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: 5d6d0ec9916bc
Sample: 5d6d0ec9916bc

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Summary
ID: 5d6d0ec9916bc
Date: Mon Sep 2 13:49:50 2019
Strain: lineage4.3.2
Drug-resistance: Sensitive

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

Lineage2FamilyMain SpoligotypeRDS
lineage4.3.2Euro-American (LAM)LAM3None

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
rrs1471853r.8t>c0.600
rrs1471853r.8t>tc1.000
rrs1471896r.51t>c1.000
rrs1471900r.55c>t1.000
rrs1471914r.69a>g1.000
rrs1471948r.103a>g1.000
rrs1472089r.244c>t0.900
rrs1472094r.249t>a1.000
rrs1472106r.261g>a1.000
rrs1472108r.263c>t1.000
rrs1472112r.267c>t0.986
rrs1472113r.268t>c1.000
rrs1472127r.282c>t1.000
rrs1472129r.284g>c1.000
rrs1472137r.292g>a1.000
rrs1472150r.305t>a1.000
rrs1472151r.306c>t1.000
rrs1472172r.327t>c1.000
rrs1472203r.358g>a0.995
rrs1472344r.499c>t0.982
rrs1472378r.533g>t0.996
rrs1472379r.534t>g0.996
rrs1472382r.537g>a0.988
rrs1472400r.555c>t0.991
rrs1472412r.567a>g0.995
rrs1472418r.573t>c0.960
rrs1472422r.577t>c0.929
rrs1472501r.656g>a0.941
rrs1472507r.662c>g1.000
rrs1472517r.672t>a1.000
rrs1472518r.673g>c1.000
rrs1472530r.685g>a0.993
rrs1472537r.692c>t0.996
rrs1472541r.696t>g1.000
rrs1472544r.699c>g0.996
rrs1472545r.700a>t0.996
rrs1472557r.712g>a1.000
rrs1472570r.725g>a1.000
rrs1472571r.726g>c0.975
rrs1472579r.734g>t0.996
rrs1472581r.736a>t1.000
rrs1472655r.810g>a1.000
rrs1472658r.813g>a1.000
rrs1472661r.816a>g1.000
rrs1472665r.820g>a1.000
rrs1472678r.833t>c1.000
rrs1472679r.834t>c1.000
rrs1472690r.845c>a1.000
rrs1472695r.850c>t1.000
rrs1472697r.852t>c1.000
rrs1472713r.868t>c1.000
rrs1472716r.871c>t1.000
rrs1472734r.889c>t1.000
rrs1472741r.896g>a1.000
rrs1472744r.899a>g1.000
rrs1472781r.936c>t0.996
rrs1472793r.948a>t1.000
rrs1472803r.958t>a1.000
rrs1472880r.1035g>ga0.980
rrs1472895r.1050c>t1.000
rrs1473008r.1163c>a0.250
rrs1473008r.1163ct>c0.917
rrs1473009r.1164t>c0.955
rrs1473035r.1190g>a1.000
rrs1473053r.1208t>a0.996
rrs1473056r.1211a>t0.996
rrs1473062r.1217t>a0.996
rrs1473068r.1223a>g0.996
rrs1473080r.1235c>a0.991
rrs1473082r.1237g>a0.995
rrs1473084r.1239t>a0.995
rrs1473131r.1286g>t0.941
rrs1473147r.1302g>c0.992
rrs1473148r.1303g>a0.992
rrs1473163r.1318c>t0.992
rrs1473164r.1319c>g0.992
rrs1473172r.1327t>c0.992
rrs1473173r.1328c>t0.992
rrs1473177r.1332g>a0.993
rrs1473192r.1347a>g0.992
rrs1473202r.1357c>t0.989
rrs1473205r.1360t>c0.989
rrs1473327r.1482a>g0.929
rrs1473328r.1483c>t0.933
rrs1473352r.1507c>t0.993
rrl1473679r.22t>c0.988
rrl1473734r.77c>t0.913
rrl1473746r.89tc>t1.000
rrl1473750r.93c>g0.957
rrl1473752r.95g>a0.957
rrl1473756r.99g>t1.000
rrl1473758r.101g>t1.000
rrl1473765r.108a>g0.974
rrl1473766r.109g>a0.976
rrl1473851r.194g>c0.996
rrl1473862r.205c>a0.996
rrl1473871r.214t>g1.000
rrl1473876r.219g>a1.000
rrl1474202r.545t>c0.727
rrl1474218r.561t>a0.996
rrl1474228r.571t>c0.996
rrl1474236r.579g>a0.996
rrl1474249r.592g>t0.996
rrl1474252r.595t>a0.996
rrl1474253r.596a>t0.996
rrl1474330r.673a>t1.000
rrl1474338r.681g>a1.000
rrl1474381r.724t>g0.964
rrl1474482r.825g>t1.000
rrl1474494r.837c>t0.996
rrl1474495r.838g>t1.000
rrl1474497r.840g>a1.000
rrl1474503r.846g>c1.000
rrl1474506r.849c>t1.000
rrl1474508r.851c>a1.000
rrl1474509r.852g>a1.000
rrl1474527r.870t>g1.000
rrl1474528r.871t>c1.000
rrl1474530r.873g>c1.000
rrl1474537r.880g>a1.000
rrl1474539r.882c>g1.000
rrl1474542r.885a>c1.000
