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.
Back to results page.
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: 5dd39ae4ed332
Sample: 5dd39ae4ed332

Download results

Summary
ID: 5dd39ae4ed332
Date: Tue Nov 19 07:38:07 2019
Strain: root
Drug-resistance: Sensitive

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

Lineage2FamilyMain SpoligotypeRDS

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
rpoC764605c.1236G>C1.000
rpoC764611c.1242G>C0.500
rpoC764620c.1251G>T0.500
rpoC764632c.1263T>C1.000
rpoC764641c.1272C>T0.933
rpoC764644c.1275G>C0.286
rpoC764650c.1281G>T1.000
rpoC764701c.1332C>G0.300
rpoC764705p.Leu446Lys0.900
rpoC764716c.1347G>C0.300
rrs1471876r.31g>a1.000
rrs1471892r.47g>a1.000
rrs1471893r.48t>g0.927
rrs1472106r.261g>a1.000
rrs1472108r.263c>a1.000
rrs1472160r.315c>t0.815
rrs1472172r.327t>c1.000
rrs1472181r.336g>a0.823
rrs1472214r.369c>g0.930
rrs1472225r.380c>a0.161
rrs1472235r.390g>c0.907
rrs1472240r.395g>c1.000
rrs1472242r.397c>t1.000
rrs1472251r.406g>a1.000
rrs1472253r.408g>t1.000
rrs1472259r.414c>a0.978
rrs1472266r.421c>a0.977
rrs1472277r.432c>g0.963
rrs1472338r.493a>c0.986
rrs1472344r.499c>t1.000
rrs1472349r.504a>t0.988
rrs1472374r.529t>a0.987
rrs1472379r.534t>g0.987
rrs1472382r.537g>t1.000
rrs1472391r.546c>t0.989
rrs1472412r.567a>c1.000
rrs1472415r.570t>a1.000
rrs1472557r.712g>a1.000
rrs1472598r.753a>t0.989
rrs1472616r.771g>a1.000
rrs1472712r.867g>a0.526
rrs1472713r.868t>c0.737
rrs1472714r.869a>t0.263
rrs1472715r.870c>a0.432
rrs1472716r.871c>t0.949
rrs1472734r.889c>t0.974
rrs1472741r.896g>a0.974
rrs1472742r.897c>t0.992
rrs1472781r.936c>t0.984
rrs1472793r.948a>t0.984
rrs1472803r.958t>a0.976
rrs1472812r.967a>c0.964
rrs1472887r.1042g>c0.955
rrs1473038r.1193a>c0.950
rrs1473044r.1199c>g0.979
rrs1473149r.1304g>c0.455
rrs1473162r.1317c>g0.538
rrs1473163r.1318c>a0.462
rrs1473164r.1319c>g1.000
rrs1473166r.1321g>a0.250
rrs1473173r.1328c>t0.890
rrs1473177r.1332g>a1.000
rrs1473192r.1347a>g0.185
rrs1473199r.1354ca>c1.000
rrs1473202r.1357c>t1.000
rrs1473205r.1360t>c0.146
rrs1473352r.1507c>g0.977
rrs1473353r.1508c>g0.956
rrs1473358r.1513g>c0.977
rrs1473359r.1514g>c0.977
rrl1473922r.265a>c1.000
rrl1474199r.542g>a1.000
rrl1474201r.544t>c1.000
rrl1474202r.545t>a1.000
rrl1474218r.561t>a1.000
rrl1474228r.571t>c1.000
rrl1474235r.578g>c1.000
rrl1474249r.592g>t1.000
rrl1474252r.595t>a0.914
rrl1474264r.607t>g1.000
rrl1474265r.608g>a1.000
rrl1474558r.901g>c0.975
rrl1474584r.927c>g0.957
rrl1474586r.929t>a0.957
rrl1474587r.930g>a0.957
rrl1474602r.945c>g0.951
rrl1474828r.1171g>c0.947
rrl1474844r.1187g>t0.848
rrl1474864r.1207c>t0.957
rrl1474866r.1209c>a0.826
rrl1474869r.1212g>t0.978
rrl1474875r.1218g>a0.978
rrl1474876r.1219t>a1.000
rrl1474883r.1226t>c1.000
rrl1475499r.1842c>g1.000
rrl1475526r.1869c>t0.823
rrl1475538r.1881t>c0.780
rrl1475539r.1882a>t1.000
rrl1475540r.1883c>t1.000
rrl1475545r.1888t>g1.000
rrl1475550r.1893a>g0.217
rrl1475553r.1896g>c0.208
rrl1475555r.1898t>g0.958
rrl1475571r.1914a>t0.951
rrl1475575r.1918c>a0.903
rrl1475577r.1920c>g0.902
rrl1475589r.1932g>a0.922
rrl1475672r.2015c>t0.971
rrl1475673r.2016t>c1.000
rrl1475685r.2028t>g1.000
rrl1475687r.2030c>t1.000
rrl1475688r.2031g>c1.000
rrl1475697r.2040c>a0.959
rrl1475702r.2045g>t0.925
rrl1475707r.2050t>c1.000
rrl1475713r.2056c>g1.000
rrl1475716r.2059a>t0.982
rrl1475803r.2146t>c0.991
rrl1475804r.2147g>c0.991
rrl1475816r.2159c>g0.992
rrl1475817r.2160a>g0.992
rrl1475881r.2224t>c1.000
rrl1475883r.2226a>c1.000
rrl1475884r.2227a>g0.211
rrl1476141r.2484a>g0.967
rrl1476153r.2496t>c0.964
rrl1476160r.2503t>g0.600
rrl1476164r.2507a>g0.962
rrl1476165r.2508t>a0.852
rrl1476252r.2595t>g0.929
rrl1476260r.2603a>g1.000
rrl1476266r.2609g>a0.909
rrl1476279r.2622g>t0.824
rrl1476280r.2623a>c0.950
rrl1476281r.2624t>a0.895
rrl1476293r.2636c>t0.947
rrl1476294r.2637a>g0.947
rrl1476295r.2638c>g0.947
rrl1476296r.2639c>t0.947
rrl1476301r.2644a>t0.750
rrl1476311r.2654g>c0.955
rrl1476312r.2655t>c0.955
rrl1476313r.2656g>a0.957
rrl1476336r.2679c>t0.156
rrl1476338r.2681c>t0.184
rrl1476339r.2682g>a0.154
rrl1476356r.2699c>t0.203
rrl1476357r.2700t>a0.759
rrl1476358r.2701t>c0.709
rrl1476359r.2702c>g0.208
rrl1476381r.2724g>c0.165
rrl1476382r.2725a>g0.772
rrl1476383r.2726t>a0.202
rrl1476384r.2727g>a0.171
rrl1476404r.2747g>a0.694
rrl1476408r.2751g>a1.000
rrl1476411r.2754g>a0.190
rrl1476442r.2785t>a0.693
rrl1476443r.2786g>t0.878
rrl1476455r.2798c>a0.892
rrl1476456r.2799a>t0.707
rrl1476463r.2806c>t0.167
rrl1476466r.2809c>t1.000
rrl1476470r.2813c>t0.892
rrl1476474r.2817c>t0.707
rrl1476481r.2824t>c1.000
rrl1476501r.2844c>t0.175
rrl1476506r.2849t>c1.000
rrl1476567r.2910c>t1.000
rrl1476572r.2915g>a0.184
rrl1476573r.2916a>t1.000
rrl1476575r.2918c>t0.806
rrl1476584r.2927c>g1.000
rrl1476586r.2929c>t0.857
rrl1476588r.2931a>t0.857
rrl1476645r.2988a>g0.641

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;