TB-Profiler result

Run: SRR21689859
Summary

Run ID: SRR21689859

Sample name:

Date: 2024-10-03T23:18:32.390244

Number of reads: 6335673

Percentage reads mapped: 99.97

Median coverage: 88.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: Sensitive

Download CSV Download TXT Download JSON
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
rpoB 761967 p.Glu721Lys 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
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 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
PPE35 2169122 c.1491C>G synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
PPE35 2169125 p.Val496Ile missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2169131 c.1482C>T synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
PPE35 2169134 c.1479G>A synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
PPE35 2169141 p.Thr491Met missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2169144 p.Val490Ala missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2169149 c.1464G>A synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289972 c.-731T>G upstream_gene_variant 1.0 pyrazinamide
kasA 2518169 p.Val19Ile missense_variant 1.0 isoniazid
ald 3087095 c.276C>T synonymous_variant 1.0 cycloserine
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247231 p.Asp240Tyr missense_variant 1.0 ethambutol Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R