TB-Profiler result

Run: SRR13861575
Summary

Run ID: SRR13861575

Sample name:

Date: 2024-04-15T19:50:04.277872

Number of reads: 277708

Percentage reads mapped: 27.8

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
gyrA 9138 p.Gln613Lys missense_variant 1.0 levofloxacin
moxifloxacin
Rv0010c 13326 c.232delC frameshift_variant 1.0 isoniazid Uncertain significance
mmpS5 779508 c.-603G>C upstream_gene_variant 1.0 clofazimine
bedaquiline
Rv1258c 1407127 p.Arg72Ser missense_variant 1.0 streptomycin
isoniazid
pyrazinamide
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.62 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 0.53 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rpsA 1834079 p.Arg180Cys missense_variant 1.0 pyrazinamide
PPE35 2168448 p.Gln722Pro missense_variant 1.0 pyrazinamide
Rv1979c 2221876 p.Val430Glu missense_variant 1.0 clofazimine
bedaquiline
kasA 2518036 c.-78delG upstream_gene_variant 0.95 isoniazid
kasA 2518088 c.-27T>A upstream_gene_variant 1.0 isoniazid
eis 2714773 p.Pro187Gln missense_variant 1.0 amikacin
kanamycin
pepQ 2859723 c.696T>C synonymous_variant 1.0 clofazimine Not assoc w R - Interim
bedaquiline
ribD 2987540 c.702G>T synonymous_variant 1.0 para-aminosalicylic_acid
fbiD 3339321 c.204G>A synonymous_variant 1.0 clofazimine
pretomanid
delamanid
ethA 4326689 p.Lys262Thr missense_variant 1.0 ethionamide
ethA 4326849 p.Pro209Thr missense_variant 1.0 ethionamide
whiB6 4338822 c.-301A>C upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin