TB-Profiler result

Run: SRR29096527
Summary

Run ID: SRR29096527

Sample name:

Date: 2024-10-04T02:52:56.336275

Number of reads: 25087

Percentage reads mapped: 27.22

Median coverage: 0.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
fgd1 491508 c.726A>C synonymous_variant 1.0 pretomanid
delamanid
clofazimine
fgd1 491512 p.Asn244Glu missense_variant 1.0 pretomanid
delamanid
clofazimine
fgd1 491523 c.741G>C synonymous_variant 1.0 pretomanid
delamanid
clofazimine
fgd1 491526 c.744T>C synonymous_variant 1.0 pretomanid
delamanid
clofazimine
fgd1 491542 c.760T>C synonymous_variant 1.0 pretomanid
delamanid
clofazimine
fgd1 491563 c.781_783delAGCinsTCG synonymous_variant 1.0 pretomanid
delamanid
clofazimine
fgd1 491595 c.813C>T synonymous_variant 1.0 pretomanid
delamanid
clofazimine
mshA 575761 c.414C>G synonymous_variant 1.0 isoniazid
ethionamide
mshA 575764 c.417C>G synonymous_variant 1.0 isoniazid
ethionamide
mshA 575771 p.Val142Thr missense_variant 1.0 isoniazid
ethionamide
mshA 575776 c.429C>T synonymous_variant 1.0 isoniazid
ethionamide
mshA 575782 c.435G>C synonymous_variant 1.0 isoniazid
ethionamide
mshA 575785 c.438T>C synonymous_variant 1.0 isoniazid
ethionamide
mshA 575795 p.Ile150Val missense_variant 1.0 isoniazid
ethionamide
mshA 575800 c.453G>C synonymous_variant 1.0 isoniazid
ethionamide
mshA 575803 c.456C>T synonymous_variant 1.0 isoniazid Not assoc w R - Interim
ethionamide
mshA 575821 c.474G>T synonymous_variant 0.93 isoniazid
ethionamide
mshA 575837 c.490C>T synonymous_variant 1.0 isoniazid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
mshA 575842 c.495G>C synonymous_variant 1.0 isoniazid
ethionamide
mshA 575864 c.517T>C synonymous_variant 1.0 isoniazid
ethionamide
mshA 575881 c.534C>T synonymous_variant 1.0 isoniazid
ethionamide
mshA 575884 c.537G>C synonymous_variant 1.0 isoniazid
ethionamide
mshA 575893 c.546C>A synonymous_variant 1.0 isoniazid
ethionamide
rpoC 764932 c.1563C>A synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 764935 c.1566T>C synonymous_variant 1.0 rifampicin
rpoC 764948 c.1579T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 764968 c.1599T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
mmpL5 775951 c.2530C>T synonymous_variant 1.0 bedaquiline
clofazimine
sigE 1364931 c.519C>T synonymous_variant 1.0 pyrazinamide
sigE 1364950 p.Ala180Ser missense_variant 1.0 pyrazinamide
sigE 1364956 c.544C>T synonymous_variant 1.0 pyrazinamide
sigE 1364962 p.Pro184Ala missense_variant 1.0 pyrazinamide
sigE 1364976 c.564T>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
sigE 1364979 c.567C>G synonymous_variant 1.0 pyrazinamide
sigE 1364980 c.568T>C synonymous_variant 1.0 pyrazinamide
sigE 1364984 p.Ala191Asp missense_variant 1.0 pyrazinamide
sigE 1364989 c.577C>T synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
sigE 1364992 p.Pro194Ala missense_variant 1.0 pyrazinamide
sigE 1365000 c.588G>A synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
sigE 1365006 c.594T>C synonymous_variant 1.0 pyrazinamide
sigE 1365018 c.606G>C synonymous_variant 1.0 pyrazinamide
sigE 1365042 c.630G>C synonymous_variant 1.0 pyrazinamide
