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: 5dc66284492bc
Sample: 5dc66284492bc

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Summary
ID: 5dc66284492bc
Date: Sat Nov 9 06:55:35 2019
Strain: lineage2.2.1
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
EthambutolRembB p.Met306Val (1.00)
Pyrazinamide
StreptomycinRrpsL p.Lys43Arg (1.00)
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
rpoB763031c.3225T>C1.000
rpoC764819p.Trp484Gly1.000
embR1416222p.Phe376Leu0.160
embR1416234p.Cys372Gly0.160
embR1416552p.Ala266Thr0.917
rrs1472164r.319g>a0.200
rrs1472172r.327t>c0.200
rrs1472193r.348a>g0.273
rrs1472197r.352a>t0.250
rrs1472210r.365a>t0.200
rrs1472214r.369c>g0.200
rrs1472225r.380c>a0.300
rrs1472234r.389t>c0.250
rrs1472235r.390g>c0.200
rrs1472240r.395g>a0.200
rrs1472242r.397c>t0.200
rrs1472251r.406g>a0.400
rrs1472256r.411t>a0.300
rrs1472259r.414c>a0.364
rrs1472286r.441c>g0.200
rrs1472289r.444t>g0.222
rrs1472290r.445c>g0.222
rrs1472314r.469a>g0.200
rrs1472324r.479g>c0.273
rrs1472325r.480g>c0.273
rrs1472328r.483g>c0.182
rrs1472344r.499c>t0.385
rrs1472349r.504a>c0.231
rrs1472373r.528g>a0.300
rrs1472374r.529t>g0.400
rrs1472379r.534t>g0.200
rrs1472382r.537g>a0.600
rrs1472389r.544g>a0.300
rrs1472391r.546c>t0.273
rrs1472400r.555c>t0.417
rrs1472415r.570t>g0.231
rrs1472422r.577t>c0.250
rrs1472530r.685g>a0.400
rrs1472571r.726g>c0.200
rrs1472581r.736a>c0.250
rrs1472584r.739a>t0.167
rrs1472598r.753a>c0.231
rrs1472634r.789t>c0.167
rrs1472655r.810g>t0.333
rrs1472660r.815t>a0.273
rrs1472661r.816a>g0.167
rrs1472666r.821g>a0.273
rrs1472673r.828t>g0.364
rrs1472674r.829t>c0.222
rrs1472675r.830t>c0.455
rrs1472677r.832c>a0.400
rrs1472682r.837t>a0.455
rrs1472683r.838t>c0.455
rrs1472686r.841g>t0.200
rrs1472687r.842a>t0.222
rrs1472690r.845c>t0.182
rrs1472694r.849c>t0.400
rrs1472697r.852t>c0.333
rrs1472714r.869a>t0.804
rrs1472715r.870c>g0.711
rrs1472716r.871c>a0.659
rrs1472734r.889c>t0.190
rrs1472741r.896g>a0.194
rrs1472742r.897c>t0.750
rrs1472754r.909g>t0.571
rrs1472770r.925c>t0.175
rrs1472781r.936c>t0.774
rrs1472793r.948a>t0.726
rrs1472803r.958t>a0.695
rrs1472812r.967a>c0.246
rrs1472824r.979t>a0.500
rrs1472826r.981g>c0.429
rrs1472887r.1042g>c0.649
rrs1472936r.1091c>t0.465
rrs1472956r.1111t>c0.676
rrs1472957r.1112c>t0.647
rrs1472958r.1113a>t0.588
rrs1472959r.1114t>a0.588
rrs1472963r.1118g>a0.588
rrs1472982r.1137g>c0.667
rrs1472987r.1142g>t0.690
rrs1472988r.1143t>a0.625
rrs1472989r.1144g>a0.656
rrs1472990r.1145a>g0.719
rrs1473002r.1157g>t0.645
rrs1473004r.1159t>a0.645
rrs1473008r.1163c>a0.645
rrs1473009r.1164t>c0.645
inhA1674556p.Gly119Cys0.400
katG2154724p.Arg463Leu1.000
ahpC2726670p.Glu160Lys0.200
ald3086788c.-32T>C1.000
alr3841652c.-232A>T0.213
alr3841654c.-234A>C0.213
alr3841662c.-242A>G0.554
alr3841663c.-243G>A0.368
embC4240361p.Glu167Gln0.200
ethA4326961c.513G>C0.200
ethA4326964c.510G>A0.200
ethA4326970c.504G>T0.200

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;