TB-Profiler result

Run: ERR2653002

Summary

Run ID: ERR2653002

Sample name:

Date: 2024-04-16T02:14:45.653012

Number of reads: 4558240

Percentage reads mapped: 99.53

Median coverage: 140.0

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 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
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
gyrA 9016 p.Thr572Asn missense_variant 0.99 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9648 p.Val783Leu missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
mshA 576574 c.1227T>C synonymous_variant 1.0 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
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
PPE35 2168149 p.Pro822Ser missense_variant 1.0 pyrazinamide 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
pncA 2289780 c.-539C>T upstream_gene_variant 1.0 pyrazinamide
ribD 2987581 p.Ser248Cys missense_variant 1.0 para-aminosalicylic_acid
Rv2680 2995848 c.-257G>A upstream_gene_variant 1.0 capreomycin
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
embA 4243412 c.180C>T synonymous_variant 1.0 ethambutol Not assoc w R - Interim
whiB6 4338596 c.-75G>A upstream_gene_variant 1.0 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338597 c.-76A>G upstream_gene_variant 0.99 capreomycin
amikacin Uncertain significance
kanamycin
whiB6 4338598 c.-77G>C upstream_gene_variant 1.0 capreomycin
amikacin Uncertain significance
kanamycin
whiB6 4338599 c.-78A>C upstream_gene_variant 1.0 capreomycin
amikacin Uncertain significance
kanamycin