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: 5ddd1e9513a5d
Sample: 5ddd1e9513a5d

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Summary
ID: 5ddd1e9513a5d
Date: Tue Nov 26 12:47:47 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
rpoB761441p.Asp545Glu1.000
rpoB763031c.3225T>C1.000
rpsL781395c.-165T>C1.000
embR1416222p.Phe376Leu0.320
embR1416234p.Cys372Gly0.348
embR1416909p.Gly147Arg0.211
rrs1471877r.32a>g0.200
rrs1472193r.348a>t0.333
rrs1472197r.352a>t0.214
rrs1472225r.380c>a0.200
rrs1472240r.395g>c0.400
rrs1472242r.397c>t0.375
rrs1472251r.406g>t0.357
rrs1472252r.407g>a0.294
rrs1472253r.408g>t0.294
rrs1472256r.411t>a0.333
rrs1472259r.414c>a0.562
rrs1472279r.434t>g0.182
rrs1472286r.441c>g0.300
rrs1472289r.444t>g0.200
rrs1472290r.445c>g0.200
rrs1472293r.448c>a0.200
rrs1472324r.479g>c0.200
rrs1472325r.480g>c0.200
rrs1472328r.483g>c0.273
rrs1472338r.493a>c0.133
rrs1472344r.499c>t0.788
rrs1472349r.504a>c0.250
rrs1472374r.529t>g0.268
rrs1472378r.533g>t0.316
rrs1472379r.534t>g0.389
rrs1472382r.537g>a0.575
rrs1472389r.544g>a0.513
rrs1472390r.545t>a0.325
rrs1472391r.546c>t0.390
rrs1472396r.551a>t0.267
rrs1472400r.555c>t0.311
rrs1472405r.560c>t0.159
rrs1472412r.567a>c0.600
rrs1472415r.570t>a0.500
rrs1472418r.573t>c0.438
rrs1472422r.577t>c0.438
rrs1472517r.672t>a0.360
rrs1472518r.673g>a0.444
rrs1472526r.681g>a0.170
rrs1472530r.685g>a0.681
rrs1472537r.692c>t0.896
rrs1472544r.699c>a0.419
rrs1472545r.700a>t0.568
rrs1472549r.704g>a0.286
rrs1472557r.712g>a0.683
rrs1472570r.725g>a0.191
rrs1472571r.726g>c0.667
rrs1472573r.728c>t0.359
rrs1472574r.729t>c0.263
rrs1472579r.734g>t0.692
rrs1472581r.736a>t0.576
rrs1472582r.737g>t0.211
rrs1472583r.738t>c0.350
rrs1472598r.753a>c0.756
rrs1472599r.754g>t0.410
rrs1472607r.762g>a0.261
rrs1472612r.767g>t0.292
rrs1472616r.771g>a0.362
rrs1472634r.789t>g0.178
rrs1472635r.790g>t0.163
rrs1472655r.810g>a0.174
rrs1472658r.813g>a0.182
rrs1472661r.816a>g0.167
rrs1473163r.1318c>t0.200
rrs1473164r.1319c>g0.200
rrl1475571r.1914a>t0.267
rrl1475574r.1917c>a0.267
rrl1475575r.1918c>t0.267
rrl1475576r.1919c>a0.267
rpsA1833540c.-2A>G1.000
rpsA1834177c.636A>C1.000
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
katG2155784p.Ala110Thr0.200
ald3086788c.-32T>C1.000
alr3841662c.-242A>G0.143
embC4242643c.2781C>T1.000
embA4243460c.228C>T1.000
ethA4326676p.Ser266Arg1.000
gid4407588c.615T>C1.000
gid4407927p.Glu92Asp1.000

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;