TB-Profiler result

Run: SRR13861663
Summary

Run ID: SRR13861663

Sample name:

Date: 2024-04-15T05:25:29.701454

Number of reads: 212706

Percentage reads mapped: 10.65

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
gyrA 7705 p.Thr135Ser missense_variant 0.77 levofloxacin
moxifloxacin
gyrA 8409 p.Leu370Ile missense_variant 0.85 levofloxacin
moxifloxacin
rplC 801215 c.408delC frameshift_variant 1.0 linezolid
sigE 1365081 c.669G>T synonymous_variant 1.0 pyrazinamide
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.87 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.87 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.87 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.88 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.89 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.89 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.89 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.89 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.89 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.89 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.89 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.89 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.89 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.89 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.89 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.89 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.89 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.87 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.87 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.46 capreomycin Not assoc w R
linezolid Uncertain significance
PPE35 2168564 c.2049T>A synonymous_variant 1.0 pyrazinamide
kasA 2519179 c.1065G>C synonymous_variant 1.0 isoniazid