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: 5c805e41b18d4
Sample: 5c805e41b18d4

Summary
ID: 5c805e41b18d4
Date: Thu Mar 7 00:05:30 2019
Strain: lineage4.9
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
StreptomycinRrrs 888G>A (0.20)
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.9Euro-American (H37Rv-like)T1None

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
rrs1472137292G>A0.400
rrs1472150305T>A0.600
rrs1472151306C>T0.462
rrs1472172327T>C0.600
rrs1472203358G>A0.400
rrs1472210365A>C0.182
rrs1472213368G>C0.182
rrs1472215370A>G0.182
rrs1472222377G>A0.200
rrs1472225380C>A0.200
rrs1472229384C>T0.167
rrs1472234389T>C0.167
rrs1472240395G>A0.167
rrs1472251406G>A0.333
rrs1472253408G>T0.167
rrs1472389544G>A0.182
rrs1472507662C>G0.300
rrs1472517672T>A0.400
rrs1472518673G>T0.364
rrs1472530685G>A0.286
rrs1472537692C>T0.333
rrs1472544699C>A0.357
rrs1472545700A>T0.357
rrs1472566721G>A0.357
rrs1472571726G>C0.385
rrs1472579734G>C0.250
rrs1472580735C>T0.231
rrs1472581736A>T0.385
rrs1472598753A>C0.400
rrs1472599754G>T0.375
rrs1472616771G>A0.500
rrs1472655810G>A0.308
rrs1472658813G>A0.200
rrs1472661816A>G0.200
rrs1472675830T>C0.167
rrs1472680835C>T0.231
rrs1472682837T>C0.231
rrs1472683838T>G0.214
rrs1472687842A>T0.214
rrs1472689844C>T0.188
rrs1472690845C>A0.250
rrs1472697852T>C0.235
rrs1472713868T>C0.190
rrs1472714869A>G0.143
rrs1472716871C>T0.182
rrs1472742897C>T0.440
rrs1472744899A>G0.269
rrs1472781936C>T0.400
rrs1472793948A>T0.333
rrs1472803958T>A0.208
rrs1472824979T>A0.188
rrs1472827982G>T0.167
rrs1472828983T>C0.167
rrs1472836991G>C0.182
rrs14728611016G>T0.167
rrs14728701025T>G0.182
rrs14728771032T>G0.154
rrs14728951050C>T0.522
rrs14729531108G>A0.182
rrs14730351190G>A0.385
rrs14730561211A>T0.333
rrs14730621217T>A0.250
rrs14730681223A>G0.273
rrs14730801235C>T0.200
rrs14731301285G>A0.200
rrs14731451300C>T0.273
rrs14731481303G>A0.167
rrs14731631318C>T0.231
rrs14731661321G>A0.357
rrs14731771332G>A0.476
rrs14731921347A>G0.400
rrs14731991354CA>C0.450
rrs14732021357C>T0.150
rrs14732051360T>C0.400
rrs14733521507C>T0.385
rrl1474218561T>A0.333
rrl1474228571T>C0.333
rrl1474249592G>T0.364
rrl14746761019T>A0.182
rrl14746771020A>G0.182
rrl14747601103A>G0.167
rrl14757832126T>G0.364
rrl14758032146T>C0.481
rrl14758042147G>C0.464
rrl14758162159C>G0.467
rrl14758172160A>G0.452
rrl14758582201T>C0.179
rrl14758662209T>A0.185
rrl14758742217C>T0.211
rrl14763322675G>C0.300
rrl14763362679C>T0.167
rrl14763382681C>T0.250
rrl14763532696G>T0.308
rrl14763572700T>C0.231
rrl14763582701T>C0.462
rrl14763592702C>G0.250
rrl14763692712C>T0.462
rrl14763722715T>C0.357
rrl14763812724G>C0.214
rrl14763822725A>G0.467
rrl14763832726T>A0.357
rrl14764082751G>A0.222
rrl14764112754G>A0.278
rrl14764252768G>T0.389
rrl14764282771C>T0.556
rrl14764292772A>C0.400
rrl14764632806C>T0.267
rrl14764662809C>T0.333
rrl14764812824T>C0.643
rrl14765062849T>C0.571

Analysis pipeline specifications

TBProfiler Version: 0.1

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;