TB-Profiler result

Run: SRR13861686
Summary

Run ID: SRR13861686

Sample name:

Date: 2024-04-15T07:53:03.199965

Number of reads: 258886

Percentage reads mapped: 25.91

Median coverage: 9.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

Download CSV Download TXT Download JSON
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
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.57 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.6 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.6 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.64 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 0.67 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.65 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.7 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.7 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.67 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.67 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.67 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.7 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.7 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.78 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.78 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.78 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.82 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1833851 p.Lys104Gln missense_variant 1.0 pyrazinamide
Rv1979c 2223241 c.-77C>G upstream_gene_variant 1.0 clofazimine
bedaquiline
pncA 2289811 c.-570C>T upstream_gene_variant 1.0 pyrazinamide
pncA 2289994 c.-753A>C upstream_gene_variant 1.0 pyrazinamide
embC 4241005 c.1143G>T synonymous_variant 1.0 ethambutol
embA 4243969 p.Val246Ala missense_variant 1.0 ethambutol