472553r.708c>t0.268
rrs1472557r.712g>a0.510
rrs1472570r.725g>a0.418
rrs1472571r.726g>c0.776
rrs1472573r.728c>t0.477
rrs1472574r.729t>c0.221
rrs1472579r.734g>t0.561
rrs1472581r.736a>t0.570
rrs1472583r.738t>a0.215
rrs1472598r.753a>c0.553
rrs1472599r.754g>a0.267
rrs1472612r.767g>t0.174
rrs1472614r.769g>t0.283
rrs1472616r.771g>a0.682
rrs1472634r.789t>g0.227
rrs1472635r.790g>t0.315
rrs1472871r.1026g>a1.000
tlyA1917972c.33A>G1.000
folC2746212p.Arg463Gly1.000
ald3086788c.-32T>C0.982
alr3841652c.-232A>T0.327
alr3841654c.-234A>C0.350
alr3841662c.-242A>G0.426
alr3841663c.-243G>A0.360
embC4242643c.2781C>T1.000
embC4242803p.Val981Leu1.000
ethR4328113p.Gly189Cys0.909

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;