TB-Profiler result

Run: SRR26112705
Summary

Run ID: SRR26112705

Sample name:

Date: 2024-04-15T15:48:19.181706

Number of reads: 3618661

Percentage reads mapped: 99.58

Median coverage: 183.0

Strain: lineage4.6.2

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.6 Euro-American None 1.0
lineage4.6.2 Euro-American RD726 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
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 0.99 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 0.97 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 574913 c.-435T>G upstream_gene_variant 0.28 ethionamide Uncertain significance
isoniazid Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 778298 c.183G>A synonymous_variant 1.0 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1253732 p.Glu268Gly missense_variant 1.0 moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv1129c 1254580 c.-46C>G upstream_gene_variant 1.0 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
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
bacA 2063187 c.1542C>T synonymous_variant 1.0 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2680 2996208 p.Ala35Asp missense_variant 0.99 capreomycin Uncertain significance
rpoA 3878654 c.-147A>G upstream_gene_variant 0.93 rifampicin Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 0.99 ethambutol Not assoc w R
embC 4242883 c.3021C>T synonymous_variant 1.0 ethambutol Not assoc w R - Interim
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin