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: 5d76151a2beb7
Sample: 5d76151a2beb7

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Summary
ID: 5d76151a2beb7
Date: Mon Sep 9 10:04:40 2019
Strain: lineage3
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
StreptomycinRrrs r.888g>a (0.76)
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage3East-African-IndianCASRD750

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA8056p.Arg252Leu1.000
gyrA9304p.Gly668Asp1.000
rpoB759746c.-61C>T1.000
rpoB762434c.2628T>G1.000
rpoB763031c.3225T>C1.000
rpsL781395c.-165T>C1.000
embR1416234p.Cys372Gly0.149
rrs1471878r.33c>t0.512
rrs1471896r.51t>c0.468
rrs1471900r.55c>t0.468
rrs1472101r.256g>a0.145
rrs1472102r.257g>a0.145
rrs1472106r.261g>a0.200
rrs1472112r.267c>t0.568
rrs1472122r.277g>a0.570
rrs1472127r.282c>t0.577
rrs1472129r.284g>c0.575
rrs1472137r.292g>a0.614
rrs1472150r.305t>a0.631
rrs1472151r.306c>t0.627
rrs1472164r.319g>a0.648
rrs1472172r.327t>c0.682
rrs1472177r.332c>t0.689
rrs1472203r.358g>a0.680
rrs1472210r.365a>c0.648
rrs1472213r.368g>c0.643
rrs1472215r.370a>g0.647
rrs1472225r.380c>a0.667
rrs1472234r.389t>c0.638
rrs1472236r.391c>g0.635
rrs1472240r.395g>a0.641
rrs1472251r.406g>a0.188
rrs1472253r.408g>t0.153
rrs1472378r.533g>t0.667
rrs1472379r.534t>g0.677
rrs1472382r.537g>a0.682
rrs1472389r.544g>a0.712
rrs1472400r.555c>t0.703
rrs1472412r.567a>c0.667
rrs1472415r.570t>g0.688
rrs1472422r.577t>c0.685
rrs1472517r.672t>a0.602
rrs1472518r.673g>t0.607
rrs1472530r.685g>a0.705
rrs1472541r.696t>g0.628
rrs1472544r.699c>a0.681
rrs1472545r.700a>t0.686
rrs1472557r.712g>a0.725
rrs1472570r.725g>a0.699
rrs1472571r.726g>c0.694
rrs1472573r.728c>t0.689
rrs1472579r.734g>t0.713
rrs1472581r.736a>t0.713
rrs1472596r.751g>t0.726
rrs1472598r.753a>t0.736
rrs1472614r.769g>t0.702
rrs1472616r.771g>a0.699
rrs1472642r.797c>t0.133
rrs1472655r.810g>a0.283
rrs1472658r.813g>a0.191
rrs1472661r.816a>g0.191
rrs1472665r.820g>a0.196
rrs1472678r.833t>c0.209
rrs1472679r.834t>c0.209
rrs1472690r.845c>a0.225
rrs1472695r.850c>t0.244
rrs1472697r.852t>c0.261
rrs1472713r.868t>c0.750
rrs1472716r.871c>t0.759
rrs1472742r.897c>t0.751
rrs1472744r.899a>g0.753
rrs1472767r.922g>a0.778
rrs1472781r.936c>t0.749
rrs1472793r.948a>t0.713
rrs1472803r.958t>a0.717
rrs1472895r.1050c>t0.707
rrs1473035r.1190g>a0.680
rrs1473053r.1208t>a0.122
rrs1473054r.1209c>t0.125
rrs1473055r.1210c>t0.128
rrs1473062r.1217t>a0.152
rrs1473068r.1223a>g0.139
rrs1473191r.1346c>t0.621
rrs1473202r.1357c>t0.642
rrs1473206r.1361g>a0.643
rrs1473226r.1381c>t0.682
rrs1473352r.1507c>t0.621
rrl1474218r.561t>a0.280
