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: 5d7b821173955
Sample: 5d7b821173955

Download results

Summary
ID: 5d7b821173955
Date: Fri Sep 13 12:49:36 2019
Strain: lineage1.1.1;lineage4.6.1;lineage4.1.1.1
Drug-resistance: Sensitive

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

Lineage2FamilyMain SpoligotypeRDS
lineage1.1.1Indo-OceanicEAI4;EAI5RD239
lineage4.6.1Euro-American (Uganda)T2RD724
lineage4.1.1.1Euro-American (X-type)X2RD183

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
rpoB762284c.2478G>C1.000
rrs1472193r.348a>t0.590
rrs1472197r.352a>t0.205
rrs1472225r.380c>g0.268
rrs1472240r.395g>c0.597
rrs1472242r.397c>t0.493
rrs1472251r.406g>t0.696
rrs1472252r.407g>a0.392
rrs1472253r.408g>t0.479
rrs1472256r.411t>a0.444
rrs1472259r.414c>a0.528
rrs1472278r.433c>t0.275
rrs1472279r.434t>g0.400
rrs1472285r.440a>g0.537
rrs1472286r.441c>g0.351
rrs1472287r.442c>t0.297
rrs1472288r.443a>t0.297
rrs1472289r.444t>g0.944
rrs1472290r.445c>t0.282
rrs1472293r.448c>a0.211
rrs1472311r.466c>t0.417
rrs1472313r.468g>a0.522
rrs1472315r.470t>g0.867
rrs1472324r.479g>a0.306
rrs1472325r.480g>t0.324
rrs1472326r.481t>g0.314
rrs1472328r.483g>c0.325
rrs1472344r.499c>t1.000
rrs1472349r.504a>c0.451
rrs1472374r.529t>g0.459
rrs1472382r.537g>a0.636
rrs1472389r.544g>a0.624
rrs1472390r.545t>a0.531
rrs1472391r.546c>t0.692
rrs1472412r.567a>c0.615
rrs1472415r.570t>a0.376
rrs1472418r.573t>c0.330
rrs1472422r.577t>c0.490
rrs1472431r.586g>a0.189
rrs1472435r.590t>c0.955
rrs1472438r.593t>c0.619
rrs1472439r.594c>t0.950
rrs1472443r.598a>t0.300
rrs1472446r.601t>g0.278
rrs1472447r.602c>t0.286
rrs1472448r.603t>c0.867
rrs1472449r.604c>t0.333
rrs1472450r.605a>g0.667
rrs1472451r.606c>g0.600
rrs1472452r.607g>a0.400
rrs1472460r.615t>c0.400
rrs1472461r.616g>c0.600
rrs1472462r.617t>c0.667
rrs1472464r.619a>g0.933
rrs1472465r.620g>a0.333
rrs1472466r.621c>a0.357
rrs1472467r.622g>c0.385
rrs1472471r.626g>a0.933
rrs1472484r.639a>t0.222
rrs1472485r.640g>a0.500
rrs1472489r.644a>t0.778
rrs1472494r.649a>g0.529
rrs1472496r.651t>a0.188
rrs1472497r.652g>a0.222
rrs1472498r.653c>t0.706
rrs1472507r.662c>a0.256
rrs1472517r.672t>c0.278
rrs1472518r.673g>t0.172
rrs1472522r.677t>g0.154
rrs1472524r.679g>a0.141
rrs1472530r.685g>a0.410
rrs1472535r.690c>t0.139
rrs1472537r.692c>t0.462
rrs1472544r.699c>a0.239
rrs1472545r.700a>g0.288
rrs1472549r.704g>a0.347
rrs1472557r.712g>a0.434
rrs1472558r.713g>a0.487
rrs1472569r.724g>a0.500
rrs1472571r.726g>c0.444
rrs1472579r.734g>t0.217
rrs1472581r.736a>c0.529
rrs1472582r.737g>t0.149
rrs1472584r.739a>t0.420
rrs1472598r.753a>c0.489
rrs1472599r.754g>a0.253
rrs1472607r.762g>a0.307
rrs1472612r.767g>t0.445
rrs1472614r.769g>t0.252
rrs1472616r.771g>a0.212
rrs1472634r.789t>g0.333
rrs1472635r.790g>t0.320
embC4241689c.1827G>C0.200
embC4241691p.Gly610Ala0.200

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;