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: 59b9b23e1d111
Sample: 59b9b23e1d111
Drug1ResistanceSupporting Mutations
IsoniazidRkasA (Gly312Ser)
Rifampicin  
Ethambutol  
Pyrazinamide  
Streptomycin  
Ethionamide  
Fluoroquinolones  
Amikacin  
Capreomycin  
Kanamycin  
Para-aminosalisylic_acid  
Linezolid  
Clofazimine  
Bedaquiline  
Multi drug resistance  
Extremely drug resistance  

Lineage2NameMain SpoligotypeRDS
lineage1Indo-OceanicEAIRD239
lineage1.2.1Indo-OceanicEAI2RD239

Mutations in candidate genes:

GeneChromosome PositionMutationLineage
gyrB5501Indel: ACCC/ACC 
gyrB6112Met291Ile 
gyrB6533Indel: GCC/GC 
gyrA7362Glu21Gln 
gyrA7585Ser95Thr 
gyrA7929Indel: GCC/GC 
gyrA8452Ala384Val 
gyrA9077Indel: CGGG/CGG 
gyrA9143Ile614Ile 
gyrA9260Leu653Leu 
gyrA9304Gly668Asp 
rpoB760078Indel: AGG/AG 
rpoB761551Indel: CGG/CG 
rpoB762515Indel: CGG/CG 
rpoB762945Indel: ACCC/ACC 
rpoB763031Ala1075Ala 
rpoC763884Ala172Val 
rpoC763886Arg173Arg 
rpoC764365Indel: CGG/CG 
rpoC766517Indel: ACC/AC 
rpoC766973Indel: GCC/GC 
rpoC767149Indel: CGG/CG 
rplC801031Indel: GT/G 
embR1417019Cys110Tyr 
embR1417152Indel: AGGG/AGG 
rrs1472997Indel: GCC/GC 
rrs1473362Indel: CGG/CG 
rrl1475003Indel: GCC/GCCC 
rrl1475205Indel: GCCC/GCC 
rrl1475682Indel: AGG/AG 
rrl1476154Indel: GCC/GC 
inhA1674813Indel: CGG/CG 
inhA1674827Indel: AGG/AG 
tlyA1917972Leu11Leu 
tlyA1918163Indel: AGG/AG 
tlyA1918396Indel: GCC/GC 
katG2154513Indel: CGG/CG 
katG2154724Arg463Leu 
katG2154878Indel: AGG/AG 
katG2155703Indel: CGGG/CG 
katG2155779Indel: GCC/GC 
kasA2518132Thr6Thr 
kasA2519017Indel: GCC/GC 
kasA2519048Gly312Ser 
eis-Rv2417c2715428Indel: GC/GCC 
ahpC2726460Glu90Lys 
folC2746242Indel: CGG/CG 
folC2746269Indel: TGG/TG 
folC2746335Indel: CGG/CG 
folC2746527Indel: CGG/CG 
folC2746596Indel: TGG/TG 
folC2746842Indel: CGG/CG 
folC2746931Indel: GCCC/GC 
folC2747022Indel: CGG/CGGG 
folC2747519Indel: AGGG/AGG 
ribD2987027Indel: CGGG/CGG 
ribD2987420Indel: CGGG/CG 
panD4043969Indel: TCC/TC 
embC4240671Thr270Ile 
embC4241044Indel: CGG/CG 
embC4242622Indel: CGG/CG 
embC4242643Arg927Arg 
embC4242717Indel: TGG/TG 
embC4242910Indel: CGG/CG 
embA4243580Val116Val 
embA4243755Indel: ACC/AC 
embA4244420Val396Val 
embA4244544Indel: GCC/GC 
embA4244850Indel: CGGG/CGG 
embA4245969Pro913Ser 
embA4246503Indel: AGGG/AGGGG 
embB4247578Leu355Leu 
embB4247646Glu378Ala 
embB4248107Indel: ACC/AC 
embB4249646Indel: CGGG/CGG 
embB4249685Indel: GCCC/GCC 
embB4249752Indel: TGGG/TGG 
ethA4326646Indel: GT/G 
ethR4328021Indel: ACC/AC 
gid4407588Ala205Ala 
gid4407813Indel: GCC/GC 
gid4407873Val110Val 


Log
Wed Sep 13 23:33:34 2017: Starting to process
Wed Sep 13 23:33:34 2017: Mapping
Wed Sep 13 23:33:46 2017: Finding mutations
Wed Sep 13 23:34:57 2017: Finalising results
Wed Sep 13 23:34:58 2017: 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.
© 2017 London School of Hygiene and Tropical Medicine;