TB-Profiler result

Run: SRR13837669
Summary

Run ID: SRR13837669

Sample name:

Date: 2024-04-15T19:49:34.207562

Number of reads: 293877

Percentage reads mapped: 95.01

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
gyrA 8780 p.Asp493Glu missense_variant 1.0 levofloxacin
moxifloxacin
Rv0010c 13273 p.Gly96Cys missense_variant 1.0 isoniazid
mshA 574744 c.-604G>A upstream_gene_variant 1.0 ethionamide
isoniazid
rpoB 761845 p.Gln680Arg missense_variant 1.0 rifampicin
rpsL 781185 c.-375T>G upstream_gene_variant 1.0 streptomycin
rpsL 781226 c.-334C>T upstream_gene_variant 1.0 streptomycin
rplC 800937 c.129A>G synonymous_variant 1.0 linezolid
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
ahpC 2726771 c.579T>A synonymous_variant 1.0 isoniazid
Rv2752c 3067057 c.-867_-866insG upstream_gene_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3087587 c.769delC frameshift_variant 1.0 cycloserine
fbiA 3641252 p.Thr237Ser missense_variant 1.0 clofazimine
pretomanid
delamanid
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
embA 4244410 p.Trp393Ser missense_variant 1.0 ethambutol Uncertain significance
whiB6 4338681 c.-160A>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin