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: 5dd3750a3bafa
Sample: 5dd3750a3bafa

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Summary
ID: 5dd3750a3bafa
Date: Tue Nov 19 04:55:23 2019
Strain: lineage4.6.2.2
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
RifampicinRrpoB p.Ser450Leu (1.00)
Ethambutol
Pyrazinamide
Streptomycin
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.6Euro-AmericanT;LAMNone
lineage4.6.2Euro-AmericanT;LAMRD726
lineage4.6.2.2Euro-American (Cameroon)LAM10-CAMRD726

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA9304p.Gly668Asp1.000
rpoC764575c.1206T>C0.143
rpoC764581c.1212T>C0.148
rpoC764582p.Leu405Met0.148
rpoC764605c.1236G>C0.169
rpoC764611c.1242G>C0.152
rpoC764620c.1251G>T0.143
rpoC764632c.1263T>C0.152
rpoC764641c.1272C>T0.132
rpoC764650c.1281G>T0.128
rpsL781395c.-165T>C1.000
rrs1471892r.47g>a0.180
rrs1472106r.261g>a0.158
rrs1472108r.263c>a0.161
rrs1472160r.315c>t0.383
rrs1472172r.327t>c0.476
rrs1472181r.336g>a0.429
rrs1472214r.369c>g0.518
rrs1472235r.390g>c0.431
rrs1472240r.395g>c0.410
rrs1472242r.397c>t0.401
rrs1472251r.406g>a0.302
rrs1472253r.408g>t0.298
rrs1472259r.414c>a0.285
rrs1472266r.421c>a0.254
rrs1472277r.432c>g0.208
rrs1472338r.493a>c0.249
rrs1472344r.499c>t0.306
rrs1472349r.504a>t0.279
rrs1472374r.529t>a0.345
rrs1472379r.534t>g0.323
rrs1472382r.537g>t0.346
rrs1472391r.546c>t0.372
rrs1472557r.712g>a0.155
rrs1472598r.753a>t0.408
rrs1472616r.771g>a0.435
rrs1472734r.889c>t0.328
rrs1472741r.896g>a0.328
rrs1472742r.897c>t0.380
rrs1472781r.936c>t0.404
rrs1472793r.948a>t0.399
rrs1472803r.958t>a0.416
rrs1472812r.967a>c0.343
rrs1472887r.1042g>c0.421
rrs1473038r.1193a>c0.347
rrs1473044r.1199c>g0.409
rrs1473173r.1328c>t0.323
rrs1473177r.1332g>a0.396
rrs1473199r.1354ca>c0.418
rrs1473202r.1357c>t0.389
rrs1473352r.1507c>g0.236
rrs1473353r.1508c>g0.228
rrs1473358r.1513g>c0.225
rrs1473359r.1514g>c0.224
rrl1474199r.542g>a0.184
rrl1474201r.544t>c0.178
rrl1474202r.545t>a0.174
rrl1474218r.561t>a0.241
rrl1474228r.571t>c0.197
rrl1474558r.901g>c0.285
rrl1474584r.927c>g0.243
rrl1474586r.929t>a0.243
rrl1474587r.930g>a0.238
rrl1474602r.945c>g0.221
rrl1474828r.1171g>c0.158
rrl1474844r.1187g>t0.227
rrl1474864r.1207c>t0.182
rrl1474866r.1209c>a0.171
rrl1474869r.1212g>t0.194
rrl1474875r.1218g>a0.184
rrl1474876r.1219t>a0.183
rrl1474883r.1226t>c0.182
rrl1475499r.1842c>g0.211
rrl1475526r.1869c>t0.338
rrl1475538r.1881t>c0.317
rrl1475539r.1882a>t0.299
rrl1475540r.1883c>t0.297
rrl1475545r.1888t>g0.299
rrl1475553r.1896g>t0.248
rrl1475555r.1898t>g0.277
rrl1475571r.1914a>t0.299
rrl1475575r.1918c>a0.274
rrl1475577r.1920c>g0.259
rrl1475589r.1932g>a0.271
rrl1475672r.2015c>t0.144
rrl1475685r.2028t>g0.155
rrl1475688r.2031g>c0.149
rrl1475697r.2040c>a0.187
rrl1475702r.2045g>t0.190
rrl1475707r.2050t>c0.196
rrl1475713r.2056c>g0.201
rrl1475716r.2059a>t0.200
rrl1475803r.2146t>c0.398
rrl1475804r.2147g>c0.403
rrl1475816r.2159c>g0.418
rrl1475817r.2160a>g0.427
rrl1476141r.2484a>g0.190
rrl1476153r.2496t>c0.193
rrl1476160r.2503t>g0.168
rrl1476164r.2507a>g0.188
rrl1476165r.2508t>a0.169
rrl1476252r.2595t>g0.303
rrl1476260r.2603a>g0.314
rrl1476266r.2609g>a0.310
rrl1476279r.2622g>t0.155
rrl1476280r.2623a>c0.171
rrl1476281r.2624t>a0.171
rrl1476293r.2636c>t0.168
rrl1476294r.2637a>g0.168
rrl1476295r.2638c>g0.170
rrl1476296r.2639c>t0.171
rrl1476301r.2644a>t0.167
rrl1476311r.2654g>c0.179
rrl1476312r.2655t>c0.179
rrl1476313r.2656g>a0.184
rrl1476336r.2679c>g0.482
rrl1476356r.2699c>g0.493
rrl1476357r.2700t>a0.480
rrl1476358r.2701t>c0.484
rrl1476382r.2725a>g0.512
rrl1476384r.2727g>t0.528
rrl1476404r.2747g>a0.430
rrl1476408r.2751g>a0.531
rrl1476442r.2785t>a0.455
rrl1476443r.2786g>t0.452
rrl1476455r.2798c>a0.455
rrl1476456r.2799a>t0.452
rrl1476466r.2809c>t0.495
rrl1476470r.2813c>t0.408
rrl1476474r.2817c>t0.415
rrl1476481r.2824t>c0.371
rrl1476506r.2849t>c0.401
rrl1476567r.2910c>t0.236
rrl1476573r.2916a>t0.199
rrl1476575r.2918c>t0.199
tlyA1917972c.33A>G1.000
thyX3067474p.Pro158Ala1.000
ald3087733p.Val305Ala1.000
alr3841654c.-234A>C0.198
alr3841662c.-242A>G0.222
alr3841663c.-243G>A0.231
embC4242643c.2781C>T1.000
embA4243230c.-3C>T1.000
embB4246584p.Arg24Pro0.526
ethA4326739c.735G>C1.000
ethR4328004c.456G>A1.000
gid4408064p.Arg47Trp1.000

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;