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: 5c80505a6f6d8
Sample: 5c80505a6f6d8

Summary
ID: 5c80505a6f6d8
Date: Wed Mar 6 23:04:30 2019
Strain: lineage4.9
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
StreptomycinRrrs 888G>A (0.23)
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
rpoB7629293123G>T0.182
rpoB7629443138C>T0.182
rpoB7629833177C>T0.167
rpoB7629893183G>C0.200
rrs1472106261G>A0.400
rrs1472108263C>T0.231
rrs1472112267C>T0.214
rrs1472127282C>T0.333
rrs1472128283G>C0.154
rrs1472129284G>A0.154
rrs1472137292G>A0.364
rrs1472147302G>A0.136
rrs1472150305T>A0.619
rrs1472151306C>T0.526
rrs1472172327T>C0.636
rrs1472203358G>A0.320
rrs1472210365A>C0.167
rrs1472214369C>G0.222
rrs1472225380C>A0.250
rrs1472235390G>C0.167
rrs1472240395G>A0.188
rrs1472251406G>A0.375
rrs1472253408G>T0.188
rrs1472259414C>A0.188
rrs1472518673G>T0.200
rrs1472530685G>A0.300
rrs1472581736A>T0.250
rrs1472616771G>A0.182
rrs1472655810G>A0.286
rrs1472679834T>C0.200
rrs1472697852T>C0.250
rrs1472713868T>C0.241
rrs1472714869A>T0.192
rrs1472715870C>A0.172
rrs1472716871C>T0.414
rrs1472742897C>T0.500
rrs1472744899A>G0.278
rrs1472754909G>T0.216
rrs1472781936C>T0.526
rrs1472793948A>T0.514
rrs1472803958T>A0.457
rrs1472812967A>C0.152
rrs1472824979T>A0.364
rrs1472826981G>C0.158
rrs1472827982G>T0.211
rrs1472828983T>C0.263
rrs1472836991G>C0.235
rrs14728591014G>A0.308
rrs14728601015C>G0.308
rrs14728611016G>T0.308
rrs14728641019C>T0.333
rrs14728691024G>C0.333
rrs14728701025T>G0.417
rrs14728731028C>A0.364
rrs14728751030T>A0.444
rrs14728771032T>G0.333
rrs14728951050C>T0.560
rrs14729511106T>C0.182
rrs14729531108G>A0.200
rrs14729891144G>A0.200
rrs14729901145A>G0.300
rrs14730041159T>A0.200
rrs14730351190G>A0.385
rrs14730561211A>T0.286
rrs14730621217T>A0.214
rrs14730681223A>G0.214
rrs14730811236C>T0.182
rrs14730891244A>C0.200
rrs14730931248C>T0.200
rrs14731211276T>C0.200
rrs14731231278A>G0.200
rrs14731451300C>T0.273
rrs14731471302G>T0.167
rrs14731481303G>A0.167
rrs14731631318C>T0.375
rrs14731661321G>A0.500
rrs14731771332G>A0.500
rrs14731921347A>G0.350
rrs14731931348G>A0.200
rrs14732021357C>T0.238
rrs14732041359C>T0.190
rrs14732051360T>C0.333
rrs14732761431A>G0.200
rrs14732831438T>C0.182
rrs14733011456T>C0.200
rrs14733051460G>T0.182
rrs14733151470T>C0.182
rrs14733161471C>T0.200
rrs14733191474C>T0.182
rrs14733521507C>T0.333
rrl1474218561T>A0.385
rrl1474228571T>C0.385
rrl1474249592G>T0.500
rrl1474252595T>A0.455
rrl1474584927C>T0.182
rrl1474632975G>T0.167
rrl1474638981C>G0.167
rrl14747601103A>G0.286
rrl14747801123C>T0.231
rrl14747941137C>T0.333
rrl14748231166C>G0.200
rrl14748531196A>G0.200
rrl14757832126T>G0.481
rrl14758032146T>C0.600
rrl14758042147G>C0.583
rrl14758162159C>G0.553
rrl14758172160A>G0.550
rrl14758582201T>C0.314
rrl14758662209T>A0.265
rrl14758742217C>T0.200
rrl14761652508T>G0.200
rrl14763322675G>C0.444
rrl14763362679C>T0.238
rrl14763382681C>T0.429
rrl14763532696G>T0.400
rrl14763572700T>C0.300
rrl14763582701T>C0.650
rrl14763592702C>G0.316
rrl14763692712C>T0.600
rrl14763722715T>C0.333
rrl14763812724G>C0.286
rrl14763822725A>G0.591
rrl14763832726T>A0.368
rrl14764112754G>A0.261
rrl14764252768G>T0.462
rrl14764282771C>T0.615
rrl14764292772A>C0.464
rrl14764632806C>T0.133
rrl14764662809C>T0.241
rrl14764812824T>C0.500
rrl14765062849T>C0.621
rrl14765132856G>T0.182
rrl14765152858C>T0.308
rrl14765232866T>C0.333
rrl14765242867C>A0.333
rrl14765252868A>G0.333
rrl14765282871A>G0.308
rrl14765362879G>A0.308
rrl14765382881A>G0.308
rrl14765392882A>G0.308
rrl14765842927C>T0.364
rrl14765852928A>G0.364
rrl14766002943A>C0.400
rrl14766082951C>G0.400
rrl14766142957A>T0.333
rrl14766162959A>G0.333
rrl14766192962C>T0.333
rrl14766282971T>G0.333
rrl14766292972C>A0.333
rrl14766332976A>G0.333
rpsA1833994453G>C0.200
rpsA1834009468C>T0.200
rpsA1834015474G>T0.200
rpsA1834024483G>C0.200
rpsA1834034165I>165V0.200
rpsA1834040167K>167R0.200
rpsA1834046169I>169L0.200

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;