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: 5dc8beafc5219
Sample: 5dc8beafc5219

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Summary
ID: 5dc8beafc5219
Date: Mon Nov 11 01:55:31 2019
Strain: lineage2.2.1
Drug-resistance: Sensitive

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

Lineage2FamilyMain SpoligotypeRDS
lineage2East-AsianBeijingRD105
lineage2.2East-Asian (Beijing)Beijing-RD207RD105;RD207
lineage2.2.1East-Asian (Beijing)Beijing-RD181RD105;RD207;RD181

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA9304p.Gly668Asp1.000
rpoB763031c.3225T>C0.974
rpoC764632c.1263T>C0.129
rpoC764641c.1272C>T0.131
rpoC764650c.1281G>T0.123
rpsL781395c.-165T>C1.000
rrs1472172r.327t>c0.384
rrs1472214r.369c>g0.364
rrs1472223r.378c>g0.200
rrs1472225r.380c>a0.179
rrs1472228r.383g>c0.202
rrs1472235r.390g>c0.255
rrs1472240r.395g>a0.192
rrs1472242r.397c>t0.243
rrs1472251r.406g>a0.255
rrs1472253r.408g>t0.245
rrs1472259r.414c>a0.242
rrs1472266r.421c>a0.247
rrs1472277r.432c>g0.261
rrs1472598r.753a>t0.275
rrs1472616r.771g>a0.363
rrs1472713r.868t>c0.145
rrs1472714r.869a>t0.173
rrs1472715r.870c>a0.169
rrs1472716r.871c>t0.231
rrs1472734r.889c>t0.333
rrs1472741r.896g>a0.333
rrs1472742r.897c>t0.375
rrs1472770r.925c>t0.210
rrs1472781r.936c>t0.427
rrs1472793r.948a>t0.396
rrs1472803r.958t>a0.268
rrs1472812r.967a>c0.247
rrs1472887r.1042g>c0.278
rrs1473035r.1190g>a0.141
rrs1473055r.1210c>t0.108
rrs1473056r.1211a>t0.108
rrs1473166r.1321g>a0.118
rrs1473259r.1414c>t0.115
rrl1475783r.2126t>g0.206
rrl1475791r.2134a>g0.296
rrl1475803r.2146t>c0.338
rrl1475804r.2147g>c0.342
rrl1475816r.2159c>g0.359
rrl1475817r.2160a>g0.367
rrl1475881r.2224t>c0.303
rrl1475883r.2226a>c0.339
rrl1475977r.2320a>g0.103
rrl1476160r.2503t>c0.111
rrl1476336r.2679c>g0.435
rrl1476356r.2699c>g0.386
rrl1476357r.2700t>a0.398
rrl1476358r.2701t>c0.200
rrl1476359r.2702c>t0.267
rrl1476368r.2711t>c0.262
rrl1476369r.2712c>t0.291
rrl1476381r.2724g>a0.326
rrl1476382r.2725a>g0.284
rrl1476384r.2727g>c0.495
rrl1476408r.2751g>a0.543
rrl1476411r.2754g>a0.514
rrl1476428r.2771c>a0.227
rrl1476443r.2786g>t0.295
rrl1476455r.2798c>g0.263
rrl1476463r.2806c>t0.391
rrl1476466r.2809c>t0.372
rrl1476470r.2813c>t0.360
rrl1476481r.2824t>c0.429
rrl1476491r.2834t>c0.110
rrl1476501r.2844c>t0.106
rrl1476506r.2849t>c0.262
rpsA1834177c.636A>C0.971
rpsA1834845c.1305 1307del0.930
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu0.974
ald3086788c.-32T>C1.000
alr3841652c.-232A>T0.250
alr3841654c.-234A>C0.266
alr3841662c.-242A>G0.281
alr3841663c.-243G>A0.289
embC4242643c.2781C>T1.000
embA4243460c.228C>T0.989
ethA4326676p.Ser266Arg0.906
gid4407588c.615T>C0.910
gid4407927p.Glu92Asp0.921

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;