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: 5de3ebed6f20b
Sample: 5de3ebed6f20b

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Summary
ID: 5de3ebed6f20b
Date: Sun Dec 1 16:38:21 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
rrs1471876r.31g>a1.000
rrs1471892r.47g>a1.000
rrs1471893r.48t>g1.000
rrs1472172r.327t>c1.000
rrs1472214r.369c>g1.000
rrs1472223r.378c>g1.000
rrs1472228r.383g>c1.000
rrs1472235r.390g>c1.000
rrs1472240r.395g>c1.000
rrs1472242r.397c>t1.000
rrs1472251r.406g>a1.000
rrs1472253r.408g>t1.000
rrs1472259r.414c>a1.000
rrs1472264r.419t>c1.000
rrs1472266r.421c>a1.000
rrs1472277r.432c>g1.000
rrs1472338r.493a>c1.000
rrs1472344r.499c>t1.000
rrs1472349r.504a>t1.000
rrs1472374r.529t>a1.000
rrs1472379r.534t>g0.995
rrs1472382r.537g>t1.000
rrs1472391r.546c>t1.000
rrs1472396r.551a>t1.000
rrs1472557r.712g>a1.000
rrs1472571r.726g>c1.000
rrs1472574r.729t>a1.000
rrs1472579r.734g>t1.000
rrs1472581r.736a>c1.000
rrs1472582r.737g>a1.000
rrs1472584r.739a>t1.000
rrs1472598r.753a>t1.000
rrs1472616r.771g>a1.000
rrs1472655r.810g>a1.000
rrs1472658r.813g>a1.000
rrs1472659r.814g>a1.000
rrs1472661r.816a>g1.000
rrs1472662r.817c>t1.000
rrs1472666r.821g>c1.000
rrs1472667r.822t>c1.000
rrs1472670r.825g>c1.000
rrs1472676r.831c>a1.000
rrs1472687r.842a>c1.000
rrs1472690r.845c>g1.000
rrs1472694r.849c>g1.000
rrs1472697r.852t>c0.978
rrs1472712r.867g>a0.982
rrs1472713r.868t>c1.000
rrs1472715r.870c>t1.000
rrs1472716r.871c>t1.000
rrs1472734r.889c>t1.000
rrs1472741r.896g>a1.000
rrs1472742r.897c>t1.000
rrs1472781r.936c>t1.000
rrs1472793r.948a>t1.000
rrs1472803r.958t>a1.000
rrs1472812r.967a>c1.000
rrs1472887r.1042g>c1.000
rrs1473038r.1193a>c1.000
rrs1473044r.1199c>g1.000
rrs1473352r.1507c>g1.000
rrs1473353r.1508c>g1.000
rrs1473358r.1513g>c1.000
rrs1473359r.1514g>c1.000
rrs1473362r.1517c>t1.000
rrl1473697r.40c>g1.000
rrl1473698r.41g>c1.000
rrl1473700r.43g>c1.000
rrl1473703r.46c>g1.000
rrl1473922r.265a>c0.992
rrl1473928r.271t>c1.000
rrl1474199r.542g>c1.000
rrl1474201r.544t>c1.000
rrl1474202r.545t>c1.000
rrl1474218r.561t>a0.989
rrl1474235r.578g>c1.000
rrl1474236r.579g>a1.000
rrl1474249r.592g>t1.000
rrl1474264r.607t>a1.000
rrl1474265r.608g>a1.000
rrl1474558r.901g>c1.000
rrl1474584r.927c>g1.000
rrl1474586r.929t>a1.000
rrl1474587r.930g>a1.000
rrl1474602r.945c>g1.000
rrl1474609r.952g>c1.000
rrl1474610r.953c>t1.000
rrl1474828r.1171g>c1.000
rrl1474833r.1176g>a1.000
rrl1474844r.1187g>t1.000
rrl1474866r.1209c>a1.000
rrl1474869r.1212g>t1.000
rrl1474875r.1218g>a1.000
rrl1474876r.1219t>a1.000
rrl1474883r.1226t>c1.000
rrl1475136r.1479g>c1.000
rrl1475137r.1480a>c1.000
rrl1475154r.1497c>a1.000
rrl1475499r.1842c>g1.000
rrl1475516r.1859t>a1.000
rrl1475518r.1861a>t1.000
rrl1475526r.1869c>a1.000
rrl1475531r.1874c>t1.000
rrl1475538r.1881t>c1.000
rrl1475539r.1882a>t1.000
rrl1475540r.1883c>t1.000
rrl1475545r.1888t>g1.000
rrl1475551r.1894t>c1.000
rrl1475553r.1896g>t0.976
rrl1475555r.1898t>g1.000
rrl1475571r.1914a>t1.000
rrl1475575r.1918c>a1.000
rrl1475577r.1920c>g1.000
rrl1475589r.1932g>a1.000
rrl1475673r.2016t>c1.000
rrl1475685r.2028t>g1.000
rrl1475687r.2030c>t1.000
rrl1475688r.2031g>c1.000
rrl1475707r.2050t>c1.000
rrl1475713r.2056c>g1.000
rrl1475716r.2059a>t0.996
rrl1475750r.2093accc>a1.000
rrl1475755r.2098t>a1.000
rrl1475775r.2118g>a1.000
rrl1475776r.2119g>t1.000
rrl1475777r.2120a>t1.000
rrl1475783r.2126t>g1.000
rrl1475803r.2146t>c1.000
rrl1475804r.2147g>c1.000
rrl1475816r.2159c>g1.000
rrl1475817r.2160a>g1.000
rrl1476141r.2484a>g1.000
rrl1476153r.2496t>c0.992
rrl1476164r.2507a>g1.000
rrl1476165r.2508t>a1.000
rrl1476313r.2656g>a1.000
rrl1476336r.2679c>g1.000
rrl1476356r.2699c>g1.000
rrl1476357r.2700t>a1.000
rrl1476358r.2701t>c1.000
rrl1476382r.2725a>g1.000
rrl1476384r.2727g>t1.000
rrl1476404r.2747g>a1.000
rrl1476408r.2751g>a1.000
rrl1476442r.2785t>a0.995
rrl1476443r.2786g>t0.995
rrl1476455r.2798c>a0.990
rrl1476456r.2799a>t0.995
rrl1476466r.2809c>t1.000
rrl1476470r.2813c>t1.000
rrl1476474r.2817c>t1.000
rrl1476481r.2824t>c1.000
rrl1476506r.2849t>c1.000
rrl1476567r.2910c>t1.000
rrl1476573r.2916a>t1.000
rrl1476575r.2918c>t1.000
rrl1476645r.2988a>g1.000

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;