TB-Profiler result

Run: SRR13861171
Summary

Run ID: SRR13861171

Sample name:

Date: 2024-04-15T14:54:12.420781

Number of reads: 224054

Percentage reads mapped: 22.43

Median coverage: 7.0

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 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
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
mshA 575194 c.-154G>T upstream_gene_variant 1.0 ethionamide
isoniazid
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.45 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.64 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.64 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.61 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.6 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.57 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.55 capreomycin Not assoc w R
linezolid Uncertain significance
fabG1 1673233 c.-207T>G upstream_gene_variant 1.0 ethionamide
isoniazid
pepQ 2859739 p.Ala227Gly missense_variant 1.0 clofazimine
bedaquiline
Rv3083 3448909 p.Leu136Ile missense_variant 1.0 ethionamide
rpoA 3878967 c.-460G>T upstream_gene_variant 1.0 rifampicin
embB 4248081 c.1569dupG frameshift_variant 1.0 ethambutol
ethA 4327644 c.-171G>A upstream_gene_variant 1.0 ethionamide