rrl1474552r.895c>g1.000
rrl1474570r.913g>t1.000
rrl1474578r.921a>g1.000
rrl1474582r.925t>c1.000
rrl1474583r.926c>t1.000
rrl1474584r.927c>g1.000
rrl1474586r.929t>a1.000
rrl1474601r.944c>t0.983
rrl1474738r.1081g>a0.824
rrl1474740r.1083g>t0.955
rrl1474747r.1090c>a0.992
rrl1474777r.1120t>c0.996
rrl1474782r.1125g>a0.996
rrl1474790r.1133c>t0.992
rrl1474794r.1137c>a0.992
rrl1474804r.1147c>t0.917
rrl1474812r.1155g>a0.992
rrl1474823r.1166c>g1.000
rrl1474827r.1170c>t1.000
rrl1474830r.1173a>t1.000
rrl1474831r.1174a>t1.000
rrl1474844r.1187g>t1.000
rrl1474866r.1209c>a1.000
rrl1474869r.1212g>t1.000
rrl1474896r.1239a>g1.000
rrl1474902r.1245t>c0.995
rrl1474904r.1247g>c1.000
rrl1474913r.1256t>a1.000
rrl1474920r.1263g>c1.000
rrl1475122r.1465c>t0.996
rrl1475129r.1472g>t0.996
rrl1475144r.1487g>c0.996
rrl1475154r.1497c>a0.996
rrl1475163r.1506t>g0.996
rrl1475175r.1518g>a0.991
rrl1475188r.1531c>t0.995
rrl1475498r.1841c>g0.900
rrl1475545r.1888t>g1.000
rrl1475550r.1893a>c0.974
rrl1475552r.1895g>c1.000
rrl1475574r.1917c>a1.000
rrl1475660r.2003a>g0.947
rrl1475672r.2015c>g0.996
rrl1475673r.2016t>c0.996
rrl1475687r.2030c>t0.992
rrl1475688r.2031g>c0.992
rrl1475696r.2039t>c0.992
rrl1475699r.2042c>t0.989
rrl1475703r.2046a>g0.993
rrl1475707r.2050t>a0.993
rrl1475713r.2056c>g0.993
rrl1475716r.2059a>g0.993
rrl1475777r.2120a>c0.952
rrl1475783r.2126t>g0.996
rrl1475803r.2146t>c0.996
rrl1475804r.2147g>c0.996
rrl1475816r.2159c>g0.993
rrl1475817r.2160a>g0.996
rrl1475858r.2201t>c1.000
rrl1475866r.2209t>a1.000
rrl1475871r.2214t>c1.000
rrl1476126r.2469c>t0.941
rrl1476128r.2471t>a0.941
rrl1476131r.2474c>t0.939
rrl1476135r.2478t>c0.957
rrl1476141r.2484a>g0.996
rrl1476153r.2496t>c0.996
rrl1476194r.2537a>g1.000
rrl1476195r.2538c>a1.000
rrl1476196r.2539c>a0.991
rrl1476200r.2543a>t1.000
rrl1476201r.2544c>t1.000
rrl1476204r.2547c>a1.000
rrl1476210r.2553g>t1.000
rrl1476211r.2554g>t1.000
rrl1476212r.2555t>c1.000
rrl1476214r.2557g>c1.000
rrl1476215r.2558c>a1.000
rrl1476225r.2568t>g0.996
rrl1476251r.2594t>c1.000
rrl1476260r.2603a>g1.000
rrl1476280r.2623a>c1.000
rrl1476293r.2636c>t0.991
rrl1476294r.2637a>g0.991
rrl1476295r.2638c>g1.000
rrl1476296r.2639c>t0.991
rrl1476297r.2640c>t0.991
rrl1476301r.2644a>c0.991
rrl1476302r.2645g>a0.991
rrl1476311r.2654g>c0.985
rrl1476312r.2655t>c0.978
rrl1476313r.2656g>a0.981
rrl1476332r.2675g>c0.993
rrl1476353r.2696g>t0.993
rrl1476358r.2701t>c0.992
rrl1476372r.2715t>c0.992
rrl1476382r.2725a>g0.975
rrl1476383r.2726t>a0.984
rrl1476408r.2751g>a0.992
rrl1476425r.2768g>t0.987
rrl1476428r.2771c>t0.991
rrl1476429r.2772a>c0.991
rrl1476466r.2809c>t1.000
rrl1476481r.2824t>c1.000
rrl1476506r.2849t>c1.000
rrl1476514r.2857c>t1.000
rrl1476519r.2862c>g1.000
rrl1476522r.2865gt>g0.982
rrl1476523r.2866t>c1.000
rrl1476524r.2867c>a0.991
rrl1476525r.2868a>g0.991
rrl1476526r.2869g>gt0.938
rrl1476530r.2873c>t1.000
rrl1476536r.2879g>a1.000
rrl1476537r.2880a>g1.000
rrl1476538r.2881a>g1.000
rrl1476540r.2883c>g0.991
rrl1476547r.2890c>t1.000
rrl1476567r.2910c>t0.992
rrl1476573r.2916a>c0.996
rrl1476577r.2920t>g0.996
rrl1476584r.2927c>t0.991
rrl1476594r.2937c>t0.993
rrl1476596r.2939c>t0.993
rrl1476601r.2944g>a0.992
rrl1476607r.2950c>t0.991
rrl1476614r.2957a>g0.991
rrl1476619r.2962c>t0.987
rrl1476621r.2964c>t0.986
rrl1476624r.2967t>g0.987
rrl1476628r.2971t>a0.987
rrl1476630r.2973a>g0.987
rrl1476637r.2980c>g0.987
rrl1476638r.2981c>t0.987

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;