TB-Profiler result

Run: SRR21685380

Summary

Run ID: SRR21685380

Sample name:

Date: 2024-03-26T23:47:20.675529

Number of reads: 1420981

Percentage reads mapped: 99.7

Median coverage: 60.0

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
dnaA 371 p.Pro124Leu missense_variant 1.0 isoniazid Not assoc w R
gyrB 4972 c.-268G>A upstream_gene_variant 1.0 levofloxacin
moxifloxacin
gyrB 5596 c.357T>G synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7294 c.-8A>C upstream_gene_variant 1.0 levofloxacin
moxifloxacin
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
Rv1129c 1254293 p.Asp81Gly missense_variant 1.0 moxifloxacin
levofloxacin
rifampicin
isoniazid
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
thyA 3074231 p.Asp81Asn missense_variant 1.0 para-aminosalicylic_acid
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
alr 3840764 c.657G>C synonymous_variant 1.0 cycloserine
embC 4242497 p.Arg879Gly missense_variant 1.0 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R