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: 5ccc3b9b62aef
Sample: 5ccc3b9b62aef

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Summary
ID: 5ccc3b9b62aef
Date: Fri May 3 14:02:14 2019
Strain: lineage6
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
StreptomycinRrrs r.888g>a (0.59)
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

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

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6446p.Ala403Ser1.000
gyrA7585p.Ser95Thr1.000
gyrA8493p.Leu398Phe1.000
gyrA8806p.Asp502Gly1.000
gyrA9143c.1842T>C1.000
gyrA9304p.Gly668Asp1.000
rpoB760855p.Thr350Ile1.000
rpoB760969p.Ser388Leu1.000
rpoB761723p.Glu639Asp1.000
rpoB763083p.Arg1093Ser0.200
rpoC766231c.2862T>C1.000
rpsL781395c.-165T>C1.000
embR1416633p.Leu239Val1.000
embR1417554c.-207C>G1.000
rrs1472137r.292g>a0.400
rrs1472150r.305t>a0.417
rrs1472151r.306c>t0.417
rrs1472172r.327t>c0.455
rrs1472203r.358g>a0.526
rrs1472507r.662c>g0.310
rrs1472517r.672t>a0.346
rrs1472518r.673g>t0.321
rrs1472530r.685g>a0.355
rrs1472537r.692c>t0.367
rrs1472544r.699c>a0.382
rrs1472545r.700a>t0.382
rrs1472566r.721g>a0.424
rrs1472571r.726g>c0.429
rrs1472579r.734g>t0.457
rrs1472581r.736a>t0.459
rrs1472598r.753a>c0.545
rrs1472599r.754g>t0.523
rrs1472616r.771g>a0.543
rrs1472655r.810g>a0.300
rrs1472658r.813g>a0.296
rrs1472661r.816a>g0.286
rrs1472670r.825g>t0.222
rrs1472673r.828t>g0.200
rrs1472675r.830t>c0.208
rrs1472677r.832c>t0.227
rrs1472690r.845c>a0.318
rrs1472697r.852t>c0.467
rrs1472713r.868t>c0.613
rrs1472716r.871c>t0.559
rrs1472742r.897c>t0.559
rrs1472744r.899a>g0.545
rrs1472781r.936c>t0.583
rrs1472793r.948a>t0.583
rrs1472803r.958t>a0.606
rrs1472895r.1050c>t0.481
rrs1473177r.1332g>a0.357
rrs1473192r.1347a>g0.400
rrs1473199r.1354ca>c0.370
rrs1473205r.1360t>c0.385
rrs1473352r.1507c>t0.357
rrl1474218r.561t>a0.630
rrl1474228r.571t>c0.593
rrl1474249r.592g>t0.516
rrl1474252r.595t>a0.548
rrl1475783r.2126t>g0.464
rrl1475803r.2146t>c0.520
rrl1475804r.2147g>c0.520
rrl1475816r.2159c>g0.520
rrl1475817r.2160a>g0.520
rrl1475858r.2201t>c0.600
rrl1475866r.2209t>a0.524
rrl1475874r.2217c>t0.308
rrl1475877r.2220c>t0.182
rrl1476250r.2593c>g0.214
rrl1476251r.2594t>c0.214
rrl1476257r.2600g>c0.214
rrl1476260r.2603a>g0.214
rrl1476332r.2675g>c0.278
rrl1476338r.2681c>t0.278
rrl1476353r.2696g>t0.263
rrl1476358r.2701t>c0.333
rrl1476369r.2712c>t0.400
rrl1476372r.2715t>c0.400
rrl1476382r.2725a>g0.471
rrl1476383r.2726t>a0.500
rrl1476425r.2768g>t0.667
rrl1476428r.2771c>t0.667
rrl1476429r.2772a>c0.692
rrl1476481r.2824t>c0.655
rrl1476506r.2849t>c0.643
tlyA1917972c.33A>G1.000
katG2155503c.609G>A1.000
kasA2518132c.18C>T1.000
ald3086788c.-32T>C1.000
ald3087084c.266 266del1.000
alr3841662c.-242A>G1.000
alr3841663c.-243G>A0.935
embC4240671p.Thr270Ile1.000
embC4241343p.Ala494Gly1.000
embC4241843p.Leu661Ile1.000
embA4244220c.988C>T1.000
embB4246864c.351C>T1.000
embB4247646p.Glu378Ala1.000
ethA4326465p.Ile337Val1.000
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;