TB-Profiler result

Run: SRR13837656
Summary

Run ID: SRR13837656

Sample name:

Date: 2025-03-05T05:01:11.569394

Number of reads: 2936417

Percentage reads mapped: 100.0

Median coverage: 97.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: HR-TB

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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 katG c.1700delT Assoc w R High-level resistance
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
katG 2154411 c.1700delT frameshift_variant 1.0 isoniazid Assoc w R High-level resistance
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 7949 c.648G>T synonymous_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8123 p.Leu274Phe missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9768 p.Gly823Cys missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
Rv0565c 657349 p.Glu41Val missense_variant 1.0 ethionamide Uncertain significance
mmaA3 738066 c.84C>T synonymous_variant 1.0 isoniazid Uncertain significance
rpoC 763734 p.Pro122Leu missense_variant 1.0 rifampicin Uncertain significance
Rv1129c 1253309 p.His409Pro missense_variant 1.0 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
rrl 1476640 n.2983C>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
tsnR 1853566 c.-40C>T upstream_gene_variant 1.0 linezolid Uncertain significance
tlyA 1918034 p.Val32Ala missense_variant 1.0 capreomycin Uncertain significance
bacA 2064615 p.Leu38Phe missense_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
katG 2155918 p.Ala65Val missense_variant 1.0 isoniazid Uncertain significance
PPE35 2168767 p.Ser616Gly missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2170815 c.-203C>G upstream_gene_variant 0.99 pyrazinamide Uncertain significance
Rv1979c 2222377 p.Val263Gly missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv2477c 2783104 c.939C>A synonymous_variant 1.0 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
ribD 2986993 p.Gly52Val missense_variant 0.99 para-aminosalicylic_acid Uncertain significance
Rv2752c 3065787 c.405G>C synonymous_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv3083 3448649 p.Arg49Pro missense_variant 1.0 ethionamide Uncertain significance
Rv3236c 3613067 p.Val17Gly missense_variant 1.0 pyrazinamide Uncertain significance
Rv3236c 3613315 c.-199T>G upstream_gene_variant 1.0 pyrazinamide Uncertain significance
fbiA 3640435 c.-108A>C upstream_gene_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
rpoA 3878982 c.-475A>T upstream_gene_variant 1.0 rifampicin Uncertain significance
clpC1 4039842 c.862_863insT frameshift_variant 1.0 pyrazinamide Uncertain significance
panD 4044103 p.Ile60Ser missense_variant 1.0 pyrazinamide Uncertain significance
embA 4245031 p.Arg600Gln missense_variant 1.0 ethambutol Uncertain significance
gid 4408218 c.-16G>T upstream_gene_variant 1.0 streptomycin Uncertain significance