TB-Profiler result

Run: SRR25515499
Summary

Run ID: SRR25515499

Sample name:

Date: 2024-10-04T19:51:35.060967

Number of reads: 7556990

Percentage reads mapped: 99.53

Median coverage: 272.0

Strain: lineage4.4.2

Spoligotype:

Drug-resistance: Other

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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
lineage4.4 Euro-American None 0.99
lineage4.4.2 Euro-American 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 rrs n.517C>T Assoc w R
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
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin Assoc w R
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 6031 c.792C>T synonymous_variant 0.99 levofloxacin
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 490824 c.42A>G synonymous_variant 1.0 pretomanid
delamanid
clofazimine
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
Rv1129c 1253456 p.Gly360Val missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472121 n.276C>T non_coding_transcript_exon_variant 1.0 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
inhA 1673952 c.-250G>A upstream_gene_variant 0.99 isoniazid
ethionamide
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2155214 p.Trp300Arg missense_variant 0.99 isoniazid Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
eis 2714570 p.Ala255Ser missense_variant 0.99 kanamycin
amikacin
Rv2681 2996608 c.-131A>G upstream_gene_variant 1.0 capreomycin
Rv2752c 3066099 p.Met31Ile missense_variant 0.98 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
ald 3086712 c.-108C>A upstream_gene_variant 0.99 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448348 c.-156G>A upstream_gene_variant 0.99 ethionamide
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3640316 c.-227_-226insT upstream_gene_variant 1.0 pretomanid
delamanid
clofazimine
rpoA 3878349 c.159C>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
clpC1 4038565 p.Asp714Asn missense_variant 0.99 pyrazinamide
embC 4238963 c.-900C>T upstream_gene_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4246508 c.3276G>A synonymous_variant 0.99 ethambutol Not assoc w R
ubiA 4268928 c.906C>T synonymous_variant 0.99 ethambutol Not assoc w R
ubiA 4269375 c.459G>A synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407535 p.Thr223Met missense_variant 0.98 streptomycin