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: 5d7b83b98b447
Sample: 5d7b83b98b447

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Summary
ID: 5d7b83b98b447
Date: Fri Sep 13 12:57:20 2019
Strain: lineage4.3;lineage4.1.1;lineage1.1.1;lineage4.6.1
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
StreptomycinRrrs r.462c>t (1.00)
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage4.3Euro-American (LAM)mainly-LAMNone
lineage4.1.1Euro-American (X-type)X1;X2;X3None
lineage1.1.1Indo-OceanicEAI4;EAI5RD239
lineage4.6.1Euro-American (Uganda)T2RD724

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB5803c.564A>G0.400
gyrB5806c.567C>G0.400
gyrB5809c.570C>G0.400
gyrB6100c.861G>C1.000
gyrB6115c.876A>G1.000
gyrB6123p.Ala295Gly1.000
gyrB6127c.888G>C1.000
gyrB6130c.891T>C1.000
gyrB6136c.897G>A1.000
gyrB6139c.900G>C1.000
gyrA7784c.483A>G1.000
gyrA7793c.492G>C1.000
gyrA7796c.495G>C1.000
gyrA7799c.498A>G1.000
gyrA7814c.513C>G1.000
gyrA7853c.552C>G1.000
gyrA8486c.1185T>C1.000
rpoB761255c.1449T>G1.000
rpoB761261c.1455G>T1.000
rpoB761306c.1500C>G1.000
rpoB761948c.2142G>C1.000
rpoB763025c.3219C>T1.000
rpoB763028c.3222T>C1.000
rpoB763031c.3225T>G1.000
rpoB763034c.3228C>G1.000
rpoB763040c.3234C>G1.000
rpoB763070c.3264T>C1.000
rpoB763085c.3279C>G1.000
rpoC763963c.594C>T0.692
rpoC764024c.655T>C1.000
rpoC764059c.690G>T1.000
rpoC764083c.714A>G1.000
rpoC764752c.1383G>C1.000
rpoC764764c.1395T>C1.000
rpoC764809c.1440C>T1.000
rpoC764815c.1446A>G1.000
rpoC764827c.1458G>C1.000
rpoC764968c.1599T>C1.000
rpoC765073c.1704G>C1.000
rpoC765076c.1707A>G0.200
rpoC765079c.1710T>G1.000
rpoC765082c.1713G>C1.000
rpoC765089c.1720T>C1.000
rpoC765103c.1734G>T1.000
rpoC766447c.3078T>C1.000
rpoC766462c.3093G>C1.000
rpoC766492c.3123T>C1.000
rpoC766522c.3153C>G1.000
rpoC766528c.3159T>C1.000
rpoC766531c.3162G>C1.000
rpoC767059c.3690T>G1.000
rpoC767062c.3693C>A1.000
rpoC767098c.3729T>C1.000
rpoC767119c.3750A>G1.000
rpoC767134c.3765C>A1.000
rpoC767158c.3789T>C1.000
rpoC767180p.Ala1271Gln1.000
rpoC767191c.3822C>G1.000
rpoC767206c.3837C>G1.000
rpoC767209c.3840T>C1.000
rpoC767212c.3843G>C1.000
rpoC767221c.3852C>G1.000
rpoC767230c.3861G>C1.000
rpoC767233c.3864T>C1.000
rpoC767263c.3894T>C1.000
rpoC767264p.Ala1299Gln1.000
rpoC767275c.3906T>C1.000
rpoC767278c.3909T>C1.000
rpoC767281c.3912C>G1.000
rpoC767284c.3915C>T1.000
rpsL781373c.-187G>C1.000
rpsL781916c.357T>C1.000
rpsL781929p.Gly124Ser1.000
rplC801321c.513C>T1.000
rplC801324c.516T>C1.000
rplC801339c.531T>C1.000
rplC801341p.Leu178Gln1.000
rplC801348c.540T>G1.000
rplC801357c.549T>C1.000
rplC801367p.Ala187Thr1.000
rrs1472193r.348a>t0.417
rrs1472197r.352a>t0.228
rrs1472225r.380c>a0.143
rrs1472240r.395g>c0.632
rrs1472242r.397c>t0.579
rrs1472251r.406g>t0.704
rrs1472252r.407g>a0.552
rrs1472253r.408g>t0.585
rrs1472256r.411t>a0.569
rrs1472259r.414c>a0.591
rrs1472278r.433c>t0.222
rrs1472279r.434t>g0.333
rrs1472285r.440a>g0.481
rrs1472286r.441c>g0.231
rrs1472287r.442c>t0.269
rrs1472288r.443a>t0.269
rrs1472289r.444t>g0.731
rrs1472290r.445c>g0.600
rrs1472303r.458g>c0.200
rrs1472313r.468g>a0.273
rrs1472315r.470t>g0.630
rrs1472324r.479g>c0.571
rrs1472325r.480g>c0.591
rrs1472326r.481t>g0.250
rrs1472328r.483g>c0.194
rrs1472329r.484a>t0.143
