TB-Profiler result

Run: SRR1173330
Summary

Run ID: SRR1173330

Sample name:

Date: 2024-10-04T09:36:20.117273

Number of reads: 187554

Percentage reads mapped: 62.43

Median coverage: 4.0

Strain: lineage4.3.3;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
lineage4.3 Euro-American (LAM) None 0.11
lineage4 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) None 0.73
lineage4.3.3 Euro-American (LAM) RD115 0.14
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
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.73 capreomycin
linezolid
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.67 capreomycin Uncertain significance
linezolid
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.6 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475761 n.2104_2106delCGCinsGT non_coding_transcript_exon_variant 0.55 capreomycin
linezolid
rrl 1475765 n.2111delG non_coding_transcript_exon_variant 0.55 capreomycin
linezolid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
rpoA 3877571 p.Pro313Ala missense_variant 0.58 rifampicin
rpoA 3877587 c.921A>G synonymous_variant 0.58 rifampicin Not assoc w R - Interim