TB-Profiler result

Run: SRR20958097
Summary

Run ID: SRR20958097

Sample name:

Date: 2024-10-04T01:11:02.062113

Number of reads: 16703207

Percentage reads mapped: 99.69

Median coverage: 444.0

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 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 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
rpsA 1834770 p.Gln410Arg missense_variant 0.99 pyrazinamide Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2290014 c.-773T>C upstream_gene_variant 1.0 pyrazinamide
eis 2715491 c.-159G>T upstream_gene_variant 1.0 kanamycin
amikacin
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0 ethionamide
alr 3841546 c.-126C>A upstream_gene_variant 1.0 cycloserine
alr 3841612 c.-193_-192insC upstream_gene_variant 1.0 cycloserine
rpoA 3878613 c.-106A>C upstream_gene_variant 0.13 rifampicin
rpoA 3878619 c.-112A>C upstream_gene_variant 0.12 rifampicin
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.14 ethambutol
embB 4247039 p.Phe176Val missense_variant 0.13 ethambutol
aftB 4269087 c.-251G>A upstream_gene_variant 1.0 ethambutol
ethA 4326582 p.Asn298His missense_variant 1.0 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R