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: 58cd0936f0766
Sample: 58cd0936f0766
Drug1ResistanceSupporting Mutations
IsoniazidRkatG (Ser315Thr)
RifampicinRrpoB (Ser450Leu)
EthambutolRembB (Met306Ile)
PyrazinamideRpncA (Ile90Ser)
StreptomycinRrrs (A1401G)
Ethionamide  
FluoroquinolonesRgyrA (Asp94Gly)
AmikacinRrrs (A1401G)
CapreomycinRrrs (A1401G)
KanamycinRrrs (A1401G)
Para-aminosalisylic_acidRfolC (Glu40Gly)
Linezolid  
Clofazimine  
Bedaquiline  
Multi drug resistanceR 
Extremely drug resistanceR 

Lineage2NameMain SpoligotypeRDS
lineage2East-AsianBeijingRD105
lineage2.1East-Asian (non-Beijing)NoneNone

Mutations in candidate genes:

GeneChromosome PositionMutationLineage
gyrB5383Glu48Glu 
gyrB5616Indel: CGG/CG 
gyrA7362Glu21Gln 
gyrA7582Asp94Gly 
gyrA7585Ser95Thr 
gyrA7929Indel: GCC/GC 
gyrA8656Indel: TC/T 
gyrA9304Gly668Asp 
gyrA9501Indel: CG/C 
gyrA9532Indel: GCC/GC 
rpoB760477Indel: GCC/GC 
rpoB761155Ser450Leu 
rpoB761559Indel: ACC/AC 
rpoB762945Indel: ACCC/ACC 
rpoB763031Ala1075Ala 
rpoB763323Indel: TAAA/TAA 
rpoC764532Indel: GCC/GC 
rpoC764817Val483Gly 
rpoC765121Gly584Gly 
rpoC765292Indel: GCC/GC 
rpoC766514Indel: GT/G 
rpoC766973Indel: GCC/GC 
rpoC767149Indel: CGG/CG 
embR1416971Indel: GCC/GC 
rrs1472144Indel: AGGG/AGG 
rrs1472997Indel: GCC/GC 
rrs1473246A1401G 
rrl1475003Indel: GCC/GCCC 
rrl1475682Indel: AGG/AG 
Rv1482c-fabG11673376Indel: GCC/GC 
rpsA1834177Arg212Arglineage2
tlyA1917972Leu11Leu 
tlyA1918044Indel: CGGG/CGG 
tlyA1918064Indel: CGG/CG 
tlyA1918608Indel: CGG/CG 
katG2154724Arg463Leu 
katG2155038Indel: GCC/GC 
katG2155168Ser315Thr 
katG2155779Indel: GCC/GC 
pncA2288973Ile90Ser 
ahpC2726436Indel: A/AG 
folC2746588Indel: GCC/GC 
folC2746842Indel: CGG/CG 
folC2747480Glu40Gly 
folC2747519Indel: AGGG/AGG 
ribD2987027Indel: CGGG/CGG 
ribD2987420Indel: CGGG/CG 
thyA3074324Indel: CTTT/CTT 
panD4043969Indel: TCC/TC 
embC4240583Indel: ACC/AC 
embC4242622Indel: CGG/CG 
embC4242643Arg927Arg 
embC4242910Indel: CGG/CG 
embA4244187Indel: ACC/AC 
embA4244544Indel: GCC/GC 
embA4244850Indel: CGGG/CGG 
embA4245927Indel: ACC/AC 
embA4246088Gln952Glnlineage2.1
embA4246503Indel: AGGG/AGGGG 
embB4246645Indel: GCC/GC 
embB4247023Indel: GCC/GC 
embB4247431Met306Ile 
embB4248107Indel: ACC/AC 
embB4248867Indel: CGG/CG 
ethR4328021Indel: ACC/AC 
gid4407588Ala205Ala 
gid4407683Indel: GC/G 
gid4407813Indel: GCC/GC 
gid4407985Gly73Ala 


Log
Sat Mar 18 10:17:26 2017: Starting to process
Sat Mar 18 10:17:27 2017: Mapping
Sat Mar 18 10:17:41 2017: Finding mutations
Sat Mar 18 10:19:15 2017: Finalising results
Sat Mar 18 10:19:16 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;