TB-Profiler result

Run: SRR6485131
Summary

Run ID: SRR6485131

Sample name:

Date: 2024-03-26T23:57:49.732147

Number of reads: 2986865

Percentage reads mapped: 99.73

Median coverage: 56.0

Strain: lineage4

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
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 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 7892 c.591G>A synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
ccsA 620619 c.729G>A synonymous_variant 1.0 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rpoB 759387 c.-420T>C upstream_gene_variant 1.0 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 778090 p.Gly131Arg missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpS5 778767 p.Asp47His missense_variant 1.0 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
embR 1416966 p.Ala128Pro missense_variant 1.0 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 0.98 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474074 n.417C>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
fabG1 1673380 c.-60C>G upstream_gene_variant 0.3 ethionamide
isoniazid
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
katG 2154450 p.Lys554Asn missense_variant 1.0 isoniazid Uncertain significance
PPE35 2170048 p.Leu189Val missense_variant 0.35 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.33 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ahpC 2726003 c.-190C>G upstream_gene_variant 1.0 isoniazid
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038318 p.Pro796Leu missense_variant 1.0 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242835 c.2973C>T synonymous_variant 1.0 ethambutol Not assoc w R - Interim
embB 4246548 p.Pro12Gln missense_variant 0.3 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.52 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.52 ethambutol Uncertain significance
embB 4246563 p.Leu17Trp missense_variant 0.44 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.42 ethambutol Not assoc w R - Interim
ethA 4327310 p.Ser55Cys missense_variant 1.0 ethionamide Uncertain significance
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