TB-Profiler result

Run: SRR8692782
Summary

Run ID: SRR8692782

Sample name:

Date: 2024-10-05T10:36:13.984281

Number of reads: 1101120

Percentage reads mapped: 34.86

Median coverage: 22.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

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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 0.98
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 rplC p.Cys154Arg Assoc w R
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
rplC 801268 p.Cys154Arg missense_variant 0.75 linezolid Assoc w R
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
Rv1258c 1406686 p.Val219Ile missense_variant 0.9 streptomycin
pyrazinamide
isoniazid
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid
rrl 1475759 n.2102C>T non_coding_transcript_exon_variant 0.48 capreomycin
linezolid
rrl 1475762 n.2105G>T non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid
rrl 1475764 n.2107A>C non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid
rrl 1475775 n.2118G>A non_coding_transcript_exon_variant 0.52 capreomycin Uncertain significance
linezolid
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.22 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1475991 n.2334T>C non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance
linezolid
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.8 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476529 n.2872A>G non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid
rrl 1476583 n.2926G>C non_coding_transcript_exon_variant 0.46 capreomycin
linezolid
rpsA 1833734 p.Ala65Ser missense_variant 0.19 pyrazinamide
rpsA 1833745 c.204G>C synonymous_variant 0.21 pyrazinamide
rpsA 1833760 c.219C>T synonymous_variant 0.22 pyrazinamide Not assoc w R - Interim
rpsA 1833787 c.246C>G synonymous_variant 0.22 pyrazinamide
rpsA 1833790 c.249T>C synonymous_variant 0.22 pyrazinamide
rpsA 1833793 c.252C>T synonymous_variant 0.22 pyrazinamide
rpsA 1833802 c.261A>G synonymous_variant 0.23 pyrazinamide
rpsA 1833808 c.267G>C synonymous_variant 0.23 pyrazinamide
rpsA 1833811 c.270G>T synonymous_variant 0.24 pyrazinamide
rpsA 1833829 c.288A>G synonymous_variant 0.26 pyrazinamide
rpsA 1833832 c.291G>A synonymous_variant 0.26 pyrazinamide
rpsA 1833838 c.297G>C synonymous_variant 0.26 pyrazinamide
rpsA 1833841 c.300C>G synonymous_variant 0.25 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.23 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.22 pyrazinamide
rpsA 1833862 c.321G>T synonymous_variant 0.22 pyrazinamide