TB-Profiler result

Run: SRR1173166
Summary

Run ID: SRR1173166

Sample name:

Date: 2024-04-14T19:27:08.061643

Number of reads: 124638

Percentage reads mapped: 43.74

Median coverage: 3.0

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 0.93
lineage4.9 Euro-American (H37Rv-like) None 0.93
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
rpoB 760328 c.522G>C synonymous_variant 0.75 rifampicin
rpoB 760331 c.525G>C synonymous_variant 0.75 rifampicin
rpoB 760340 c.534G>T synonymous_variant 0.69 rifampicin Not assoc w R - Interim
rpoB 760361 c.555T>C synonymous_variant 0.69 rifampicin Not assoc w R - Interim
rpoB 760370 c.564C>G synonymous_variant 0.67 rifampicin
rpoB 760376 p.Asp190Glu missense_variant 0.64 rifampicin Uncertain significance
rpoB 760380 p.Thr192Leu missense_variant 0.6 rifampicin
rpoC 763723 c.354G>C synonymous_variant 0.46 rifampicin
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.62 capreomycin
linezolid
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.69 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475249 n.1592T>C non_coding_transcript_exon_variant 0.6 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.6 capreomycin
linezolid
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.6 capreomycin
linezolid