TB-Profiler result

Run: SRR13837651
Summary

Run ID: SRR13837651

Sample name:

Date: 2024-04-15T22:29:20.144975

Number of reads: 293853

Percentage reads mapped: 97.01

Median coverage: 10.0

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 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 fbiC c.170dupA Assoc w R - Interim Confers DLM-PMD cross-resistance
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
fbiC 1303099 c.170dupA frameshift_variant 1.0 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-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
Rv0010c 13883 c.-325T>A upstream_gene_variant 1.0 isoniazid
rpoC 766128 p.Ala920Gly missense_variant 1.0 rifampicin
sigE 1364655 p.Met81Ile missense_variant 1.0 pyrazinamide
Rv1258c 1407463 c.-123G>C upstream_gene_variant 1.0 streptomycin
isoniazid
pyrazinamide
rrl 1474235 n.578G>T non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1475139 n.1482C>T non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476248 n.2591G>A non_coding_transcript_exon_variant 0.92 capreomycin Uncertain significance
linezolid
rrl 1476576 n.2919C>G non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
kasA 2518209 p.Thr32Arg missense_variant 1.0 isoniazid
fbiD 3339396 c.279C>T synonymous_variant 1.0 clofazimine
pretomanid
delamanid
mtrA 3627293 p.Glu19Asp missense_variant 1.0 bedaquiline
rifampicin
rpoA 3878048 p.Ala154Ser missense_variant 1.0 rifampicin
panD 4044922 c.-641G>T upstream_gene_variant 1.0 pyrazinamide
gid 4407792 c.411G>C synonymous_variant 1.0 streptomycin