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: 5cc4c52dd1894
Sample: 5cc4c52dd1894

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Summary
ID: 5cc4c52dd1894
Date: Sat Apr 27 22:11:27 2019
Strain: lineage4.3.4.1
Drug-resistance: Sensitive

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

Lineage2FamilyMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.3Euro-American (LAM)mainly-LAMNone
lineage4.3.4Euro-American (LAM)LAMRD174
lineage4.3.4.1Euro-American (LAM)LAM1;LAM2RD174

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA9304p.Gly668Asp1.000
rpoC764995c.1626C>G1.000
rpsL781395c.-165T>C1.000
rrs1471896r.51t>c0.364
rrs1472150r.305t>a0.357
rrs1472151r.306c>a0.357
rrs1472160r.315c>t0.429
rrs1472164r.319g>a0.500
rrs1472177r.332c>t0.647
rrs1472225r.380c>a0.667
rrs1472240r.395g>a0.545
rrs1472251r.406g>a0.545
rrs1472253r.408g>t0.545
rrs1472259r.414c>a0.545
rrs1472544r.699c>t0.235
rrs1472549r.704g>a0.278
rrs1472557r.712g>a0.278
rrs1472570r.725g>a0.263
rrs1472571r.726g>c0.263
rrs1472573r.728c>t0.263
rrs1472579r.734g>a0.278
rrs1472581r.736a>c0.278
rrs1472582r.737g>a0.278
rrs1472598r.753a>c0.455
rrs1472599r.754g>a0.435
rrs1472600r.755c>t0.455
rrs1472616r.771g>a0.385
rrs1472655r.810g>a0.320
rrs1472658r.813g>a0.320
rrs1472659r.814g>a0.320
rrs1472734r.889c>t0.394
rrs1472741r.896g>a0.364
rrs1472742r.897c>t0.364
rrs1472779r.934g>a0.371
rrs1472793r.948a>t0.375
rrs1472803r.958t>a0.379
rrs1472895r.1050c>t0.290
rrs1473001r.1156g>c0.353
rrs1473005r.1160c>t0.364
rrs1473009r.1164t>g0.343
rrs1473035r.1190g>a0.394
rrs1473055r.1210c>t0.414
rrs1473062r.1217t>a0.400
rrs1473068r.1223a>g0.400
rrs1473080r.1235c>t0.310
rrl1475803r.2146t>c0.333
rrl1475804r.2147g>c0.333
rrl1475816r.2159c>g0.412
rrl1475817r.2160a>g0.412
rrl1475843r.2186g>a0.389
rrl1475853r.2196c>t0.438
rrl1475858r.2201t>c0.438
rrl1475874r.2217c>t0.375
rrl1476332r.2675g>c0.385
rrl1476337r.2680c>t0.417
rrl1476358r.2701t>c0.467
rrl1476372r.2715t>c0.476
rrl1476382r.2725a>g0.542
rrl1476383r.2726t>a0.542
rrl1476425r.2768g>a0.577
rrl1476428r.2771c>t0.577
rrl1476481r.2824t>c0.643
rrl1476506r.2849t>c0.700
rrl1476514r.2857c>t0.571
rrl1476519r.2862c>g0.571
rrl1476524r.2867c>a0.571
rrl1476525r.2868a>g0.571
rrl1476530r.2873c>t0.571
rrl1476536r.2879g>a0.667
rrl1476537r.2880a>g0.667
rrl1476538r.2881a>g0.615
rrl1476540r.2883c>g0.615
rrl1476547r.2890c>t0.615
rrl1476567r.2910c>t0.615
rrl1476572r.2915g>c0.600
tlyA1917972c.33A>G1.000
ahpC2726323p.Pro44Arg1.000
ald3086788c.-32T>C1.000
alr3841006p.Asp139His1.000
embC4242643c.2781C>T1.000
gid4408156p.Leu16Arg1.000

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;