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: 5cce0af733264
Sample: 5cce0af733264

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Summary
ID: 5cce0af733264
Date: Sat May 4 22:59:18 2019
Strain: lineage6
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
EthambutolRembC p.Ala307Thr (1.00)
Pyrazinamide
StreptomycinRrrs r.888g>a (0.52)
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage6West-Africa 2AFRI 1RD702
lineageBOV AFRI???

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6446p.Ala403Ser1.000
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA8493p.Leu398Phe1.000
gyrA8806p.Asp502Gly1.000
gyrA9143c.1842T>C1.000
gyrA9304p.Gly668Asp1.000
rpoB760855p.Thr350Ile1.000
rpoB760969p.Ser388Leu1.000
rpoB763031c.3225T>C1.000
rpoC766231c.2862T>C1.000
rpsL781395c.-165T>C1.000
embR1416633p.Leu239Val1.000
embR1417554c.-207C>G1.000
rrs1472137r.292g>a0.458
rrs1472150r.305t>a0.440
rrs1472151r.306c>t0.440
rrs1472172r.327t>c0.478
rrs1472203r.358g>a0.478
rrs1472507r.662c>g0.400
rrs1472517r.672t>a0.429
rrs1472518r.673g>t0.429
rrs1472530r.685g>a0.484
rrs1472537r.692c>t0.455
rrs1472544r.699c>a0.512
rrs1472545r.700a>t0.512
rrs1472566r.721g>a0.615
rrs1472571r.726g>c0.625
rrs1472579r.734g>t0.585
rrs1472581r.736a>t0.585
rrs1472598r.753a>c0.636
rrs1472599r.754g>t0.636
rrs1472616r.771g>a0.622
rrs1472655r.810g>a0.296
rrs1472658r.813g>a0.259
rrs1472661r.816a>g0.259
rrs1472670r.825g>t0.182
rrs1472673r.828t>g0.182
rrs1472675r.830t>c0.182
rrs1472677r.832c>t0.182
rrs1472690r.845c>a0.160
rrs1472697r.852t>c0.382
rrs1472713r.868t>c0.512
rrs1472716r.871c>t0.512
rrs1472742r.897c>t0.558
rrs1472744r.899a>g0.558
rrs1472781r.936c>t0.532
rrs1472793r.948a>t0.558
rrs1472803r.958t>a0.500
rrs1472895r.1050c>t0.439
rrs1473177r.1332g>a0.222
rrs1473192r.1347a>g0.259
rrs1473205r.1360t>c0.292
rrs1473352r.1507c>t0.333
rrl1474218r.561t>a0.679
rrl1474228r.571t>c0.679
rrl1474249r.592g>t0.633
rrl1474252r.595t>a0.633
rrl1475783r.2126t>g0.812
rrl1475803r.2146t>c0.700
rrl1475804r.2147g>c0.700
rrl1475816r.2159c>g0.609
rrl1475817r.2160a>g0.609
rrl1475858r.2201t>c0.636
rrl1475866r.2209t>a0.583
rrl1476332r.2675g>c0.278
rrl1476338r.2681c>t0.263
rrl1476353r.2696g>t0.375
rrl1476358r.2701t>c0.375
rrl1476369r.2712c>t0.379
rrl1476372r.2715t>c0.429
rrl1476382r.2725a>g0.414
rrl1476383r.2726t>a0.393
rrl1476425r.2768g>t0.486
rrl1476428r.2771c>t0.515
rrl1476429r.2772a>c0.515
rrl1476481r.2824t>c0.625
rrl1476506r.2849t>c0.607
rrl1476514r.2857c>t0.214
rrl1476519r.2862c>g0.214
inhA1674434p.Val78Ala1.000
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
katG2155503c.609G>A0.950
kasA2518132c.18C>T1.000
ald3086788c.-32T>C1.000
ald3087084c.266 266del0.929
alr3841654c.-234A>C0.304
alr3841662c.-242A>G1.000
alr3841663c.-243G>A0.923
embC4241343p.Ala494Gly1.000
embC4241843p.Leu661Ile1.000
embC4242643c.2781C>T1.000
embA4244379p.Pro383Ser1.000
embB4246864c.351C>T1.000
embB4247646p.Glu378Ala1.000
ethA4326465p.Ile337Val1.000
gid4408034p.Glu57Lys1.000

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;