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: 5d3e6774dcdd4
Sample: 5d3e6774dcdd4

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Summary
ID: 5d3e6774dcdd4
Date: Mon Jul 29 04:28:41 2019
Strain: root
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
StreptomycinRrrs r.888g>a (1.00)
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
rrs1471896r.51t>c1.000
rrs1471900r.55c>t1.000
rrs1471911r.66c>a1.000
rrs1472089r.244c>t0.846
rrs1472094r.249t>a1.000
rrs1472106r.261g>a0.995
rrs1472112r.267c>t1.000
rrs1472113r.268t>c1.000
rrs1472127r.282c>t0.995
rrs1472127r.282cgg>c0.981
rrs1472128r.283g>a1.000
rrs1472129r.284g>c1.000
rrs1472130r.285g>a1.000
rrs1472137r.292g>a1.000
rrs1472150r.305t>a1.000
rrs1472151r.306c>t1.000
rrs1472172r.327t>c1.000
rrs1472203r.358g>a1.000
rrs1472344r.499c>t1.000
rrs1472378r.533g>t0.995
rrs1472379r.534t>c1.000
rrs1472380r.535g>c1.000
rrs1472396r.551a>t1.000
rrs1472400r.555c>t1.000
rrs1472507r.662c>g1.000
rrs1472517r.672t>a1.000
rrs1472518r.673g>t1.000
rrs1472530r.685g>a1.000
rrs1472537r.692c>t1.000
rrs1472544r.699c>a1.000
rrs1472545r.700a>t1.000
rrs1472557r.712g>a0.988
rrs1472566r.721g>a1.000
rrs1472571r.726g>c1.000
rrs1472579r.734g>c1.000
rrs1472580r.735c>t1.000
rrs1472581r.736a>t0.994
rrs1472598r.753a>c1.000
rrs1472599r.754g>t0.996
rrs1472616r.771g>a1.000
rrs1472647r.802c>t1.000
rrs1472655r.810g>a1.000
rrs1472658r.813g>a1.000
rrs1472661r.816a>g1.000
rrs1472680r.835c>t1.000
rrs1472682r.837t>c1.000
rrs1472683r.838t>g1.000
rrs1472687r.842a>t1.000
rrs1472689r.844c>t1.000
rrs1472690r.845c>a1.000
rrs1472713r.868t>c1.000
rrs1472716r.871c>t1.000
rrs1472742r.897c>t1.000
rrs1472744r.899a>g1.000
rrs1472781r.936c>t0.987
rrs1472793r.948a>t1.000
rrs1472803r.958t>a1.000
rrs1472895r.1050c>t1.000
rrs1473035r.1190g>a1.000
rrs1473053r.1208t>a1.000
rrs1473056r.1211a>t1.000
rrs1473062r.1217t>a1.000
rrs1473068r.1223a>g1.000
rrs1473081r.1236c>t1.000
rrs1473166r.1321g>a1.000
rrs1473177r.1332g>a0.996
rrs1473192r.1347a>g0.996
rrs1473205r.1360t>c1.000
rrs1473316r.1471c>a1.000
rrs1473318r.1473g>a1.000
rrs1473319r.1474c>t1.000
rrs1473327r.1482a>g1.000
rrs1473328r.1483c>t1.000
rrs1473352r.1507c>t1.000
rrl1473679r.22t>c1.000
rrl1474218r.561t>a1.000
rrl1474228r.571t>c1.000
rrl1474249r.592g>t1.000
rrl1474252r.595t>a1.000
rrl1474753r.1096ac>a1.000
rrl1474869r.1212g>c1.000
rrl1474892r.1235g>a1.000
rrl1474896r.1239a>g1.000
rrl1474902r.1245t>c1.000
rrl1474903r.1246t>c1.000
rrl1474904r.1247g>c1.000
rrl1474913r.1256t>a1.000
rrl1474920r.1263g>c1.000
rrl1475124r.1467a>t1.000
rrl1475129r.1472g>t1.000
rrl1475145r.1488c>a1.000
rrl1475149r.1492g>a1.000
rrl1475154r.1497c>a1.000
rrl1475158r.1501c>t1.000
rrl1475162r.1505g>t0.995
rrl1475163r.1506t>c0.995
rrl1475175r.1518g>a1.000
rrl1475498r.1841c>g1.000
rrl1475574r.1917c>a0.992
rrl1475783r.2126t>g1.000
rrl1475803r.2146t>c1.000
rrl1475804r.2147g>c1.000
rrl1475816r.2159c>g1.000
rrl1475817r.2160a>g1.000
rrl1475858r.2201t>c1.000
rrl1475866r.2209t>a1.000
rrl1475874r.2217c>t1.000
rrl1476126r.2469c>t1.000
rrl1476130r.2473g>a1.000
rrl1476135r.2478t>c1.000
rrl1476141r.2484a>g0.996
rrl1476153r.2496t>c1.000
rrl1476165r.2508t>g1.000
rrl1476194r.2537a>g1.000
rrl1476195r.2538c>a0.944
rrl1476196r.2539c>a1.000
rrl1476200r.2543a>t1.000
rrl1476201r.2544c>t1.000
rrl1476204r.2547c>a1.000
rrl1476210r.2553g>t1.000
rrl1476211r.2554g>t1.000
rrl1476212r.2555t>c1.000
rrl1476214r.2557g>c1.000
rrl1476215r.2558c>a1.000
rrl1476225r.2568t>g1.000
rrl1476227r.2570c>t1.000
rrl1476229r.2572c>t1.000
rrl1476250r.2593c>g1.000
rrl1476251r.2594t>c1.000
rrl1476257r.2600g>c0.995
rrl1476260r.2603a>g1.000
rrl1476280r.2623a>c1.000
rrl1476293r.2636c>t1.000
rrl1476294r.2637a>g1.000
rrl1476295r.2638c>g1.000
rrl1476296r.2639c>t1.000
rrl1476297r.2640c>t1.000
rrl1476301r.2644a>t1.000
rrl1476302r.2645g>a1.000
rrl1476311r.2654g>c1.000
rrl1476312r.2655t>c1.000
rrl1476313r.2656g>a1.000
rrl1476332r.2675g>c1.000
rrl1476338r.2681c>t1.000
rrl1476353r.2696g>t1.000
rrl1476358r.2701t>c1.000
rrl1476369r.2712c>t1.000
rrl1476372r.2715t>c1.000
rrl1476382r.2725a>g0.992
rrl1476383r.2726t>a1.000
rrl1476425r.2768g>t1.000
rrl1476428r.2771c>t1.000
rrl1476429r.2772a>c1.000
rrl1476481r.2824t>c1.000
rrl1476506r.2849t>c1.000
rrl1476514r.2857c>t1.000
rrl1476637r.2980c>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;