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: 5ddf8737bd3b0
Sample: 5ddf8737bd3b0

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Summary
ID: 5ddf8737bd3b0
Date: Thu Nov 28 08:43:20 2019
Strain: lineage1
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
StreptomycinRrrs r.462c>t (0.24)
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage1Indo-OceanicEAIRD239

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB5819c.580C>T1.000
gyrB6112p.Met291Ile1.000
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA8452p.Ala384Val1.000
gyrA9143c.1842T>C1.000
gyrA9304p.Gly668Asp1.000
rpoB763031c.3225T>C1.000
rpoC763884p.Ala172Val0.982
rpoC763886c.517C>A1.000
rpsL781395c.-165T>C1.000
embR1416783p.Ala189Ser1.000
embR1417019p.Cys110Tyr1.000
embR1417554c.-207C>G1.000
rrs1472193r.348a>t0.339
rrs1472214r.369c>g0.294
rrs1472225r.380c>a0.198
rrs1472235r.390g>c0.292
rrs1472240r.395g>c0.564
rrs1472242r.397c>t0.550
rrs1472251r.406g>t0.443
rrs1472252r.407g>a0.304
rrs1472253r.408g>t0.520
rrs1472256r.411t>a0.359
rrs1472259r.414c>a0.535
rrs1472277r.432c>g0.246
rrs1472278r.433c>t0.143
rrs1472279r.434t>c0.155
rrs1472285r.440a>g0.255
rrs1472286r.441c>g0.200
rrs1472287r.442c>t0.244
rrs1472289r.444t>g0.500
rrs1472290r.445c>g0.409
rrs1472298r.453g>c0.175
rrs1472313r.468g>a0.297
rrs1472315r.470t>g0.500
rrs1472324r.479g>c0.450
rrs1472325r.480g>c0.488
rrs1472327r.482g>a0.160
rrs1472328r.483g>c0.192
rrs1472344r.499c>t0.800
rrs1472349r.504a>c0.289
rrs1472374r.529t>g0.301
rrs1472378r.533g>t0.324
rrs1472379r.534t>g0.366
rrs1472382r.537g>a0.594
rrs1472389r.544g>a0.583
rrs1472390r.545t>a0.290
rrs1472391r.546c>t0.486
rrs1472400r.555c>t0.303
rrs1472412r.567a>c0.678
rrs1472415r.570t>g0.521
rrs1472422r.577t>c0.467
rrs1472431r.586g>a0.262
rrs1472435r.590t>c0.694
rrs1472438r.593t>c0.676
rrs1472439r.594c>t0.706
rrs1472447r.602c>t0.250
rrs1472448r.603t>c0.520
rrs1472449r.604c>t0.280
rrs1472450r.605a>g0.320
rrs1472451r.606c>g0.520
rrs1472460r.615t>c0.308
rrs1472461r.616g>c0.500
rrs1472462r.617t>c0.250
rrs1472464r.619a>g0.500
rrs1472465r.620g>a0.222
rrs1472471r.626g>a0.519
rrs1472484r.639a>t0.235
rrs1472485r.640g>a0.229
rrs1472489r.644a>t0.395
rrs1472494r.649a>g0.139
rrs1472497r.652g>a0.167
rrs1472498r.653c>t0.361
rrs1472504r.659a>t0.156
rrs1472505r.660g>a0.156
rrs1472507r.662c>a0.125
rrs1472517r.672t>a0.534
rrs1472518r.673g>t0.327
rrs1472530r.685g>a0.691
rrs1472537r.692c>t0.341
rrs1472541r.696t>g0.407
rrs1472544r.699c>a0.404
rrs1472545r.700a>t0.578
rrs1472557r.712g>a0.427
rrs1472570r.725g>a0.315
rrs1472571r.726g>c0.689
rrs1472573r.728c>t0.371
rrs1472579r.734g>t0.485
rrs1472581r.736a>t0.540
rrs1472584r.739a>t0.225
rrs1472598r.753a>c0.505
rrs1472599r.754g>a0.219
rrs1472612r.767g>t0.236
rrs1472614r.769g>t0.239
rrs1472616r.771g>a0.601
rrs1472634r.789t>g0.209
rrs1472635r.790g>t0.256
inhA1674814p.Gly205Ser1.000
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
kasA2518132c.18C>T1.000
eis2715422c.-90G>A1.000
ald3086788c.-32T>C1.000
alr3841652c.-232A>T0.276
alr3841654c.-234A>C0.304
alr3841662c.-242A>G0.371
alr3841663c.-243G>A0.330
embC4240671p.Thr270Ile1.000
embC4241042p.Asn394Asp1.000
embC4242643c.2781C>T1.000
embA4245969p.Pro913Ser1.000
embB4247582p.Ala357Thr1.000
embB4247646p.Glu378Ala1.000
ethA4326120p.Arg452Ser1.000
gid4407588c.615T>C1.000
gid4407796p.Ser136Leu1.000
gid4407835p.Trp123Ser1.000
gid4407873c.330C>A1.000

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;