TB-Profiler result

Run: ERR12544298
Summary

Run ID: ERR12544298

Sample name:

Date: 2024-10-04T12:17:54.922579

Number of reads: 2707649

Percentage reads mapped: 99.9

Median coverage: 130.5

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.Leu449Gln Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
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
rpoB 761152 p.Leu449Gln missense_variant 0.14 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
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
Rv0010c 13829 c.-271T>A upstream_gene_variant 0.14 isoniazid
Rv0010c 13834 c.-276A>T upstream_gene_variant 0.16 isoniazid
mshA 576488 p.Val381His missense_variant 0.17 isoniazid
ethionamide
rpoC 766237 c.2868T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
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
atpE 1461037 c.-8_-7insT upstream_gene_variant 1.0 bedaquiline
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
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2170035 p.Val193Ala missense_variant 0.27 pyrazinamide Uncertain significance
PPE35 2170048 p.Leu189Val missense_variant 0.38 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.36 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2680 2995848 c.-257G>A upstream_gene_variant 1.0 capreomycin
Rv2680 2996084 c.-21A>C upstream_gene_variant 0.44 capreomycin Uncertain significance
Rv2681 2997962 c.1224A>C synonymous_variant 0.12 capreomycin
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
rpoA 3878567 c.-60C>G upstream_gene_variant 0.44 rifampicin
rpoA 3878578 c.-71C>A upstream_gene_variant 0.23 rifampicin Uncertain significance
rpoA 3878599 c.-92C>G upstream_gene_variant 0.42 rifampicin
rpoA 3878639 c.-132C>G upstream_gene_variant 0.26 rifampicin Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244510 c.1278G>A synonymous_variant 1.0 ethambutol Not assoc w R - Interim
embB 4246544 p.Thr11Pro missense_variant 0.31 ethambutol Uncertain significance
embB 4246548 p.Pro12Gln missense_variant 0.31 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.3 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.3 ethambutol Uncertain significance
embB 4246563 p.Leu17Trp missense_variant 0.3 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.3 ethambutol Not assoc w R - Interim
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R