TB-Profiler result

Run: SRR28240082
Summary

Run ID: SRR28240082

Sample name:

Date: 2025-02-11T19:58:17.482590

Number of reads: 2797213

Percentage reads mapped: 99.5

Median coverage: 69.0

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) RD219 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 0.98 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 775764 p.Val906Ala missense_variant 1.0 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
fbiC 1304155 c.1225C>A synonymous_variant 1.0 pretomanid
delamanid
clofazimine
embR 1416759 c.589C>T synonymous_variant 1.0 ethambutol Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1473645 n.-12delT upstream_gene_variant 1.0 capreomycin Uncertain significance
linezolid
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2222842 c.322delG frameshift_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2752c 3067180 c.-989C>A upstream_gene_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
lpqB 3623610 p.Ala434Val missense_variant 1.0 rifampicin Uncertain significance
bedaquiline
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244637 p.Val469Met missense_variant 1.0 ethambutol Uncertain significance
embB 4246544 p.Thr11Pro missense_variant 0.15 ethambutol Uncertain significance
embB 4246548 p.Pro12Gln missense_variant 0.14 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.16 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.16 ethambutol Uncertain significance
embB 4246563 p.Leu17Trp missense_variant 0.18 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.18 ethambutol Not assoc w R - Interim
ethA 4328471 c.-998A>G upstream_gene_variant 1.0 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
gid 4407834 p.Trp123Cys missense_variant 1.0 streptomycin Uncertain significance