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: 5db4e3accb789
Sample: 5db4e3accb789

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Summary
ID: 5db4e3accb789
Date: Sun Oct 27 01:42:49 2019
Strain: lineage4.6.1.1
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
EthambutolRembB p.Ala356Val (0.33)
Pyrazinamide
StreptomycinRrrs r.888g>a (0.98)
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.6Euro-AmericanT;LAMNone
lineage4.6.1Euro-American (Uganda)T2RD724
lineage4.6.1.1Euro-AmericanT2-UgandaRD724

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7433c.132G>C0.200
gyrA7457c.156T>C0.200
gyrA7526c.225G>T0.231
gyrA7532c.231T>C0.231
gyrA7539p.Thr80Ala0.769
gyrA7547c.246C>T0.214
gyrA7585p.Ser95Thr1.000
gyrA7601c.300C>G0.231
gyrA7793c.492G>C0.167
gyrA7797c.496C>T0.154
gyrA7820c.519G>C0.143
gyrA7835c.534A>G0.167
gyrA8294c.993T>C0.150
gyrA8324c.1023T>C0.158
gyrA8339c.1038A>G0.176
gyrA8340p.Ala347Ser0.176
gyrA8360c.1059G>A0.188
gyrA9230c.1929T>C0.188
gyrA9236c.1935G>C0.200
gyrA9242c.1941A>C0.188
gyrA9248c.1947G>C0.176
gyrA9252p.Val651Ile0.167
gyrA9266c.1965C>T0.154
gyrA9304p.Gly668Asp1.000
rpoB760184c.378A>G0.300
rpoB760196c.390C>G0.273
rpoB760235c.429T>C0.429
rpoB760244c.438G>C0.529
rpoB760274c.468G>A0.500
rpoB760295c.489C>T0.538
rpoB760307c.501T>C0.417
rpoB760310c.504G>C0.417
rpoB761249c.1443A>G0.600
rpoB761255c.1449T>C0.500
rpoB761261c.1455G>T0.583
rpoB761264c.1458C>G0.583
rpoB761282c.1476C>G0.700
rpoB761492c.1686G>C0.200
rpoB761666c.1860G>C0.273
rpoB761690c.1884G>C0.300
rpoB761765c.1959T>C0.200
rpoB761772p.His656Ala0.200
rpoB761778p.Asn658Asp0.200
rpoB762008c.2202C>G0.200
rpoB762014c.2208C>T0.200
rpoB762083c.2277T>C0.400
rpoB762101c.2295C>G0.300
rpoB762233c.2427G>T0.200
rpoB762266c.2460T>C0.300
rpoB762278c.2472C>T0.250
rpoB762281c.2475G>A0.273
rpoB762284c.2478G>C0.273
rpoB762293c.2487T>C0.300
rpoB763115c.3309T>C0.300
rpoC763441c.72C>T0.231
rpoC763444c.75T>C0.231
rpoC763456c.87A>G0.250
rpoC763486c.117T>G0.364
rpoC763636c.267T>C0.273
rpoC763660c.291T>G0.214
rpoC763669c.300C>G0.214
rpoC763675c.306C>G0.231
rpoC763771c.402C>T0.214
rpoC763780c.411C>G0.273
rpoC763792p.Glu141Asp0.273
rpoC763801c.432C>G0.300
rpoC763807c.438T>C0.273
rpoC763836p.Ala156Val0.300
rpoC764140c.771C>T0.364
rpoC764159c.790C>T0.364
rpoC764167c.798G>A0.364
rpoC764815c.1446A>G0.300
rpoC764923c.1554A>G0.200
rpoC764932c.1563C>G0.182
rpoC765383p.Met672Leu0.231
rpoC765391c.2022C>T0.286
rpoC765406c.2037G>T0.267
rpoC765409c.2040T>C0.267
rpoC765412c.2043T>C0.286
rpoC765421c.2052C>G0.357
rpoC765452p.Ala695Ser0.417
rpoC765466c.2097C>T0.364
rpoC765478c.2109T>C0.308
rpoC765529c.2160C>T0.273
rpoC765562c.2193G>C0.267
rpoC765578c.2209C>T0.333
rpoC765622p.Glu751Asp0.250
rpoC765625c.2256C>T0.222
rpoC765628c.2259G>C0.235
rpoC765658c.2289C>T0.308
rpoC765892c.2523T>C0.583
rpoC765904c.2535C>T0.600
rpoC765934c.2565C>T0.286
rpoC765952c.2583G>T0.200
rpoC767098c.3729T>C0.273
rpsL781766c.207C>T0.200
rpsL781772c.213C>G0.182
rrs1471923r.78t>c0.188
rrs1471925r.80t>c0.200
rrs1471970r.125g>a0.353
