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: 5dd379224880d
Sample: 5dd379224880d

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Summary
ID: 5dd379224880d
Date: Tue Nov 19 05:13:18 2019
Strain: lineage4.6.2.2
Drug-resistance: MDR

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRahpC c.-48G>A (1.00)
RifampicinRrpoB p.His445Cys (1.00)
EthambutolRembB p.Gly406Asp (1.00)
PyrazinamideRpncA p.Ser32Ile (0.68)
StreptomycinRrpsL p.Lys43Arg (0.98)
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.Ser95Thr0.991
gyrA9304p.Gly668Asp1.000
rpsL781395c.-165T>C1.000
rrs1471876r.31g>a0.171
rrs1471892r.47g>a0.148
rrs1471893r.48t>g0.144
rrs1472160r.315c>t0.310
rrs1472172r.327t>c0.383
rrs1472181r.336g>a0.329
rrs1472214r.369c>g0.413
rrs1472235r.390g>c0.296
rrs1472240r.395g>c0.283
rrs1472242r.397c>t0.283
rrs1472251r.406g>a0.210
rrs1472253r.408g>t0.201
rrs1472259r.414c>a0.220
rrs1472266r.421c>a0.199
rrs1472277r.432c>g0.154
rrs1472338r.493a>c0.285
rrs1472344r.499c>t0.324
rrs1472349r.504a>t0.313
rrs1472374r.529t>a0.321
rrs1472379r.534t>g0.311
rrs1472382r.537g>t0.304
rrs1472391r.546c>t0.328
rrs1472598r.753a>t0.335
rrs1472616r.771g>a0.403
rrs1472734r.889c>t0.320
rrs1472741r.896g>a0.318
rrs1472742r.897c>t0.335
rrs1472781r.936c>t0.341
rrs1472793r.948a>t0.338
rrs1472803r.958t>a0.337
rrs1472812r.967a>c0.311
rrs1472887r.1042g>c0.309
rrs1473038r.1193a>c0.232
rrs1473044r.1199c>g0.250
rrs1473173r.1328c>t0.229
rrs1473177r.1332g>a0.258
rrs1473202r.1357c>t0.269
rrl1474199r.542g>a0.243
rrl1474201r.544t>c0.237
rrl1474202r.545t>a0.237
rrl1474218r.561t>a0.309
rrl1474228r.571t>c0.261
rrl1474235r.578g>c0.244
rrl1474249r.592g>t0.226
rrl1474252r.595t>a0.224
rrl1474264r.607t>g0.197
rrl1474265r.608g>a0.198
rrl1474558r.901g>c0.270
rrl1474584r.927c>g0.236
rrl1474586r.929t>a0.236
rrl1474587r.930g>a0.215
rrl1474602r.945c>g0.210
rrl1474844r.1187g>t0.220
rrl1474864r.1207c>t0.183
rrl1474866r.1209c>a0.183
rrl1474869r.1212g>t0.170
rrl1474875r.1218g>a0.170
rrl1474876r.1219t>a0.171
rrl1474883r.1226t>c0.167
rrl1475499r.1842c>g0.239
rrl1475526r.1869c>t0.358
rrl1475538r.1881t>c0.333
rrl1475539r.1882a>t0.322
rrl1475540r.1883c>t0.328
rrl1475545r.1888t>g0.322
rrl1475553r.1896g>t0.298
rrl1475555r.1898t>g0.311
rrl1475571r.1914a>t0.322
rrl1475575r.1918c>a0.306
rrl1475577r.1920c>g0.293
rrl1475589r.1932g>a0.295
rrl1475672r.2015c>t0.150
rrl1475673r.2016t>c0.150
rrl1475685r.2028t>g0.175
rrl1475687r.2030c>t0.177
rrl1475688r.2031g>c0.177
rrl1475697r.2040c>a0.213
rrl1475702r.2045g>t0.213
rrl1475707r.2050t>c0.217
rrl1475713r.2056c>g0.211
rrl1475716r.2059a>t0.213
rrl1475803r.2146t>c0.318
rrl1475804r.2147g>c0.322
rrl1475816r.2159c>g0.323
rrl1475817r.2160a>g0.321
rrl1476141r.2484a>g0.250
rrl1476153r.2496t>c0.257
rrl1476160r.2503t>g0.219
rrl1476164r.2507a>g0.239
rrl1476165r.2508t>a0.233
rrl1476252r.2595t>g0.202
rrl1476260r.2603a>g0.211
rrl1476266r.2609g>a0.211
rrl1476301r.2644a>t0.133
rrl1476311r.2654g>c0.137
rrl1476312r.2655t>c0.136
rrl1476313r.2656g>a0.157
rrl1476336r.2679c>g0.355
rrl1476356r.2699c>g0.331
rrl1476357r.2700t>a0.328
rrl1476358r.2701t>c0.341
rrl1476382r.2725a>g0.375
rrl1476384r.2727g>t0.378
rrl1476404r.2747g>a0.329
rrl1476408r.2751g>a0.382
rrl1476442r.2785t>a0.322
rrl1476443r.2786g>t0.342
rrl1476455r.2798c>a0.306
rrl1476456r.2799a>t0.290
rrl1476466r.2809c>t0.316
rrl1476470r.2813c>t0.314
rrl1476474r.2817c>t0.290
rrl1476481r.2824t>c0.303
rrl1476506r.2849t>c0.262
tlyA1917972c.33A>G1.000
katG2153948722Q>722*1.000
katG2154096c.2016T>G1.000
thyX3067474p.Pro158Ala1.000
alr3841652c.-232A>T0.234
alr3841654c.-234A>C0.238
alr3841662c.-242A>G0.307
alr3841663c.-243G>A0.271
embC4242550c.2688C>G1.000
embC4242643c.2781C>T1.000
embB4246584p.Arg24Pro0.345
ethA4326739c.735G>C1.000
ethR4328004c.456G>A1.000

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;