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: 5dde7b44e3a8f
Sample: 5dde7b44e3a8f

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Summary
ID: 5dde7b44e3a8f
Date: Wed Nov 27 13:36:02 2019
Strain: lineage2.2.1
Drug-resistance: MDR

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRkatG p.Trp300Gly (1.00)
RifampicinRrpoB p.His445Gly (1.00)
EthambutolRembB p.Met306Leu (1.00)
PyrazinamideRpncA p.His82Arg (1.00)
Streptomycin
Ethionamide
FluoroquinolonesRgyrA p.Ala90Val (0.80), gyrA p.Asp94Gly (0.20)
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
gyrB5858p.Asn207Tyr0.250
gyrA7362p.Glu21Gln1.000
gyrA7618p.Arg106Leu0.231
gyrA9304p.Gly668Asp1.000
gyrA9312p.Leu671Met0.308
gyrA9329c.2028C>T0.167
rpoB759500c.-307A>T0.273
rpoB760137p.Ala111Thr0.130
rpoB763031c.3225T>C1.000
rpoC763861c.492C>T0.200
rpoC763943p.Asp192Tyr0.150
rpoC765874c.2505G>T0.150
rpoC765884p.Ser839Thr0.167
rpoC766339c.2970C>T0.400
Rv0678779016c.27G>A0.150
Rv0678779255p.Arg89Gln0.154
rpsL781395c.-165T>C1.000
rplC801079p.Ala91Thr0.231
embR1416222p.Phe376Leu0.292
embR1416234p.Cys372Gly0.298
rrs1472207r.362a>t0.182
rrl1473442c.-216G>A0.192
inhA1674521p.Pro107Leu0.333
rpsA1833406c.-136A>G0.190
rpsA1833835c.294C>T0.154
rpsA1834177c.636A>C1.000
tlyA1917972c.33A>G1.000
tlyA1918167c.228G>A0.176
tlyA1918692c.753G>A0.121
katG2153947p.Gln722Leu0.136
katG2154724p.Arg463Leu1.000
katG2155524c.588G>A0.188
pncA2289152c.90G>A0.154
eis2714783184Q>184*0.154
ahpC2726620p.Glu143Ala0.364
ahpC2726625145Q>145*0.417
folC2746220p.Ala460Val0.174
folC2746301p.Ala433Val0.200
folC2747372p.Thr76Ile0.167
ribD2987091p.Val85Met1.000
ribD2987160p.Ala108Ser0.167
thyX3067409c.537G>T0.200
thyX3068028c.-83G>C0.200
thyA3074115c.357C>A0.154
thyA3074305p.Ala56Val0.147
ald3086788c.-32T>C1.000
fbiA3640342c.-201C>T1.000
fbiA3641402p.Cys287Tyr0.150
alr3840892p.Thr177Ser0.211
alr3841652c.-232A>T0.321
alr3841654c.-234A>C0.321
alr3841662c.-242A>G0.452
alr3841663c.-243G>A0.419
embC4240153c.291G>A0.121
embC4241247p.Arg462Gln0.136
embC4241588p.Phe576Leu0.174
embA4243386p.Asp52Asn1.000
embA4243460c.228C>T1.000
embA4244867c.1635C>T0.188
embA4245799856W>856*0.235
embA4246331c.3099C>A0.158
embA4246370c.3138G>A0.182
embB4246855c.342G>A0.167
embB4247555p.Leu348Met0.167
embB4247623c.1110G>A0.167
embB4247825p.Ala438Thr0.125
ethA4326523c.951A>T0.138
ethA4326988c.486G>T0.167
ethR4327701c.153C>T0.143
gid4407588c.615T>C1.000
gid4407927p.Glu92Asp1.000
gid4407966c.237C>T0.188
gid4408054p.Leu50Arg1.000
gid4408296c.-94C>A0.207

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;