rrs1472030r.185g>t0.375
rrs1472031r.186g>t0.353
rrs1472033r.188a>g0.353
rrs1472034r.189t>c0.353
rrs1472040r.195t>c0.389
rrs1472061r.216a>t0.286
rrs1472075r.230a>g0.308
rrs1472557r.712g>a0.907
rrs1472570r.725g>a0.918
rrs1472571r.726g>c0.902
rrs1472573r.728c>t0.918
rrs1472579r.734g>t0.940
rrs1472581r.736a>t0.951
rrs1472596r.751g>t0.984
rrs1472598r.753a>t0.980
rrs1472614r.769g>t0.984
rrs1472616r.771g>a0.980
rrs1472655r.810g>a0.690
rrs1472695r.850c>t0.823
rrs1472697r.852t>c0.382
rrs1472713r.868t>c0.966
rrs1472716r.871c>t0.970
rrs1472742r.897c>t0.986
rrs1472744r.899a>g0.986
rrs1472767r.922g>a0.993
rrs1472781r.936c>t0.988
rrs1472793r.948a>t0.940
rrs1472803r.958t>a0.891
rrs1472880r.1035g>ga0.800
rrs1472895r.1050c>t0.969
rrs1472969r.1124a>g0.500
rrs1472970r.1125c>g0.500
rrs1473105r.1260g>a0.500
rrs1473120r.1275c>ct0.583
rrs1473123r.1278a>t0.583
rrs1473327r.1482a>g0.724
rrs1473328r.1483c>t0.765
rrs1473352r.1507c>t0.976
rrl1474130r.473c>t0.500
rrl1474447r.790g>a0.300
rrl1475355r.1698c>t0.364
rrl1475505r.1848g>a0.364
rrl1475526r.1869c>a0.300
rrl1475783r.2126t>g0.214
rrl1475803r.2146t>c0.969
rrl1475804r.2147g>c0.965
rrl1475816r.2159c>g0.970
rrl1475817r.2160a>g0.966
rrl1475858r.2201t>c0.953
rrl1475866r.2209t>a0.949
rrl1475877r.2220c>t0.560
rrl1476047r.2390g>a0.200
rrl1476049r.2392c>t0.167
rrl1476115r.2458t>c0.200
rrl1476311r.2654g>c0.550
rrl1476312r.2655t>c0.550
rrl1476313r.2656g>a0.667
rrl1476332r.2675g>c0.956
rrl1476353r.2696g>t0.963
rrl1476358r.2701t>c0.963
rrl1476369r.2712c>t0.961
rrl1476372r.2715t>c0.961
rrl1476382r.2725a>g0.962
rrl1476383r.2726t>a0.972
rrl1476408r.2751g>a0.984
rrl1476425r.2768g>t0.976
rrl1476428r.2771c>t0.965
rrl1476429r.2772a>c0.966
rrl1476466r.2809c>t0.979
rrl1476481r.2824t>c0.970
rrl1476506r.2849t>c0.960
rrl1476514r.2857c>t0.700
rrl1476580r.2923g>a0.500
rrl1476597r.2940g>a0.600
rrl1476619r.2962c>t0.400
rrl1476689r.3032a>t0.200
rrl1476690r.3033c>t0.200
rrl1476693r.3036g>a0.200
rrl1476695r.3038t>a0.200
rpsA1833619c.78A>C0.250
rpsA1833661c.120A>G0.385
rpsA1833667c.126C>G0.357
rpsA1833703c.162C>T0.417
rpsA1833724c.183C>G0.333
rpsA1833727c.186G>C0.333
rpsA1833745c.204G>C0.353
rpsA1833760c.219C>T0.312
rpsA1833790c.249T>C0.300
rpsA1833802c.261A>G0.300
rpsA1833808c.267G>C0.364
rpsA1833811c.270G>T0.308
rpsA1833847c.306C>G0.286
rpsA1833856c.315A>G0.385
rpsA1833859c.318C>T0.385
rpsA1833874c.333T>C0.400
rpsA1833895c.354G>C0.389
rpsA1833928c.387G>C0.500
rpsA1834348c.807T>C0.250
rpsA1834732c.1191T>C0.273
embC4240747c.885C>T0.182
embC4242643c.2781C>T1.000
embB4247437c.924A>G0.200
embB4247452c.939C>G0.182
embB4247470c.957T>C0.273
embB4247497c.984T>C0.364
embB4247500c.987C>G0.333
embB4247506c.993C>G0.333
embB4247512c.999T>C0.364
embB4247527c.1014G>C0.300
embB4247539c.1026T>C0.231
embB4247550p.Ala346Asp0.267
embB4247554c.1041T>C0.294
embB4247566c.1053C>G0.333
embB4247572c.1059A>C0.353
embB4247590c.1077A>G0.357
embB4247629c.1116C>G0.333
embB4247632c.1119C>G0.308
embB4247638c.1125G>C0.333

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;