TB-Profiler result

Run: SRR13837668
Summary

Run ID: SRR13837668

Sample name:

Date: 2024-04-16T03:24:42.578415

Number of reads: 293867

Percentage reads mapped: 95.02

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
gyrB 5785 c.546C>T synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrB 6314 c.1076dupC frameshift_variant 1.0 levofloxacin Uncertain significance
moxifloxacin
ccsA 620129 p.Gly80Ala missense_variant 1.0 capreomycin
amikacin
kanamycin
rpoB 761845 p.Gln680Arg missense_variant 1.0 rifampicin
rpsL 781185 c.-375T>G upstream_gene_variant 1.0 streptomycin
rplC 800937 c.129A>G synonymous_variant 1.0 linezolid
embR 1416298 c.1050G>C synonymous_variant 1.0 ethambutol
embR 1417588 c.-241C>T upstream_gene_variant 1.0 ethambutol
bacA 2064860 c.-132A>G upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
Rv1979c 2223395 c.-231G>T upstream_gene_variant 1.0 clofazimine
bedaquiline
rpoA 3877496 p.Glu338* stop_gained 1.0 rifampicin
embC 4238901 c.-962T>A upstream_gene_variant 1.0 ethambutol
embC 4240480 c.618G>A synonymous_variant 1.0 ethambutol
embB 4249447 c.2934G>A synonymous_variant 1.0 ethambutol Not assoc w R - Interim
whiB6 4338681 c.-160A>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin