TB-Profiler result

Run: SRR13837647
Summary

Run ID: SRR13837647

Sample name:

Date: 2024-03-27T04:22:01.549600

Number of reads: 295127

Percentage reads mapped: 96.43

Median coverage: 10.0

Strain: lineage4.9

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
lineage4.9 Euro-American (H37Rv-like) 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
dnaA 750 c.750C>T synonymous_variant 1.0 isoniazid Not assoc w R - Interim
dnaA 1200 c.1200C>T synonymous_variant 1.0 isoniazid
gyrA 9494 p.Tyr731* stop_gained 1.0 levofloxacin
moxifloxacin
fbiC 1303155 c.225G>C synonymous_variant 1.0 clofazimine
pretomanid
delamanid
fbiC 1304225 p.Gly432Asp missense_variant 1.0 clofazimine
pretomanid
delamanid
fbiC 1305046 p.Ser706Pro missense_variant 0.93 clofazimine
pretomanid
delamanid
embR 1416546 p.Thr268Ser missense_variant 1.0 ethambutol
rrs 1471511 n.-335C>A upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
kasA 2518563 p.Ala150Gly missense_variant 1.0 isoniazid
kasA 2519015 p.Ser301Ala missense_variant 1.0 isoniazid
Rv2477c 2783171 c.871delT frameshift_variant 0.86 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
Rv3236c 3612913 p.Leu68Phe missense_variant 1.0 pyrazinamide
lpqB 3624794 c.117G>C synonymous_variant 1.0 bedaquiline
rifampicin
ethA 4327132 c.342C>T synonymous_variant 1.0 ethionamide Not assoc w R - Interim
gid 4408070 p.Trp45Arg missense_variant 1.0 streptomycin Uncertain significance