TB Profiler
This tool processes raw sequence data to infer strain type and identify known drug resistance markers.
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: 5b687ccc297be
Sample: 5b687ccc297be
Drug1ResistanceSupporting Mutations
Isoniazid  
Rifampicin  
Ethambutol  
Pyrazinamide  
StreptomycinRrrs (C462T)
Ethionamide  
Fluoroquinolones  
Amikacin  
Capreomycin  
Kanamycin  
Para-aminosalisylic_acid  
Linezolid  
Clofazimine  
Bedaquiline  
Multi drug resistance  
Extremely drug resistance  

Lineage2NameMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.9Euro-American (H37Rv-like)T1None

Mutations in candidate genes:

GeneChromosome PositionMutationLineage
rpoB762857Val1017Val 
rpoB762860Thr1018Thr 
rpoB762863Val1019Val 
rpoB762929Gly1041Gly 
rpoB762989Arg1061Arg 
rpoB762995Gly1063Gly 
rpoC763468Thr33Thr 
rpoC763486Leu39Leu 
rpoC763528Gly53Gly 
rpoC763546Glu59Glu 
rpoC763570Arg67Arg 
rpoC763594Cys75Cys 
rpoC764650Arg427Arg 
rpoC764695Gly442Gly 
rpoC764716Leu449Leu 
rpoC764752Val461Val 
rpoC764764His465His 
rpoC765613His748Gln 
rpoC765625Arg752Arg 
rpoC765628Ala753Ala 
rpoC765631Asp754Glu 
rpoC765658Gly763Gly 
rpoC765700Ile777Ile 
rrs1471923T78C 
rrs1471934A89G 
rrs1471969T124C 
rrs1471970G125A 
rrs1472028A183T 
rrs1472030G185A 
rrs1472031G186A 
rrs1472034T189C 
rrs1472044G199C 
rrs1472053Indel: AGCGC/AGC 
rrs1472061A216T 
rrs1472075A230G 
rrs1472307C462T 
rrs1472969A1124G 
rrs1472970C1125G 
rrs1472977G1132C 
rrs1472978T1133C 
rrs1473104C1259T 
rrs1473105G1260A 
rrs1473123A1278T 
rrs1473145C1300T 
rrs1473166G1321A 
rrs1473288Indel: CT/CTTT 
rrl1473668... 
rrl1473756... 
rrl1473758... 
rrl1473806... 
rrl1473813... 
rrl1473839... 
rrl1473877... 
rrl1473898... 
rrl1474140... 
rrl1474151... 
rrl1474181... 
rrl1474249... 
rrl1474639... 
rrl1474794... 
rrl1474812... 
rrl1474823... 
rrl1474831... 
rrl1474904... 
rrl1474991... 
rrl1475006... 
rrl1475061... 
rrl1475088... 
rrl1475199... 
rrl1475206... 
rrl1475209... 
rrl1475213... 
rrl1475333... 
rrl1475355... 
rrl1475369... 
rrl1475419... 
rrl1475483... 
rrl1475505... 
rrl1475526... 
rrl1475599... 
rrl1475608... 
rrl1475638... 
rrl1475642... 
rrl1475657... 
rrl1475659... 
rrl1475763... 
rrl1475881... 
rrl1475988... 
rrl1476095... 
rrl1476105... 
rrl1476115... 
rrl1476117... 
rrl1476224... 
rrl1476281... 
rrl1476583... 
rrl1476584... 
rrl1476597... 
rrl1476608... 
rrl1476628... 
rpsA1833589Ile16Ile 
rpsA1833595Ser18Ser 
rpsA1833619Ile26Ile 
rpsA1833661Glu40Glu 
rpsA1833667Thr42Thr 
rpsA1833928Thr129Thr 
rpsA1833940Val133Val 
rpsA1833970Gly143Gly 
rpsA1833979Gly146Gly 
rpsA1834000Val153Val 
rpsA1834015Val158Val 
rpsA1834021Asp160Asp 


Log
Mon Aug 6 17:52:28 2018: Starting to process
Mon Aug 6 17:52:28 2018: Mapping
Mon Aug 6 17:54:32 2018: Finding mutations
Mon Aug 6 17:54:47 2018: Finalising results
Mon Aug 6 17:54:49 2018: End

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.
© 2018 London School of Hygiene and Tropical Medicine;