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: 5d771df9ee383
Sample: 5d771df9ee383

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Summary
ID: 5d771df9ee383
Date: Tue Sep 10 04:53:35 2019
Strain: lineage2.2.1
Drug-resistance: MDR

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRkatG p.Ser315Thr (1.00)
RifampicinRrpoB p.Ser450Leu (1.00)
EthambutolRembB p.Gly406Asp (1.00)
Pyrazinamide
StreptomycinRrpsL p.Lys43Arg (1.00)
EthionamideRethA c.639 640del (1.00)
FluoroquinolonesRgyrA p.Ala90Val (0.90)
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
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
rpoB761998p.Leu731Pro1.000
rpoB763031c.3225T>C1.000
rpsL781395c.-165T>C1.000
rrs1471896r.51t>c0.804
rrs1471900r.55c>t0.787
rrs1472127r.282c>t0.564
rrs1472129r.284g>c0.564
rrs1472137r.292g>a0.617
rrs1472150r.305t>a0.661
rrs1472151r.306c>t0.643
rrs1472172r.327t>c0.745
rrs1472203r.358g>a0.698
rrs1472210r.365a>c0.688
rrs1472213r.368g>c0.652
rrs1472215r.370a>g0.652
rrs1472225r.380c>a0.646
rrs1472234r.389t>c0.541
rrs1472236r.391c>g0.541
rrs1472240r.395g>a0.514
rrs1472344r.499c>t0.608
rrs1472379r.534t>g0.655
rrs1472382r.537g>a0.655
rrs1472400r.555c>t0.643
rrs1472517r.672t>a0.286
rrs1472518r.673g>c0.375
rrs1472530r.685g>a0.324
rrs1472537r.692c>t0.324
rrs1472541r.696t>g0.324
rrs1472544r.699c>g0.324
rrs1472545r.700a>t0.324
rrs1472557r.712g>a0.326
rrs1472570r.725g>a0.326
rrs1472571r.726g>c0.326
rrs1472573r.728c>t0.326
rrs1472574r.729t>c0.256
rrs1472579r.734g>c0.326
rrs1472581r.736a>t0.326
rrs1472583r.738t>a0.267
rrs1472598r.753a>c0.659
rrs1472616r.771g>a0.614
rrs1472655r.810g>a0.364
rrs1472658r.813g>a0.310
rrs1472661r.816a>g0.289
rrs1472713r.868t>c0.219
rrs1472716r.871c>t0.286
rrs1472734r.889c>t0.620
rrs1472741r.896g>a0.613
rrs1472744r.899a>g0.625
rrs1472767r.922g>a0.617
rrs1472779r.934g>a0.598
rrs1472781r.936c>t0.598
rrs1472786r.941c>t0.605
rrs1472793r.948a>t0.583
rrs1472803r.958t>a0.590
rrs1472824r.979t>a0.238
rrs1472827r.982g>t0.132
rrs1472828r.983t>c0.132
rrs1472895r.1050c>t0.667
rrs1473035r.1190g>a0.148
rrs1473352r.1507c>t0.653
rrl1473384c.-274A>G0.250
rrl1474790r.1133c>t0.522
rrl1474798r.1141c>t0.549
rrl1474800r.1143t>c0.559
rrl1474804r.1147c>t0.569
rrl1474823r.1166c>g0.617
rrl1474827r.1170c>t0.633
rrl1474830r.1173a>c0.620
rrl1474831r.1174a>c0.633
rrl1474844r.1187g>t0.688
rrl1474866r.1209c>a0.705
rrl1474896r.1239a>g0.667
rrl1474902r.1245t>c0.629
rrl1474904r.1247g>c0.632
rrl1474913r.1256t>a0.587
rrl1474920r.1263g>a0.565
rrl1475672r.2015c>g0.391
rrl1475673r.2016t>c0.400
rrl1475687r.2030c>t0.439
rrl1475696r.2039t>c0.462
rrl1475703r.2046a>g0.474
rrl1475707r.2050t>a0.450
rrl1475716r.2059a>g0.439
rrl1475747r.2090a>g0.192
rrl1475803r.2146t>c0.595
rrl1475804r.2147g>c0.611
rrl1475816r.2159c>g0.550
rrl1475817r.2160a>g0.564
rrl1475843r.2186g>a0.595
rrl1475849r.2192g>a0.564
rrl1475853r.2196c>t0.590
rrl1475858r.2201t>c0.564
rrl1476246r.2589g>a0.296
rrl1476251r.2594t>c0.300
rrl1476252r.2595t>c0.250
rrl1476260r.2603a>g0.417
rrl1476280r.2623a>c0.459
rrl1476293r.2636c>t0.472
rrl1476294r.2637a>g0.486
rrl1476295r.2638c>g0.486
rrl1476296r.2639c>t0.486
rrl1476297r.2640c>a0.486
rrl1476302r.2645g>a0.447
rrl1476311r.2654g>c0.459
rrl1476312r.2655t>c0.459
rrl1476313r.2656g>a0.474
rrl1476332r.2675g>c0.729
rrl1476338r.2681c>t0.738
rrl1476353r.2696g>t0.747
rrl1476358r.2701t>c0.762
rrl1476372r.2715t>c0.773
rrl1476382r.2725a>g0.800
rrl1476383r.2726t>a0.797
rrl1476408r.2751g>a0.782
rrl1476425r.2768g>a0.784
rrl1476428r.2771c>t0.804
rrl1476466r.2809c>t0.739
rrl1476481r.2824t>c0.736
rrl1476506r.2849t>c0.750
rpsA1834177c.636A>C1.000
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
pncA2289150p.Ile31Thr1.000
ald3086788c.-32T>C1.000
embA4243460c.228C>T1.000
gid4407588c.615T>C1.000
gid4407927p.Glu92Asp1.000

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;