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: 5dd56e0153e5d
Sample: 5dd56e0153e5d

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Summary
ID: 5dd56e0153e5d
Date: Wed Nov 20 16:48:03 2019
Strain: lineage5
Drug-resistance: Sensitive

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

Lineage2FamilyMain SpoligotypeRDS
lineage5West-Africa 1AFRI 2;AFRI 3RD711

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6446p.Ala403Ser1.000
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA9143c.1842T>C1.000
gyrA9304p.Gly668Asp1.000
gyrA9566c.2265C>T1.000
rpoB763031c.3225T>C1.000
rpoC766987c.3618G>A0.200
rpsL781395c.-165T>C1.000
embR1416222p.Phe376Leu0.237
embR1416234p.Cys372Gly0.263
embR1417554c.-207C>G1.000
rrs1472225r.380c>g0.250
rrs1472251r.406g>c0.333
rrs1472256r.411t>c0.167
rrs1472258r.413a>g0.250
rrs1472259r.414c>a0.500
rrs1472271r.426t>c0.200
rrs1472274r.429a>g0.200
rrs1472279r.434t>g0.375
rrs1472289r.444t>g0.700
rrs1472290r.445c>g0.571
rrs1472293r.448c>a0.300
rrs1472328r.483g>c0.200
rrs1472330r.485g>t0.364
rrs1472338r.493a>c0.429
rrs1472339r.494c>t0.150
rrs1472344r.499c>t1.000
rrs1472349r.504a>c0.227
rrs1472374r.529t>g0.190
rrs1472378r.533g>t0.150
rrs1472379r.534t>g0.562
rrs1472382r.537g>a0.545
rrs1472389r.544g>a0.636
rrs1472391r.546c>t0.217
rrs1472396r.551a>t0.348
rrs1472400r.555c>t0.565
rrs1472405r.560c>t0.292
rrs1472412r.567a>g0.714
rrs1472415r.570t>g0.300
rrs1472507r.662c>g0.318
rrs1472517r.672t>a0.267
rrs1472518r.673g>a0.242
rrs1472526r.681g>a0.234
rrs1472530r.685g>a0.638
rrs1472537r.692c>t0.733
rrs1472544r.699c>a0.378
rrs1472545r.700a>t0.394
rrs1472546r.701g>a0.244
rrs1472549r.704g>a0.200
rrs1472556r.711c>t0.244
rrs1472557r.712g>a0.441
rrs1472566r.721g>a0.171
rrs1472571r.726g>c0.500
rrs1472573r.728c>t0.528
rrs1472574r.729t>c0.355
rrs1472579r.734g>a0.696
rrs1472581r.736a>t0.433
rrs1472582r.737g>t0.364
rrs1472583r.738t>c0.167
rrs1472598r.753a>c0.714
rrs1472599r.754g>t0.565
rrs1472607r.762g>a0.214
rrs1472612r.767g>t0.276
rrs1472616r.771g>a0.241
rrs1472634r.789t>c0.400
rrs1472635r.790g>t0.409
fabG11673338c.-102G>A1.000
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
pncA2289002c.240G>A1.000
ald3087084c.266 266del1.000
alr3840932c.489G>A1.000
alr3841662c.-242A>G1.000
alr3841663c.-243G>A0.818
embC4242643c.2781C>T1.000
embA4244220c.988C>T1.000
embA4245147p.Pro639Ser1.000
ethA4327103p.Gly124Asp1.000
gid4407588c.615T>C1.000

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;