TB-Profiler result

Run: SRR1208340
Summary

Run ID: SRR1208340

Sample name:

Date: 2024-10-05T08:55:40.482126

Number of reads: 6019897

Percentage reads mapped: 98.93

Median coverage: 74.0

Strain: 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
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
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
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471656 n.-190G>A upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tlyA 1917972 c.33A>G synonymous_variant 0.97 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.98 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223724 c.-560C>G upstream_gene_variant 1.0 bedaquiline
clofazimine
embB 4247128 c.615C>T synonymous_variant 1.0 ethambutol Not assoc w R - Interim
embB 4247530 c.1017G>T synonymous_variant 1.0 ethambutol