TB-Profiler result

Run: ERR144585
Summary

Run ID: ERR144585

Sample name:

Date: 2024-04-15T23:32:28.734431

Number of reads: 4707386

Percentage reads mapped: 99.69

Median coverage: 101.0

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 0.97
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 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781481 c.-79C>A upstream_gene_variant 0.97 streptomycin Uncertain significance
Rv1129c 1253179 c.1356A>C synonymous_variant 0.88 moxifloxacin
levofloxacin
rifampicin
isoniazid Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.93 capreomycin Not assoc w R
linezolid Not assoc w R
fabG1 1673162 c.-278T>C upstream_gene_variant 0.94 ethionamide
isoniazid
tsnR 1854300 p.Leu232Pro missense_variant 0.1 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.93 capreomycin
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 0.94 ethionamide Uncertain significance
whiB7 3569174 c.-495A>G upstream_gene_variant 0.93 streptomycin
amikacin
kanamycin
Rv3236c 3612047 p.Ala357Val missense_variant 0.98 pyrazinamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.12 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246820 p.Pro103Thr missense_variant 0.96 ethambutol Uncertain significance
ethA 4326505 c.969C>G synonymous_variant 0.98 ethionamide Not assoc w R - Interim
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R