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: 5d6487af99176
Sample: 5d6487af99176

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Summary
ID: 5d6487af99176
Date: Tue Aug 27 02:32:50 2019
Strain: lineage4.3.3
Drug-resistance: Sensitive

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

Lineage2FamilyMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.3Euro-American (LAM)mainly-LAMNone
lineage4.3.3Euro-American (LAM)LAM;TRD115

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6408p.Glu390Gly1.000
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA8040p.Gly247Ser1.000
gyrA9304p.Gly668Asp1.000
rpoC764995c.1626C>G0.992
rpsL781395c.-165T>C1.000
rrs1472225r.380c>g0.128
rrs1472400r.555c>t0.188
rrs1472412r.567a>g0.207
rrs1472435r.590t>c0.148
rrs1472438r.593t>g0.130
rrs1472461r.616g>c0.120
rrs1472464r.619a>g0.174
rrs1472472r.627g>t0.125
rrs1472473r.628g>t0.125
rrs1472495r.650c>a0.125
rrs1472507r.662c>g0.241
rrs1472530r.685g>a0.511
rrs1472537r.692c>t0.152
rrs1472545r.700a>t0.111
rrs1472549r.704g>a0.167
rrs1472557r.712g>a0.308
rrs1472558r.713g>a0.292
rrs1472569r.724g>a0.289
rrs1472571r.726g>c0.500
rrs1472574r.729t>g0.190
rrs1472580r.735c>a0.333
rrs1472581r.736a>c0.513
rrs1472583r.738t>g0.250
rrs1472584r.739a>t0.348
rrs1472594r.749g>a0.204
rrs1472597r.752g>a0.216
rrs1472598r.753a>c0.532
rrs1472616r.771g>a0.340
rrs1472648r.803g>c0.269
rrs1472673r.828t>g0.263
rrs1472675r.830t>c0.222
rrs1472677r.832c>a0.222
rrs1472682r.837t>a0.278
rrs1472683r.838t>c0.278
rrs1472687r.842a>t0.235
rrs1472707r.862a>t0.148
rrs1472714r.869a>g0.296
rrs1472715r.870c>t0.296
rrs1472716r.871c>a0.280
rrs1472734r.889c>t0.312
rrs1472741r.896g>a0.312
rrs1472742r.897c>t0.355
rrs1472759r.914t>a0.281
rrs1472767r.922g>a0.357
rrs1472781r.936c>t0.387
rrs1472793r.948a>t0.379
rrs1472803r.958t>a0.333
rrs1472805r.960c>a0.300
rrs1472806r.961a>t0.300
rrs1472828r.983t>c0.200
rrs1472887r.1042g>c0.320
rrs1472892r.1047t>c0.308
rrs1473145r.1300c>t0.174
rrs1473166r.1321g>a0.185
rrs1473276r.1431a>g0.175
rrs1473290r.1445c>t0.156
rrs1473301r.1456t>c0.159
rrs1473304r.1459c>t0.114
rrs1473316r.1471c>t0.136
rrl1474218r.561t>g0.222
rrl1475499r.1842c>t0.182
rrl1475526r.1869c>a0.182
rrl1475531r.1874c>t0.182
rrl1475536r.1879c>a0.182
rrl1475539r.1882a>t0.182
rrl1475545r.1888t>g0.167
rrl1475550r.1893a>g0.167
rrl1475562r.1905c>t0.200
rrl1475586r.1929c>t0.200
rrl1475589r.1932g>a0.200
rrl1475803r.2146t>c0.250
rrl1475804r.2147g>c0.250
rrl1475816r.2159c>g0.267
rrl1475817r.2160a>g0.267
rrl1476322r.2665c>a0.517
rrl1476358r.2701t>c0.471
rrl1476368r.2711t>c0.486
rrl1476369r.2712c>t0.486
rrl1476372r.2715t>c0.462
rrl1476382r.2725a>g0.488
rrl1476383r.2726t>a0.476
rrl1476408r.2751g>a0.476
rrl1476442r.2785t>a0.415
rrl1476443r.2786g>t0.386
rrl1476455r.2798c>a0.340
rrl1476456r.2799a>t0.340
rrl1476466r.2809c>t0.347
rrl1476481r.2824t>c0.353
rrl1476506r.2849t>c0.292
tlyA1917972c.33A>G1.000
kasA2518919p.Gly269Ser1.000
thyA3073868p.Thr202Ala1.000
ald3086788c.-32T>C1.000
embC4242643c.2781C>T1.000
gid4408156p.Leu16Arg1.000

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;