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: 5db500a9adcdd
Sample: 5db500a9adcdd

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Summary
ID: 5db500a9adcdd
Date: Sun Oct 27 02:33:21 2019
Strain: lineage4.6.1.2
Drug-resistance: MDR

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRfabG1 c.-15C>T (1.00)
RifampicinRrpoB p.Gln432Lys (1.00)
Ethambutol
PyrazinamideRpncA p.His137Arg (1.00)
StreptomycinRgid c.102 102del (1.00)
EthionamideRfabG1 c.-15C>T (1.00)
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.6Euro-AmericanT;LAMNone
lineage4.6.1Euro-American (Uganda)T2RD724
lineage4.6.1.2Euro-AmericanT2RD724

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
gyrA7539p.Thr80Ala1.000
gyrA7585p.Ser95Thr1.000
gyrA9276c.1975C>T1.000
gyrA9304p.Gly668Asp1.000
rpoC764810p.Pro481Thr1.000
rpoC766767p.His1133Pro1.000
rpsL781395c.-165T>C1.000
embR1416410p.Leu313Arg1.000
rrs1471896r.51t>c0.730
rrs1471900r.55c>t0.722
rrs1471914r.69a>g0.279
rrs1472106r.261g>a0.133
rrs1472108r.263c>t0.158
rrs1472112r.267c>t0.140
rrs1472113r.268t>c0.210
rrs1472127r.282c>t0.725
rrs1472129r.284g>c0.745
rrs1472137r.292g>a0.808
rrs1472150r.305t>a0.838
rrs1472151r.306c>t0.838
rrs1472172r.327t>c0.844
rrs1472203r.358g>a0.798
rrs1472530r.685g>a0.386
rrs1472537r.692c>t0.393
rrs1472541r.696t>g0.379
rrs1472544r.699c>g0.367
rrs1472545r.700a>t0.397
rrs1472557r.712g>a0.862
rrs1472570r.725g>a0.868
rrs1472571r.726g>c0.868
rrs1472579r.734g>t0.867
rrs1472581r.736a>t0.874
rrs1472695r.850c>t0.370
rrs1472697r.852t>c0.408
rrs1472713r.868t>c0.842
rrs1472716r.871c>t0.839
rrs1472734r.889c>t0.901
rrs1472741r.896g>a0.906
rrs1472744r.899a>g0.906
rrs1472781r.936c>t0.916
rrs1472793r.948a>t0.816
rrs1472803r.958t>a0.807
rrs1472824r.979t>a0.172
rrs1472880r.1035g>ga0.277
rrs1472895r.1050c>t0.839
rrs1473163r.1318c>t0.342
rrs1473164r.1319c>g0.342
rrs1473172r.1327t>c0.385
rrs1473173r.1328c>t0.391
rrs1473177r.1332g>a0.385
rrs1473192r.1347a>g0.348
rrs1473202r.1357c>t0.377
rrs1473205r.1360t>c0.368
rrs1473327r.1482a>g0.213
rrs1473328r.1483c>t0.213
rrs1473352r.1507c>t0.825
rrl1474812r.1155g>a0.739
rrl1474823r.1166c>g0.743
rrl1474827r.1170c>t0.754
rrl1474830r.1173a>t0.754
rrl1474831r.1174a>t0.757
rrl1474844r.1187g>t0.841
rrl1474866r.1209c>a0.841
rrl1474869r.1212g>t0.835
rrl1474896r.1239a>g0.853
rrl1474902r.1245t>c0.808
rrl1474904r.1247g>c0.795
rrl1474913r.1256t>a0.757
rrl1474920r.1263g>c0.742
rrl1475783r.2126t>g0.680
rrl1475803r.2146t>c0.827
rrl1475804r.2147g>c0.827
rrl1475816r.2159c>g0.826
rrl1475817r.2160a>g0.842
rrl1475858r.2201t>c0.812
rrl1475866r.2209t>a0.806
rrl1475871r.2214t>c0.776
rrl1476225r.2568t>g0.896
rrl1476251r.2594t>c0.930
rrl1476260r.2603a>g0.938
rrl1476280r.2623a>c0.915
rrl1476293r.2636c>t0.296
rrl1476311r.2654g>c0.361
rrl1476312r.2655t>c0.324
rrl1476313r.2656g>a0.366
rrl1476332r.2675g>c0.864
rrl1476353r.2696g>t0.883
rrl1476358r.2701t>c0.892
rrl1476372r.2715t>c0.906
rrl1476382r.2725a>g0.908
rrl1476383r.2726t>a0.911
rrl1476408r.2751g>a0.942
rrl1476425r.2768g>t0.913
rrl1476428r.2771c>t0.905
rrl1476429r.2772a>c0.912
rrl1476466r.2809c>t0.897
rrl1476481r.2824t>c0.866
rrl1476506r.2849t>c0.796
rrl1476514r.2857c>t0.397
rrl1476519r.2862c>g0.236
rpsA1833503c.-39G>A1.000
tlyA1917972c.33A>G1.000
katG2155541p.Trp191Gly1.000
embC4242643c.2781C>T1.000
embA4245055p.Thr608Asn1.000
ethA4327107p.His123Tyr1.000
ethR4328171p.Val208Ala1.000

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;