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: 5d7b84e199c86
Sample: 5d7b84e199c86

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Summary
ID: 5d7b84e199c86
Date: Fri Sep 13 13:02:11 2019
Strain: lineage4.3
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
StreptomycinRrrs r.462c>t (0.75)
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage4.3Euro-American (LAM)mainly-LAMNone

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7853c.552C>G0.600
gyrA9182c.1881T>C1.000
gyrA9191c.1890G>C1.000
gyrA9200c.1899A>G1.000
gyrA9204p.Ser635Thr1.000
rpoB760046c.240G>C1.000
rpoB760060p.Tyr85Leu1.000
rpoB760067c.261G>C1.000
rpoB760070c.264T>G1.000
rpoB760091c.285G>C1.000
rpoB760101c.295T>C1.000
rpoB760112c.306T>C1.000
rpoB760118c.312T>G1.000
rpoB760121c.315T>C1.000
rpoB760130p.Asp108Glu1.000
rpoB760139c.333A>G1.000
rpoB760142c.336C>G1.000
rpoB760181c.375T>C1.000
rpoB760184c.378A>G1.000
rpoB760196c.390C>G1.000
rpoB760591p.Val262Ala1.000
rpoB760611c.805T>C1.000
rpoB760646c.840C>G1.000
rpoB760655c.849A>G1.000
rpoB761570c.1764T>C1.000
rpoB761573c.1767C>G1.000
rpoB761579c.1773G>C1.000
rpoB761588c.1782C>T1.000
rpoC764968c.1599T>C1.000
rpoC765553c.2184C>T0.455
rpoC765556c.2187G>C0.455
rpoC765559c.2190G>C0.455
rpoC765613p.His748Gln1.000
rpoC765625c.2256C>G1.000
rpoC765628c.2259G>C1.000
rpoC765631p.Asp754Glu1.000
rpoC766447c.3078T>C1.000
rpoC766462c.3093G>C1.000
rpoC766795c.3426C>T1.000
rpoC766801c.3432C>G1.000
rpoC766804c.3435A>G1.000
rpoC766900c.3531T>C1.000
rpoC766933c.3564A>G1.000
rpoC767033c.3664T>A1.000
rplC800814c.6A>G1.000
rplC800817c.9A>T1.000
rplC800844c.36T>C1.000
rplC801367p.Ala187Thr1.000
rplC801402c.594T>C1.000
rplC801405c.597T>C1.000
rplC801423c.615G>C1.000
rplC801426c.618C>G1.000
rplC801427p.Met207Val1.000
rplC801438c.630T>C1.000
rplC801442p.Ile212Val1.000
rrs1472193r.348a>t0.390
rrs1472197r.352a>t0.261
rrs1472225r.380c>g0.154
rrs1472240r.395g>c0.568
rrs1472242r.397c>t0.525
rrs1472251r.406g>t0.581
rrs1472252r.407g>a0.425
rrs1472253r.408g>t0.500
rrs1472256r.411t>a0.475
rrs1472259r.414c>a0.525
rrs1472278r.433c>t0.400
rrs1472279r.434t>c0.524
rrs1472285r.440a>g0.609
rrs1472286r.441c>g0.190
rrs1472287r.442c>t0.400
rrs1472289r.444t>g0.800
rrs1472290r.445c>g0.650
rrs1472298r.453g>c0.200
rrs1472311r.466c>t0.400
rrs1472313r.468g>a0.333
rrs1472315r.470t>g0.765
rrs1472324r.479g>c0.684
rrs1472325r.480g>c0.700
rrs1472327r.482g>a0.136
rrs1472328r.483g>c0.174
rrs1472344r.499c>t0.935
rrs1472349r.504a>c0.510
rrs1472374r.529t>g0.514
rrs1472382r.537g>a0.683
rrs1472389r.544g>a0.755
rrs1472390r.545t>a0.627
rrs1472391r.546c>t0.711
rrs1472412r.567a>c0.720
rrs1472415r.570t>g0.456
