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: 5d48410c2f1fa
Sample: 5d48410c2f1fa

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Summary
ID: 5d48410c2f1fa
Date: Mon Aug 5 15:48:10 2019
Strain: root
Drug-resistance: Sensitive

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

Lineage2FamilyMain SpoligotypeRDS

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
rpoB761258c.1452G>A1.000
rpoB761261c.1455G>T1.000
rpoB761264c.1458C>G1.000
rpoC767041c.3672G>A1.000
rrs1471855r.10g>a1.000
rrs1471867r.22c>a1.000
rrs1471876r.31g>a0.996
rrs1471877r.32a>t0.996
rrs1471878r.33c>t0.996
rrs1471892r.47g>a0.992
rrs1471893r.48t>g0.996
rrs1471896r.51t>c1.000
rrs1472106r.261g>a0.994
rrs1472112r.267c>t1.000
rrs1472113r.268t>c1.000
rrs1472127r.282c>t1.000
rrs1472128r.283g>c1.000
rrs1472129r.284g>c1.000
rrs1472130r.285g>c1.000
rrs1472135r.290c>t1.000
rrs1472138r.293c>t1.000
rrs1472147r.302g>a1.000
rrs1472150r.305t>a1.000
rrs1472153r.308g>a1.000
rrs1472164r.319g>a1.000
rrs1472172r.327t>c1.000
rrs1472177r.332c>t1.000
rrs1472240r.395g>c1.000
rrs1472242r.397c>t1.000
rrs1472251r.406g>t1.000
rrs1472252r.407g>a1.000
rrs1472253r.408g>t1.000
rrs1472256r.411t>a1.000
rrs1472259r.414c>a0.994
rrs1472344r.499c>t1.000
rrs1472349r.504a>c1.000
rrs1472374r.529t>g1.000
rrs1472382r.537g>a1.000
rrs1472389r.544g>a1.000
rrs1472390r.545t>a1.000
rrs1472391r.546c>t1.000
rrs1472412r.567a>c1.000
rrs1472517r.672t>a0.995
rrs1472530r.685g>a1.000
rrs1472537r.692c>t1.000
rrs1472541r.696t>g1.000
rrs1472545r.700a>t1.000
rrs1472553r.708c>t1.000
rrs1472571r.726g>c1.000
rrs1472572r.727t>c1.000
rrs1472574r.729t>c1.000
rrs1472580r.735c>a0.979
rrs1472594r.749g>c1.000
rrs1472598r.753a>t1.000
rrs1472616r.771g>a1.000
rrs1472655r.810g>a1.000
rrs1472658r.813g>t1.000
rrs1472659r.814g>c1.000
rrs1472660r.815t>g1.000
rrs1472664r.819a>t1.000
rrs1472679r.834t>c1.000
rrs1472697r.852t>g1.000
rrs1472707r.862a>g1.000
rrs1472714r.869a>c1.000
rrs1472715r.870c>g1.000
rrs1472716r.871c>a1.000
rrs1472742r.897c>t1.000
rrs1472754r.909g>t1.000
rrs1472781r.936c>t1.000
rrs1472793r.948a>t1.000
rrs1472887r.1042g>c0.995
rrs1472912r.1067c>t1.000
rrs1472917r.1072g>a1.000
rrs1473044r.1199c>g1.000
rrs1473051r.1206t>c1.000
rrs1473053r.1208t>a1.000
rrs1473062r.1217t>a1.000
rrs1473068r.1223a>g1.000
rrs1473145r.1300c>t1.000
rrs1473148r.1303g>a1.000
rrs1473163r.1318c>t1.000
rrs1473166r.1321g>a1.000
rrs1473177r.1332g>a1.000
rrs1473191r.1346c>t1.000
rrs1473192r.1347a>g1.000
rrs1473202r.1357c>t1.000
rrs1473205r.1360t>c1.000
rrs1473206r.1361g>a1.000
rrs1473346r.1501g>a1.000
rrs1473352r.1507c>g1.000
rrs1473353r.1508c>g1.000
rrs1473358r.1513g>c1.000
rrs1473359r.1514g>c1.000
rrs1473365r.1520c>t1.000
rrl1474218r.561t>a1.000
rrl1474221r.564t>c1.000
rrl1474228r.571t>a1.000
rrl1474249r.592g>a1.000
rrl1474252r.595t>a1.000
rrl1474582r.925t>c1.000
rrl1474583r.926c>g0.996
rrl1474584r.927c>g0.996
rrl1474586r.929t>a1.000
rrl1474837r.1180a>g1.000
rrl1474844r.1187g>t1.000
rrl1474864r.1207c>t1.000
rrl1474866r.1209c>a0.996
rrl1474869r.1212g>t1.000
rrl1474875r.1218g>a1.000
rrl1474876r.1219t>a1.000
rrl1475154r.1497c>a0.992
rrl1475526r.1869c>a1.000
rrl1475538r.1881t>c0.995
rrl1475539r.1882a>t1.000
rrl1475540r.1883c>t1.000
rrl1475545r.1888t>g1.000
rrl1475550r.1893a>c1.000
rrl1475551r.1894t>g1.000
rrl1475555r.1898t>g1.000
rrl1475564r.1907c>a1.000
rrl1475574r.1917c>g1.000
rrl1475575r.1918c>t1.000
rrl1475576r.1919c>g1.000
rrl1475791r.2134a>g1.000
rrl1475803r.2146t>c1.000
rrl1475804r.2147g>c1.000
rrl1475816r.2159c>g1.000
rrl1475817r.2160a>g1.000
rrl1476126r.2469c>t1.000
rrl1476131r.2474c>t1.000
rrl1476141r.2484a>g1.000
rrl1476153r.2496t>c1.000
rrl1476154r.2497g>t1.000
rrl1476164r.2507a>g1.000
rrl1476165r.2508t>a1.000
rrl1476336r.2679c>t1.000
rrl1476356r.2699c>a1.000
rrl1476357r.2700t>c1.000
rrl1476358r.2701t>c1.000
rrl1476359r.2702c>g1.000
rrl1476369r.2712c>t1.000
rrl1476381r.2724g>c1.000
rrl1476382r.2725a>g1.000
rrl1476383r.2726t>g0.995
rrl1476384r.2727g>t0.990
rrl1476408r.2751g>a1.000
rrl1476411r.2754g>a1.000
rrl1476425r.2768g>a1.000
rrl1476428r.2771c>t1.000
rrl1476442r.2785t>a1.000
rrl1476443r.2786g>t1.000
rrl1476455r.2798c>a0.982
rrl1476456r.2799a>t0.982
rrl1476463r.2806c>t1.000
rrl1476466r.2809c>t1.000
rrl1476506r.2849t>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;