TB-Profiler result

Run: SRR20139562
Summary

Run ID: SRR20139562

Sample name:

Date: 2024-10-03T17:35:11.433253

Number of reads: 2176327

Percentage reads mapped: 99.72

Median coverage: 74.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: RR-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
lineage4.8 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 rpoB p.Thr427Ile Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
p.Ile491Phe Assoc w R
isoniazid
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Ala3Glu Assoc w R - Interim
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
rpoB 761086 p.Thr427Ile missense_variant 1.0 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoB 761277 p.Ile491Phe missense_variant 1.0 rifampicin Assoc w R
pncA 2289234 p.Ala3Glu missense_variant 1.0 pyrazinamide Assoc w R - Interim
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol 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
dnaA 1465 p.Glu489Lys missense_variant 1.0 isoniazid Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 574913 c.-435T>G upstream_gene_variant 0.19 isoniazid Uncertain significance
ethionamide Uncertain significance
mshA 576732 p.Asp462Ala missense_variant 1.0 isoniazid
ethionamide
rpoC 763348 c.-22C>T upstream_gene_variant 1.0 rifampicin Uncertain significance
rpoC 765689 p.Leu774Val missense_variant 1.0 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpR5 779302 p.Arg105Gly missense_variant 1.0 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1253726 p.Arg270Pro missense_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
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
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2155843 p.Trp90Ser missense_variant 1.0 isoniazid
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pepQ 2860451 c.-33G>A upstream_gene_variant 1.0 bedaquiline
clofazimine
Rv2752c 3067180 c.-989C>A upstream_gene_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326788 p.Leu229Arg missense_variant 0.87 ethionamide Uncertain significance
whiB6 4338593 c.-73delT upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
whiB6 4338596 c.-75G>C upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407991 p.Gly71Glu missense_variant 0.93 streptomycin Uncertain significance