TB-Profiler result

Run: SRR20958131
Summary

Run ID: SRR20958131

Sample name:

Date: 2024-10-05T10:44:32.305910

Number of reads: 13861512

Percentage reads mapped: 99.84

Median coverage: 383.0

Strain: lineage4.8;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
lineage4.8 Euro-American (mainly T) RD219 0.42
lineage4.9 Euro-American (H37Rv-like) None 0.6
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 0.4 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mmaA3 738075 c.75A>C synonymous_variant 0.43 isoniazid
mmpL5 775639 p.Ile948Val missense_variant 0.46 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 0.41 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 0.44 capreomycin Not assoc w R
linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 0.42 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.41 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223604 c.-440C>T upstream_gene_variant 0.41 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.43 capreomycin
ald 3087141 c.322T>C synonymous_variant 0.46 cycloserine
embC 4242643 c.2781C>T synonymous_variant 0.38 ethambutol Not assoc w R
embA 4246277 c.3045G>A synonymous_variant 0.41 ethambutol Not assoc w R - Interim
embB 4247028 p.Leu172Arg missense_variant 0.18 ethambutol
embB 4247039 p.Phe176Val missense_variant 0.13 ethambutol
ethA 4328212 c.-740delC upstream_gene_variant 0.44 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 0.41 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
gid 4407945 c.258C>T synonymous_variant 0.42 streptomycin Not assoc w R - Interim