TB-Profiler result

Run: SRR28045545
Summary

Run ID: SRR28045545

Sample name:

Date: 2024-05-22T14:18:32.319109

Number of reads: 8541884

Percentage reads mapped: 99.72

Median coverage: 237.0

Strain: lineage4.9

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 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) 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
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
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
gyrB 5389 c.150C>A synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv1258c 1407298 p.Ala15Ser missense_variant 1.0 streptomycin
isoniazid
pyrazinamide
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1476704 n.3053delC non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
pncA 2289866 c.-625T>G upstream_gene_variant 1.0 pyrazinamide
eis 2715807 c.-475G>A upstream_gene_variant 1.0 amikacin
kanamycin
whiB7 3568428 c.252A>C synonymous_variant 0.11 streptomycin
amikacin
kanamycin
mtrB 3625489 c.1121_1124dupGCAC frameshift_variant 0.14 bedaquiline Uncertain significance
rifampicin Uncertain significance
embB 4247028 p.Leu172Arg missense_variant 0.28 ethambutol
embB 4247033 p.Ser174Arg missense_variant 0.21 ethambutol
ethA 4327415 p.Ala20Asp missense_variant 1.0 ethionamide Uncertain significance
ethA 4328236 c.-763A>G upstream_gene_variant 0.99 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R