sigE 1365048 c.636G>A synonymous_variant 1.0 pyrazinamide
sigE 1365051 c.639G>A synonymous_variant 1.0 pyrazinamide
sigE 1365063 c.651A>G synonymous_variant 1.0 pyrazinamide
sigE 1365069 c.657C>T synonymous_variant 1.0 pyrazinamide
katG 2155691 c.421T>C synonymous_variant 1.0 isoniazid
katG 2155696 p.Ala139Val missense_variant 1.0 isoniazid
katG 2155716 c.396T>G synonymous_variant 1.0 isoniazid
katG 2155722 c.390G>C synonymous_variant 1.0 isoniazid
katG 2155728 c.384G>C synonymous_variant 1.0 isoniazid
katG 2155742 p.Gly124Arg missense_variant 1.0 isoniazid
katG 2155747 p.Ala122Gly missense_variant 1.0 isoniazid
katG 2155749 c.363C>T synonymous_variant 1.0 isoniazid Not assoc w R - Interim
katG 2155752 c.360C>T synonymous_variant 1.0 isoniazid
katG 2155764 p.His116Glu missense_variant 1.0 isoniazid
katG 2155769 p.Ile115Val missense_variant 1.0 isoniazid
katG 2155770 c.342C>G synonymous_variant 1.0 isoniazid
katG 2155782 c.330C>A synonymous_variant 1.0 isoniazid
katG 2155794 p.Ala106Ser missense_variant 1.0 isoniazid
katG 2155800 c.312G>C synonymous_variant 1.0 isoniazid
katG 2155805 p.Ile103Val missense_variant 1.0 isoniazid Uncertain significance
katG 2155806 c.306T>C synonymous_variant 1.0 isoniazid
katG 2155815 c.297G>C synonymous_variant 1.0 isoniazid
katG 2155824 c.288C>G synonymous_variant 1.0 isoniazid
lpqB 3624614 c.297A>T synonymous_variant 0.93 rifampicin
bedaquiline
lpqB 3624635 p.His92Arg missense_variant 0.93 rifampicin Uncertain significance
bedaquiline
lpqB 3624643 p.Ile90Leu missense_variant 0.93 rifampicin
bedaquiline
lpqB 3624646 c.265T>C synonymous_variant 0.93 rifampicin
bedaquiline
lpqB 3624649 c.262T>C synonymous_variant 0.93 rifampicin
bedaquiline
lpqB 3624650 c.261G>A synonymous_variant 0.93 rifampicin
bedaquiline
lpqB 3624656 c.255C>T synonymous_variant 0.93 rifampicin
bedaquiline
lpqB 3624673 p.Ala80Ser missense_variant 0.93 rifampicin
bedaquiline
lpqB 3624675 p.Asn79Ser missense_variant 0.93 rifampicin
bedaquiline
lpqB 3624680 c.231T>G synonymous_variant 0.93 rifampicin
bedaquiline
lpqB 3624701 c.210T>G synonymous_variant 0.93 rifampicin
bedaquiline
lpqB 3624704 c.207G>C synonymous_variant 0.93 rifampicin
bedaquiline
lpqB 3624719 c.192C>T synonymous_variant 0.93 rifampicin
bedaquiline
lpqB 3624725 c.186G>T synonymous_variant 0.93 rifampicin
bedaquiline
lpqB 3624734 c.177A>G synonymous_variant 0.9 rifampicin
bedaquiline
embB 4247491 c.978G>C synonymous_variant 0.92 ethambutol
embB 4247497 c.984T>C synonymous_variant 0.93 ethambutol
embB 4247511 p.Tyr333Phe missense_variant 0.88 ethambutol
embB 4247527 c.1014G>C synonymous_variant 0.88 ethambutol
embB 4247536 c.1023C>G synonymous_variant 0.87 ethambutol
embB 4247554 c.1041T>C synonymous_variant 0.86 ethambutol
embB 4247555 p.Leu348Ile missense_variant 0.86 ethambutol
embB 4247566 c.1053C>A synonymous_variant 0.85 ethambutol
embB 4247572 c.1059A>C synonymous_variant 0.85 ethambutol
embB 4247578 c.1065_1066insATCTGT conservative_inframe_insertion 0.85 ethambutol
embB 4247581 c.1069_1074delGCCGGG conservative_inframe_deletion 0.85 ethambutol
embB 4247590 c.1077A>G synonymous_variant 0.85 ethambutol Not assoc w R - Interim