TB-Profiler result

Run: SRR21732809
Summary

Run ID: SRR21732809

Sample name:

Date: 2024-04-14T15:52:56.684796

Number of reads: 8544166

Percentage reads mapped: 99.63

Median coverage: 289.0

Strain: lineage4

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
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
mshA 576456 p.Val370Gly missense_variant 0.33 ethionamide
isoniazid
mshA 576651 p.Asp435Ala missense_variant 0.29 ethionamide
isoniazid
mshA 576657 p.Leu437Arg missense_variant 0.17 ethionamide
isoniazid
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
embR 1416436 p.Gln304His missense_variant 0.17 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
inhA 1674999 c.798C>G synonymous_variant 1.0 ethionamide
isoniazid
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154980 c.1132C>T synonymous_variant 1.0 isoniazid Not assoc w R - Interim
PPE35 2169122 c.1491C>G synonymous_variant 0.98 pyrazinamide Not assoc w R - Interim
PPE35 2169125 c.1486_1488delGTTinsAC frameshift_variant&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 0.99 pyrazinamide Uncertain significance
PPE35 2169149 c.1464G>A synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
PPE35 2170811 c.-199C>T upstream_gene_variant 1.0 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
eis 2714450 p.Trp295Arg missense_variant 1.0 amikacin
kanamycin
Rv2752c 3066064 p.Ile43Ser missense_variant 1.0 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv3083 3449145 c.642G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
alr 3840794 c.627T>C synonymous_variant 1.0 cycloserine
panD 4044406 c.-125C>G upstream_gene_variant 1.0 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245835 p.Leu868Arg missense_variant 0.15 ethambutol
aftB 4268076 p.Met254Ala missense_variant 1.0 ethambutol Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R