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: 5906af9de86d7
Sample: 5906af9de86d7
Drug1ResistanceSupporting Mutations
IsoniazidRfabG1 (C-15T promoter)
RifampicinRrpoB (Ser450Leu)
Ethambutol  
Pyrazinamide  
Streptomycin  
EthionamideRfabG1 (C-15T promoter)
Fluoroquinolones  
Amikacin  
Capreomycin  
Kanamycin  
Para-aminosalisylic_acid  
Linezolid  
Clofazimine  
Bedaquiline  
Multi drug resistanceR 
Extremely drug resistance  

Lineage2NameMain SpoligotypeRDS
lineage1Indo-OceanicEAIRD239
lineage1.1Indo-OceanicEAI3;EAI4;EAI5;EAI6RD239
lineage1.1.1Indo-OceanicEAI4;EAI5RD239

Mutations in candidate genes:

GeneChromosome PositionMutationLineage
gyrB5320Indel: CAAA/CAAAA 
gyrB5501Indel: ACCC/ACC 
gyrB5616Indel: CGG/CG 
gyrB5780Indel: GAAA/GAAAA 
gyrB6112Met291Ile 
gyrB6211Indel: GA/G 
gyrB6448Indel: GAAA/GAA 
gyrA7362Glu21Gln 
gyrA7585Ser95Thr 
gyrA8452Ala384Val 
gyrA8661Asp454Asn 
gyrA9143Ile614Ile 
gyrA9304Gly668Asp 
gyrA9368Indel: GC/G 
gyrA9501Indel: CG/C 
rpoB760477Indel: GCC/GC 
rpoB761155Ser450Leu 
rpoB761325Indel: GAAA/GAAAA 
rpoB761482Indel: CGGG/CGG 
rpoB761770Met655Thr 
rpoB762515Indel: CGG/CG 
rpoB762665Indel: GCCC/GCC 
rpoB762945Indel: ACCC/ACC 
rpoB763031Ala1075Ala 
rpoC763884Ala172Val 
rpoC763886Arg173Arg 
rpoC764365Indel: CGG/CG 
rpoC765171Pro601Leu 
rpoC766283Indel: ACC/AC 
rpoC766973Indel: GCC/GC 
rpoC767149Indel: CGG/CG 
rplC801031Indel: GT/G 
embR1417019Cys110Tyr 
embR1417152Indel: AGGG/AGG 
rrs1472338Indel: ACC/AC 
rrl1474262Indel: CG/C 
rrl1474595Indel: GTT/GTTT 
rrl1474709... 
rrl1475003Indel: GCC/GCCC 
rrl1475205Indel: GCCC/GCC 
rrl1475667Indel: GTTT/GTTTT 
rrl1476000Indel: GTTT/GTTTT 
rrl1476027Indel: GAAA/GAAAA 
rrl1476173Indel: AGG/AG 
rrl1476478Indel: GTTT/GTTTT 
Rv1482c-fabG11673376Indel: GCC/GC 
Rv1482c-fabG11673425C-15T 
inhA1674827Indel: AGG/AG 
inhA1674923Indel: CGG/CG 
rpsA1833690Indel: AGG/AG 
rpsA1834315Val258Val 
rpsA1834319Val260Ile 
rpsA1834890Indel: CGG/CG 
rpsA1834940Indel: GA/G 
tlyA1917972Leu11Leu 
tlyA1918608Indel: CGG/CG 
katG2154449Indel: CTTT/CTTTT 
katG2154724Arg463Leu 
katG2154878Indel: AGG/AG 
katG2155122Asn330Lys 
katG2155355Indel: GAAA/GAAAA 
katG2155541Trp191Gly 
katG2155611Indel: GAAAA/GAAAAA 
katG2155779Indel: GCC/GC 
katG2155805Indel: TAAA/TAAAA 
katG2156080Indel: GTTT/GTTTT 
pncA2289102Indel: GTT/GTTT 
kasA2518123Gln3Gln 
kasA2518132Thr6Thr 
kasA2518598Indel: GCC/GC 
kasA2518947Indel: TGG/TG 
ahpC2726660Indel: CAA/CA 
folC2746335Indel: CGG/CG 
ribD2986863Indel: GCC/GC 
ribD2987341Indel: AC/A 
ribD2987614Indel: GAAA/GAAAA 
thyA3073885Indel: ACC/A 
thyA3073958Indel: GAAA/GAAAA 
thyA3074324Indel: CTTT/CTT 
panD4043969Indel: TCC/TC 
embC4240671Thr270Ile 
embC4241042Asn394Asp 
embC4241263Indel: CGG/CG 
embC4241821Indel: GTTT/GTTTT 
embC4242622Indel: CGG/CG 
embC4242643Arg927Arg 
embC4242910Indel: CGG/CG,CGGG 
embA4243720Pro163Leu 
embA4243791Indel: GCCC/GC 
embA4243848Val206Met 
embA4244096Gly288Gly 
embA4244227Indel: GAA/GAAA 
embA4244544Indel: GCC/GC 
embA4245170Indel: GA/G 
embA4245969Pro913Ser 
embB4246530Indel: GC/G 
embB4246623Indel: G/GT 
embB4247646Glu378Ala 
embB4247717Leu402Val 
embB4248107Indel: ACC/AC 
embB4248798Indel: GTTT/GTT 
embB4248996Indel: GTT/GTTT 
embB4249231Indel: ACCC/ACC 
embB4249685Indel: GCCC/GCCCC 
ethA4326846Indel: TGGG/TGG 
ethA4326902Indel: AC/A 
ethA4326986His163Arg 
ethA4327068Indel: GAAA/GAAAA 
ethR4327968Indel: GTTT/GTTTT 
ethR4328030Indel: CGG/CG 
gid4407588Ala205Ala 
gid4407615Indel: CAAA/CAAAA 
gid4407813Indel: GCC/GC 
gid4407873Val110Val 


Log
Mon May 1 04:46:37 2017: Starting to process
Mon May 1 04:46:37 2017: Mapping
Mon May 1 04:46:49 2017: Finding mutations
Mon May 1 04:48:01 2017: Finalising results
Mon May 1 04:48:02 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;