TB-Profiler result

Run: SRR26399449

Summary

Run ID: SRR26399449

Sample name:

Date: 2024-10-03T23:11:29.233614

Number of reads: 6727906

Percentage reads mapped: 99.37

Median coverage: 143.0

Strain: lineage4.1.2

Spoligotype:

Drug-resistance: HR-TB


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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 1.0
lineage4.1.2 Euro-American None 1.0
lineage4 Euro-American 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 katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin gid c.351delG Assoc w R
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
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid Assoc w R High-level resistance
gid 4407851 c.351delG frameshift_variant 1.0 streptomycin Assoc w R
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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13631 c.-73T>C upstream_gene_variant 0.72 isoniazid Uncertain significance
fgd1 490892 p.Val37Gly missense_variant 1.0 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 1.0 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
embR 1417140 p.Ala70Ser missense_variant 1.0 ethambutol Not assoc w R
embR 1418018 c.-671C>T upstream_gene_variant 1.0 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
inhA 1673249 c.-953C>T upstream_gene_variant 1.0 isoniazid
ethionamide
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2169202 p.Ser471Ala missense_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
folC 2747022 p.Val193Ile missense_variant 0.99 para-aminosalicylic_acid
Rv2752c 3065377 p.Val272Ala missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3449642 p.Asn380Ser missense_variant 1.0 ethionamide Uncertain significance
whiB7 3568921 c.-242G>C upstream_gene_variant 1.0 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3641164 p.Ile208Val missense_variant 0.99 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
ddn 3986755 c.-89G>C upstream_gene_variant 0.99 pretomanid
delamanid
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 1.0 ethambutol Not assoc w R
embC 4242993 p.Thr1044Met missense_variant 0.17 ethambutol Uncertain significance
ethA 4326041 p.Leu478Arg missense_variant 0.77 ethionamide Uncertain significance
ethA 4327265 p.Thr70Ser missense_variant 1.0 ethionamide Uncertain significance
ethR 4327628 c.80_81delTGinsC frameshift_variant&missense_variant 1.0 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin