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: 5cc54e3817675
Sample: 5cc54e3817675

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Summary
ID: 5cc54e3817675
Date: Sun Apr 28 07:56:17 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
rrs1471896r.51t>c0.951
rrs1471900r.55c>t0.951
rrs1472127r.282c>t1.000
rrs1472129r.284g>c1.000
rrs1472137r.292g>a1.000
rrs1472150r.305t>a1.000
rrs1472151r.306c>t1.000
rrs1472172r.327t>c0.974
rrs1472203r.358g>a0.969
rrs1472210r.365a>c0.857
rrs1472344r.499c>t1.000
rrs1472379r.534t>g1.000
rrs1472382r.537g>a1.000
rrs1472400r.555c>t1.000
rrs1472530r.685g>a0.727
rrs1472537r.692c>t0.727
rrs1472541r.696t>g0.727
rrs1472544r.699c>g0.727
rrs1472545r.700a>t0.727
rrs1472557r.712g>a0.933
rrs1472570r.725g>a0.939
rrs1472571r.726g>c0.939
rrs1472573r.728c>t0.941
rrs1472581r.736a>t0.976
rrs1472598r.753a>c0.926
rrs1472616r.771g>a0.964
rrs1472734r.889c>t0.960
rrs1472741r.896g>a0.960
rrs1472744r.899a>g0.960
rrs1472767r.922g>a0.923
rrs1472779r.934g>a0.923
rrs1472781r.936c>t0.923
rrs1472786r.941c>t0.923
rrs1472793r.948a>t0.923
rrs1472803r.958t>a0.923
rrs1472895r.1050c>t0.983
rrs1473035r.1190g>a0.929
rrs1473053r.1208t>a0.929
rrs1473056r.1211a>t0.923
rrs1473062r.1217t>a0.923
rrs1473068r.1223a>g0.923
rrs1473070r.1225g>a0.923
rrs1473089r.1244a>c0.923
rrs1473093r.1248c>t0.923
rrs1473094r.1249t>c1.000
rrs1473099r.1254t>a1.000
rrs1473352r.1507c>t0.947
rrl1474779r.1122g>a0.800
rrl1474780r.1123c>t0.800
rrl1474782r.1125g>a0.833
rrl1474790r.1133c>t0.929
rrl1474798r.1141c>t0.941
rrl1474804r.1147c>t0.951
rrl1474823r.1166c>g0.957
rrl1474827r.1170c>t0.957
rrl1474831r.1174a>c0.961
rrl1474844r.1187g>t0.983
rrl1474866r.1209c>a0.965
rrl1474869r.1212g>t0.965
rrl1474896r.1239a>g0.977
rrl1474902r.1245t>c0.970
rrl1474904r.1247g>c0.968
rrl1474913r.1256t>a0.963
rrl1474920r.1263g>a0.958
rrl1475803r.2146t>c1.000
rrl1475804r.2147g>c1.000
rrl1475816r.2159c>g1.000
rrl1475817r.2160a>g1.000
rrl1475843r.2186g>a1.000
rrl1475849r.2192g>a1.000
rrl1475853r.2196c>t1.000
rrl1475858r.2201t>c1.000
rrl1476332r.2675g>c1.000
rrl1476338r.2681c>t1.000
rrl1476353r.2696g>t1.000
rrl1476358r.2701t>c1.000
rrl1476372r.2715t>c0.982
rrl1476382r.2725a>g0.981
rrl1476383r.2726t>a0.982
rrl1476408r.2751g>a0.984
rrl1476425r.2768g>a0.984
rrl1476428r.2771c>t0.984
rrl1476466r.2809c>t1.000
rrl1476481r.2824t>c1.000
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;