TB-Profiler result

Run: SRR29230907
Summary

Run ID: SRR29230907

Sample name:

Date: 2025-02-11T18:53:24.365009

Number of reads: 2203456

Percentage reads mapped: 99.88

Median coverage: 65.0

Strain: lineage3.1.2;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
lineage3 East-African-Indian RD750 0.22
lineage3.1.2 East-African-Indian RD750 0.24
lineage4 Euro-American None 0.83
lineage4.9 Euro-American (H37Rv-like) None 0.76
lineage3.1 East-African-Indian RD750 0.35
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
gyrA 7362 p.Glu21Gln missense_variant 0.21 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.18 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.16 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.18 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.22 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 0.2 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.18 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 0.22 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.27 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 0.18 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1473543 n.-115C>T upstream_gene_variant 0.14 capreomycin
linezolid
tsnR 1853400 c.-206G>A upstream_gene_variant 0.33 linezolid
tlyA 1917972 c.33A>G synonymous_variant 0.26 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.31 isoniazid Not assoc w R
katG 2156482 c.-371G>A upstream_gene_variant 0.28 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 0.22 pyrazinamide Not assoc w R
PPE35 2168604 p.Pro670Leu missense_variant 0.15 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.23 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289047 c.195C>T synonymous_variant 0.31 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.34 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.17 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.22 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.19 rifampicin Not assoc w R
bedaquiline Uncertain significance
lpqB 3625114 c.-204G>A upstream_gene_variant 0.16 rifampicin
bedaquiline
panD 4044340 c.-59G>T upstream_gene_variant 0.32 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 0.18 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.21 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
glpK 4139183 c.572dupG frameshift_variant 0.38 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.3 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.22 ethambutol Not assoc w R
gid 4407588 c.615A>G synonymous_variant 0.2 streptomycin Not assoc w R
gid 4407758 p.Ser149Arg missense_variant 0.22 streptomycin Uncertain significance