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: 5dafe64eec936
Sample: 5dafe64eec936

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Summary
ID: 5dafe64eec936
Date: Wed Oct 23 06:34:58 2019
Strain: root
Drug-resistance: Sensitive

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

Lineage2FamilyMain SpoligotypeRDS

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7763c.462T>C0.526
gyrA7787c.486G>A1.000
gyrA7793c.492G>C1.000
gyrA7799c.498A>G1.000
gyrA7832c.531G>T0.992
gyrA7835c.534A>G1.000
gyrA7838c.537C>T1.000
gyrA7852p.Gly184Val0.762
gyrA7859c.558A>C1.000
gyrA7865c.564T>C1.000
rpoB760235c.429T>C0.375
rpoB760244c.438G>C1.000
rpoB760274c.468G>A0.996
rpoB760307c.501T>C1.000
rpoB760328c.522G>C1.000
rpoB760331c.525G>C1.000
rpoB760340c.534G>C1.000
rpoB760358c.552C>G1.000
rpoB760361c.555T>C0.988
rpoB760370c.564C>G1.000
rpoB760376p.Asp190Glu1.000
rpoB760380p.Thr192Leu1.000
rpoB760724c.918T>C1.000
rpoB760730c.924T>C1.000
rpoB760755p.His317Asn1.000
rpoB760759p.Val318Ala1.000
rpoB760763c.957C>T1.000
rpoB760769c.963C>G1.000
rpoB760796p.Glu330Asp1.000
rpoB760805c.999G>C1.000
rpoB760817c.1011A>G0.917
rpoB760820c.1014T>C1.000
rpoB760826c.1020C>G1.000
rpoB760830c.1024T>C1.000
rpoB760845p.Thr347Ser1.000
rpoB760850c.1044G>C1.000
rpoB760856c.1050C>G1.000
rpoB760859c.1053T>G1.000
rpoB760862c.1056G>C1.000
rpoB760868c.1062C>G1.000
rpoB760886c.1080A>G1.000
rpoB760913c.1107C>T1.000
rpoB760919c.1113C>G1.000
rpoB760928c.1122G>C1.000
rpoB760946c.1140A>G1.000
rpoB761906c.2100C>G1.000
rpoB761909c.2103T>C1.000
rpoB761912c.2106T>C1.000
rpoB761915p.Asp703Glu1.000
rpoB761916p.Asp704Asn1.000
rpoB761921c.2115C>T1.000
rpoB761936c.2130C>T1.000
rpoB761954c.2148C>G1.000
rpoB761955p.Ile717Val0.990
rpoB762014c.2208C>T1.000
rpoB762017c.2211A>G1.000
rpoB762053c.2247T>C0.982
rpoB762065c.2259T>C0.994
rpoB762083c.2277T>C1.000
rpoB762086c.2280G>C0.996
rpoB762101c.2295C>G1.000
rpoB762114p.Ile770Val1.000
rpoB762134c.2328C>G1.000
rpoB762138c.2332C>T1.000
rpoB762149c.2343G>C1.000
rpoB762161c.2355C>G0.996
rpoB762167c.2361T>G1.000
rpoB762179c.2373C>A1.000
rpoB762185c.2379G>C1.000
rpoB762192c.2386C>T0.996
rpoB762218c.2412T>G1.000
rpoB762449c.2643C>A1.000
rpoB762452c.2646G>C1.000
rpoB762470c.2664G>C1.000
rpoB762833c.3027C>T0.545
rpoB762857c.3051C>G0.996
rpoB762860c.3054G>C0.996
rpoB762911c.3105C>T0.993
rpoB762929c.3123G>T0.996
rpoB762989c.3183G>A1.000
rpoB762995c.3189G>T1.000
rpoB763031c.3225T>G1.000
rpoB763034c.3228C>G0.997
rpoB763040c.3234C>G1.000
rpoB763053c.3247T>C0.990
rpoB763070c.3264T>C0.993
rpoB763085c.3279C>G1.000
rpoB763115c.3309T>C1.000
rpoB763127c.3321G>C1.000
rpoB763136c.3330C>G1.000
rpoB763158c.3352C>T1.000
rpoB763166c.3360A>G1.000
rpoB763169c.3363A>G1.000
rpsL781751c.192G>C1.000
rpsL781754c.195G>C1.000
rpsL781760c.201T>C1.000
rpsL781763c.204C>G1.000
rpsL781811c.252C>T1.000
rpsA1834435c.894G>C1.000
rpsA1834456c.915T>G1.000
rpsA1834465c.924T>C0.996
rpsA1834468c.927A>G1.000
rpsA1834474c.933C>G1.000
rpsA1834489c.948T>C1.000
rpsA1834498c.957C>T1.000
rpsA1834522c.981C>T1.000
rpsA1834528c.987T>C0.996

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;