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: 5dc36d534fa45
Sample: 5dc36d534fa45

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Summary
ID: 5dc36d534fa45
Date: Thu Nov 7 01:04:34 2019
Strain: lineage3.1.2
Drug-resistance: Sensitive

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

Lineage2FamilyMain SpoligotypeRDS
lineage3East-African-IndianCASRD750
lineage3.1East-African-IndianNon-CAS1-DelhiRD750
lineage3.1.2East-African-IndianCAS;CAS2RD750

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
gyrA8592p.Gln431Lys0.200
gyrA8991p.His564Asn0.200
gyrA9304p.Gly668Asp1.000
gyrA9658p.Thr786Asn0.200
gyrA9782c.2481C>A0.200
rpoB759526c.-281G>T0.200
rpoB759746c.-61C>T1.000
rpoB761265p.Asn487Tyr0.250
rpoB761493563E>563*0.222
rpoB762411p.Gln869Glu0.200
rpoB762434c.2628T>G1.000
rpoB763141p.Pro1112His0.211
rpoC763355c.-15G>A0.200
rpoC763402c.33C>A0.200
rpoC763926c.558 559del0.364
rpsL781395c.-165T>C0.941
rplC801239p.Val144Glu0.200
embR1416222p.Phe376Leu0.267
embR1416234p.Cys372Gly0.290
rrl1474645r.988g>t0.200
rrl1474824r.1167a>t0.200
rrl1475803r.2146t>c0.286
rrl1475804r.2147g>c0.286
rrl1475816r.2159c>g0.286
rrl1475817r.2160a>g0.286
rrl1475841r.2184t>g0.200
rrl1475858r.2201t>c0.200
rrl1476353r.2696g>t0.273
rrl1476358r.2701t>c0.300
rrl1476425r.2768g>t0.214
rrl1476428r.2771c>t0.267
rrl1476463r.2806c>t0.308
rrl1476481r.2824t>c0.364
inhA1674282c.81G>T0.250
rpsA1833808c.267G>T0.200
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
katG2155906p.Ala69Glu0.200
pncA2288716p.Arg176Ser0.200
pncA2288942c.300G>T0.200
pncA2288998p.His82Asn0.200
kasA2518462c.349 351del0.300
kasA2518519c.405G>T0.200
ahpC2726105c.-88G>A1.000
ahpC2726153c.-40G>T0.200
ahpC2726163c.-30G>T0.200
ahpC2726430p.Ala80Ser0.200
folC2747373p.Thr76Ser0.200
ribD2986948p.Asp37Val0.200
thyA3074022p.Phe150Leu0.200
thyA3074032p.His147Leu0.200
ald3086788c.-32T>C1.000
ald3087596c.777A>G0.200
fbiA3640858p.Asp106Asn0.200
fbiA3640921p.Gln127Lys0.200
fbiA3641494p.Glu318Lys0.200
alr3840492p.Leu310Gln0.200
alr3841652c.-232A>T0.333
alr3841662c.-242A>G0.231
alr3841663c.-243G>A0.273
embC4239999p.Ala46Asp0.200
embC4241184p.Thr441Lys0.200
embC4241266c.1404C>A0.200
embC4242075p.Arg738Gln1.000
embC4242643c.2781C>T1.000
embA4243202c.-31C>T0.200
embA4244459c.1227G>T0.200
embA4245601p.Pro790Leu0.333
embB4249025p.Asp838Tyr0.200
embB4249227p.Pro905Gln0.200
embB4249733p.Pro1074Thr0.200
ethR4327842p.Asp98Glu0.200
gid4407588c.615T>C1.000
gid4407932p.Leu91Ile0.200

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;