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: 5da4c80473bc6
Sample: 5da4c80473bc6

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Summary
ID: 5da4c80473bc6
Date: Mon Oct 14 20:10:51 2019
Strain: lineageBOV
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
StreptomycinRrrs r.888g>a (0.50)
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineageBOVM. bovisBOV 1;BOV 2None
lineageBOV AFRI???

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
rrs1471876r.31g>a0.216
rrs1471877r.32a>t0.216
rrs1471878r.33c>t0.485
rrs1471892r.47g>a0.370
rrs1471893r.48t>g0.194
rrs1471896r.51t>c0.407
rrs1471898r.53a>t0.296
rrs1471900r.55c>t0.407
rrs1471911r.66c>a0.476
rrs1472172r.327t>c0.947
rrs1472203r.358g>a0.480
rrs1472210r.365a>t0.800
rrs1472214r.369c>g0.909
rrs1472344r.499c>t1.000
rrs1472378r.533g>t0.276
rrs1472379r.534t>c0.286
rrs1472380r.535g>c0.286
rrs1472389r.544g>a0.680
rrs1472390r.545t>a0.680
rrs1472391r.546c>t0.680
rrs1472396r.551a>t0.240
rrs1472400r.555c>t0.240
rrs1472612r.767g>t0.545
rrs1472616r.771g>a1.000
rrs1472648r.803g>c0.353
rrs1472713r.868t>c0.600
rrs1472715r.870c>t0.400
rrs1472716r.871c>t0.600
rrs1472719r.874g>a0.200
rrs1472734r.889c>t0.444
rrs1472741r.896g>a0.400
rrs1472742r.897c>g0.250
rrs1472744r.899a>g0.667
rrs1472767r.922g>a0.229
rrs1472781r.936c>a0.212
rrs1472785r.940g>a0.185
rrs1472786r.941c>g0.129
rrs1472793r.948a>t0.756
rrs1472803r.958t>a0.500
rrs1472805r.960c>a0.184
rrs1472806r.961a>t0.184
rrs1472813r.968a>g0.194
rrs1472887r.1042g>c0.571
rrs1472895r.1050c>t0.389
rrs1473035r.1190g>a0.600
rrs1473038r.1193a>c0.421
rrs1473044r.1199c>g0.526
rrs1473053r.1208t>a0.842
rrs1473056r.1211a>t0.417
rrs1473062r.1217t>a0.462
rrs1473068r.1223a>g0.900
rrs1473070r.1225g>c0.400
rrs1473071r.1226c>a0.500
rrs1473080r.1235c>t0.400
rrs1473081r.1236c>t0.600
rrs1473177r.1332g>a0.867
rrs1473192r.1347a>g0.619
rrs1473194r.1349a>g0.286
rrs1473199r.1354ca>c0.810
rrs1473205r.1360t>c0.462
rrs1473226r.1381c>t0.467
rrs1473352r.1507c>t0.654
rrs1473353r.1508c>g0.250
rrs1473358r.1513g>c0.235
rrs1473359r.1514g>c0.278
rrl1474218r.561t>a1.000
rrl1474221r.564t>c0.500
rrl1474228r.571t>c0.286
rrl1474249r.592g>t0.889
rrl1474252r.595t>a1.000
rrl1474551r.894g>c0.200
rrl1474555r.898t>a0.400
rrl1474558r.901g>a0.500
rrl1474563r.906g>a0.375
rrl1474573r.916c>t0.556
rrl1474576r.919t>a0.556
rrl1474583r.926c>t0.286
rrl1474584r.927c>g1.000
rrl1474586r.929t>a1.000
rrl1474594r.937g>c0.375
rrl1474597r.940t>a0.375
rrl1474837r.1180a>g0.600
rrl1474844r.1187g>t1.000
rrl1474864r.1207c>t0.600
rrl1474866r.1209c>a1.000
rrl1474869r.1212g>t1.000
rrl1474875r.1218g>a0.571
rrl1474876r.1219t>a0.667
rrl1475571r.1914a>t0.500
rrl1475574r.1917c>a1.000
rrl1475575r.1918c>t0.500
rrl1475576r.1919c>a0.500
rrl1475783r.2126t>g1.000
rrl1475803r.2146t>c0.905
rrl1475804r.2147g>c0.905
rrl1475816r.2159c>g0.920
rrl1475817r.2160a>g0.951
rrl1475858r.2201t>c0.697
rrl1475866r.2209t>a0.394
rrl1475874r.2217c>t0.300
rrl1476250r.2593c>g1.000
rrl1476251r.2594t>c1.000
rrl1476252r.2595t>a0.600
rrl1476257r.2600g>c1.000
rrl1476260r.2603a>g1.000
rrl1476280r.2623a>c1.000
rrl1476332r.2675g>c0.133
rrl1476336r.2679c>t0.867
rrl1476338r.2681c>t0.138
rrl1476353r.2696g>t0.207
rrl1476358r.2701t>c0.240
rrl1476368r.2711t>c0.148
rrl1476369r.2712c>t1.000
rrl1476372r.2715t>c0.138
rrl1476381r.2724g>a0.160
rrl1476382r.2725a>g0.400
rrl1476383r.2726t>a0.600
rrl1476408r.2751g>a0.448
rrl1476411r.2754g>a0.655
rrl1476425r.2768g>t0.739
rrl1476428r.2771c>a0.158
rrl1476429r.2772a>c0.889
rrl1476442r.2785t>a0.190
rrl1476443r.2786g>t0.190
rrl1476455r.2798c>a0.190
rrl1476456r.2799a>t0.190
rrl1476463r.2806c>t0.250
rrl1476481r.2824t>c0.857
rrl1476506r.2849t>c0.765
rrl1476565r.2908g>a1.000
rrl1476566r.2909a>g1.000
rrl1476567r.2910c>t1.000

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;