rrs1472418r.573t>c0.326
rrs1472422r.577t>c0.471
rrs1472435r.590t>c0.789
rrs1472438r.593t>c0.368
rrs1472439r.594c>t0.789
rrs1472443r.598a>t0.353
rrs1472446r.601t>g0.235
rrs1472447r.602c>t0.250
rrs1472448r.603t>c0.714
rrs1472450r.605a>g0.643
rrs1472451r.606c>g0.286
rrs1472452r.607g>a0.429
rrs1472461r.616g>c0.250
rrs1472462r.617t>c0.692
rrs1472464r.619a>g0.769
rrs1472466r.621c>a0.333
rrs1472467r.622g>c0.333
rrs1472471r.626g>a0.786
rrs1472485r.640g>a0.643
rrs1472489r.644a>t0.786
rrs1472494r.649a>g0.500
rrs1472498r.653c>t0.600
rrs1472507r.662c>g0.261
rrs1472517r.672t>a0.689
rrs1472518r.673g>t0.189
rrs1472530r.685g>a0.736
rrs1472537r.692c>t0.637
rrs1472541r.696t>g0.478
rrs1472544r.699c>a0.282
rrs1472545r.700a>t0.699
rrs1472553r.708c>t0.389
rrs1472557r.712g>a0.270
rrs1472558r.713g>a0.333
rrs1472569r.724g>a0.227
rrs1472571r.726g>c0.583
rrs1472573r.728c>t0.250
rrs1472579r.734g>t0.440
rrs1472581r.736a>t0.511
rrs1472584r.739a>t0.245
rrs1472596r.751g>t0.161
rrs1472598r.753a>c0.410
rrs1472599r.754g>t0.241
rrs1472607r.762g>a0.424
rrs1472612r.767g>t0.339
rrs1472614r.769g>t0.130
rrs1472616r.771g>a0.262
rrs1472634r.789t>g0.234
rrs1472635r.790g>a0.237
rpsA1833554p.Thr5Ala1.000
rpsA1834021c.480C>T1.000
rpsA1834030c.489C>G1.000
kasA2518459c.345T>C1.000
kasA2518462c.348A>C1.000
kasA2518468c.354A>C1.000
kasA2518474c.360G>A1.000
kasA2518480c.366T>C1.000
kasA2518483c.369C>G1.000
kasA2518504c.390T>C1.000
embC4240780c.918T>C1.000
embC4240783c.921G>C1.000
embC4240789c.927T>C1.000
embC4240819c.957A>G1.000
embC4240828c.966G>A1.000
embC4240831c.969T>G1.000
embC4241038c.1176G>C1.000
embC4241089c.1227C>G1.000
embC4241770c.1908T>C1.000
embC4241791c.1929G>C1.000
embC4241794c.1932C>G1.000
embC4241797c.1935C>T1.000
embC4241809c.1947A>C1.000
embC4242859c.2997C>T1.000
embC4242862c.3000A>G1.000
embC4242863p.Tyr1001Asn1.000
embC4242883c.3021C>G1.000
embC4242892c.3030G>C1.000
embC4242901c.3039G>C1.000
embC4242919c.3057A>G1.000
embA4244585c.1353A>G1.000
embA4244670p.Ala480Leu1.000
embA4244675c.1443A>G1.000
embA4244678c.1446G>C1.000
embA4244681c.1449A>C1.000
embA4244690c.1458G>A1.000
embA4244702c.1470C>G1.000
embA4244708c.1476C>G1.000
embA4245137c.1905T>C1.000
embA4245146c.1914G>A1.000
embA4245149c.1917C>G1.000
embA4245153p.Ile641Val1.000
embA4245182c.1950T>C1.000
embA4245198p.Leu656Ile1.000
embA4245207c.1975T>C1.000
embA4245215c.1983A>C1.000
embA4245222p.Tyr664Gln1.000
embA4245248c.2016G>C1.000
embA4245257c.2025A>G1.000
embB4247866c.1353G>C0.400
embB4247875c.1362G>C0.273
embB4247876c.1363C>T0.273
embB4248304c.1791G>C1.000
embB4248316c.1803C>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;