rrs1472330r.485g>a0.152
rrs1472344r.499c>t0.866
rrs1472349r.504a>c0.310
rrs1472374r.529t>g0.310
rrs1472378r.533g>t0.235
rrs1472379r.534t>g0.195
rrs1472382r.537g>a0.506
rrs1472389r.544g>a0.568
rrs1472390r.545t>a0.391
rrs1472391r.546c>t0.558
rrs1472400r.555c>t0.219
rrs1472412r.567a>c0.466
rrs1472415r.570t>a0.328
rrs1472418r.573t>c0.288
rrs1472422r.577t>c0.515
rrs1472431r.586g>a0.250
rrs1472435r.590t>c0.667
rrs1472438r.593t>c0.407
rrs1472439r.594c>t0.667
rrs1472443r.598a>t0.231
rrs1472446r.601t>g0.160
rrs1472448r.603t>c0.550
rrs1472449r.604c>t0.200
rrs1472450r.605a>g0.350
rrs1472451r.606c>g0.316
rrs1472452r.607g>a0.263
rrs1472460r.615t>c0.211
rrs1472461r.616g>c0.316
rrs1472462r.617t>c0.368
rrs1472464r.619a>g0.579
rrs1472465r.620g>a0.211
rrs1472466r.621c>a0.250
rrs1472467r.622g>c0.250
rrs1472471r.626g>a0.647
rrs1472484r.639a>t0.222
rrs1472485r.640g>a0.368
rrs1472489r.644a>t0.647
rrs1472494r.649a>g0.412
rrs1472496r.651t>a0.200
rrs1472497r.652g>a0.250
rrs1472498r.653c>t0.533
rrs1472507r.662c>a0.286
rrs1472517r.672t>a0.646
rrs1472518r.673g>t0.200
rrs1472530r.685g>a0.653
rrs1472537r.692c>t0.573
rrs1472541r.696t>g0.547
rrs1472544r.699c>a0.282
rrs1472545r.700a>t0.694
rrs1472549r.704g>a0.169
rrs1472553r.708c>t0.429
rrs1472557r.712g>a0.355
rrs1472570r.725g>a0.189
rrs1472571r.726g>c0.845
rrs1472572r.727t>c0.419
rrs1472573r.728c>t0.183
rrs1472574r.729t>c0.431
rrs1472579r.734g>t0.383
rrs1472580r.735c>a0.171
rrs1472581r.736a>t0.460
rrs1472582r.737g>a0.299
rrs1472583r.738t>a0.322
rrs1472584r.739a>g0.306
rrs1472594r.749g>c0.355
rrs1472598r.753a>c0.585
rrs1472599r.754g>a0.220
rrs1472607r.762g>a0.220
rrs1472612r.767g>t0.252
rrs1472614r.769g>t0.146
rrs1472616r.771g>a0.588
rrs1472634r.789t>c0.232
rrs1472635r.790g>a0.314
rrl1474249r.592g>t1.000
rrl1474794r.1137c>t1.000
rrl1475355r.1698c>t1.000
rrl1475369r.1712g>t1.000
rrl1475402r.1745c>t1.000
rrl1475419r.1762c>t1.000
rrl1475758r.2101ac>a1.000
rrl1475763r.2106c>t1.000
rrl1475765r.2108ag>a1.000
rpsA1833886c.345C>G1.000
rpsA1833928c.387G>C1.000
rpsA1833940c.399C>G1.000
rpsA1833971c.430C>T1.000
rpsA1833979c.438T>C1.000
rpsA1834000c.459G>C1.000
rpsA1834021c.480C>T1.000
rpsA1834030c.489C>G1.000
rpsA1834081c.540C>T1.000
rpsA1834096c.555G>C1.000
rpsA1834099c.558C>G1.000
rpsA1834102c.561T>C1.000
rpsA1834105c.564C>G1.000
rpsA1834108c.567C>G1.000
rpsA1834123c.582C>G1.000
rpsA1834513c.972C>G1.000
rpsA1834528c.987T>C1.000
rpsA1834540c.999G>C1.000
rpsA1834546c.1005T>C1.000
rpsA1834555c.1014T>G1.000
rpsA1834609c.1068T>C1.000
rpsA1834618c.1077G>C1.000
rpsA1834633c.1092A>G1.000
rpsA1834639c.1098T>C1.000
rpsA1834654p.Glu371Asp1.000
rpsA1834690c.1149T>C1.000
tlyA1918310p.Asn124Ser1.000
katG2155626c.486C>G1.000
katG2155632c.480T>G1.000
katG2155637p.Leu159Ile1.000
katG2155641p.Lys157Asn1.000
katG2155661p.Val151Ile1.000
kasA2518480c.366T>C1.000
kasA2518483c.369C>G1.000
kasA2518504c.390T>C1.000
kasA2518506p.Ala131Glu1.000
kasA2518519c.405G>C1.000
kasA2518528c.414C>G1.000
kasA2518540c.426T>C1.000
thyX3067814c.132A>G1.000
thyX3067842p.Leu35Arg0.200
alr3840248c.1173G>C1.000
embC4241770c.1908T>C1.000
embB4247776c.1263G>T1.000
embB4247797c.1284C>G1.000
embB4247800c.1287A>T1.000
embB4247803c.1290G>C1.000

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;