rrl1474236r.579g>a0.250
rrl1474252r.595t>a0.268
rrl1474255r.598c>t0.250
rrl1474269r.612c>t0.179
rrl1474330r.673a>t0.469
rrl1474839r.1182c>t0.440
rrl1474844r.1187g>t0.444
rrl1474864r.1207c>t0.467
rrl1474866r.1209c>a0.463
rrl1474869r.1212g>t0.481
rrl1474892r.1235g>a0.468
rrl1474896r.1239a>g0.478
rrl1474902r.1245t>c0.506
rrl1474903r.1246t>a0.500
rrl1474904r.1247g>c0.500
rrl1474913r.1256t>a0.489
rrl1474920r.1263g>c0.461
rrl1475137r.1480a>t0.424
rrl1475144r.1487g>c0.424
rrl1475145r.1488c>t0.431
rrl1475163r.1506t>g0.414
rrl1475171r.1514c>t0.403
rrl1475175r.1518g>a0.409
rrl1475188r.1531c>t0.391
rrl1475498r.1841c>g0.349
rrl1475574r.1917c>a0.659
rrl1475713r.2056c>g0.694
rrl1475716r.2059a>g0.694
rrl1475803r.2146t>c0.837
rrl1475804r.2147g>c0.837
rrl1475816r.2159c>g0.855
rrl1475817r.2160a>g0.860
rrl1475858r.2201t>c0.873
rrl1475866r.2209t>a0.865
rrl1476135r.2478t>c0.780
rrl1476141r.2484a>g0.783
rrl1476153r.2496t>c0.770
rrl1476165r.2508t>g0.704
rrl1476179r.2522c>t0.673
rrl1476225r.2568t>g0.790
rrl1476229r.2572c>t0.787
rrl1476251r.2594t>c0.824
rrl1476260r.2603a>g0.823
rrl1476268r.2611a>t0.817
rrl1476275r.2618t>a0.800
rrl1476279r.2622g>a0.813
rrl1476280r.2623a>c0.813
rrl1476293r.2636c>t0.671
rrl1476294r.2637a>g0.671
rrl1476295r.2638c>g0.662
rrl1476296r.2639c>t0.653
rrl1476297r.2640c>t0.627
rrl1476301r.2644a>c0.627
rrl1476302r.2645g>a0.627
rrl1476311r.2654g>c0.633
rrl1476312r.2655t>c0.633
rrl1476313r.2656g>a0.625
rrl1476332r.2675g>c0.812
rrl1476353r.2696g>t0.831
rrl1476358r.2701t>c0.820
rrl1476369r.2712c>t0.832
rrl1476372r.2715t>c0.833
rrl1476382r.2725a>g0.814
rrl1476383r.2726t>a0.826
rrl1476408r.2751g>a0.807
rrl1476425r.2768g>t0.767
rrl1476428r.2771c>t0.757
rrl1476429r.2772a>c0.763
rrl1476466r.2809c>t0.786
rrl1476481r.2824t>c0.797
rrl1476506r.2849t>c0.796
rrl1476514r.2857c>t0.652
rrl1476517r.2860c>t0.647
rrl1476519r.2862c>g0.647
rrl1476524r.2867c>a0.647
rrl1476525r.2868a>g0.655
rrl1476530r.2873c>t0.647
rrl1476536r.2879g>a0.663
rrl1476537r.2880a>g0.663
rrl1476538r.2881a>g0.655
rrl1476540r.2883c>g0.663
rrl1476547r.2890c>t0.755
rrl1476567r.2910c>t0.731
rrl1476572r.2915g>a0.713
rrl1476573r.2916a>t0.713
rrl1476584r.2927c>t0.673
rpsA1833485c.-57C>T1.000
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
katG2156132c.-21C>A1.000
pncA2289047c.195G>A1.000
ahpC2726105c.-88G>A1.000
ald3086788c.-32T>C1.000
alr3841652c.-232A>T0.355
alr3841654c.-234A>C0.364
alr3841662c.-242A>G0.411
alr3841663c.-243G>A0.389
embC4242075p.Arg738Gln1.000
embC4242643c.2781C>T1.000
embB4246584p.Arg24Pro0.269
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;