TB-Profiler result

Run: SRR1208658
Summary

Run ID: SRR1208658

Sample name:

Date: 2024-05-17T15:03:39.916983

Number of reads: 6840

Percentage reads mapped: 0.15

Median coverage: 0.0

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 rrs n.888G>A Uncertain significance Mutation from literature
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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.65 streptomycin Uncertain significance Mutation from literature
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
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.71 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472129 n.284G>A non_coding_transcript_exon_variant 0.8 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.43 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472150 n.305T>G non_coding_transcript_exon_variant 1.0 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.68 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.73 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.89 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1472223 n.378C>G non_coding_transcript_exon_variant 0.56 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.78 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1472228 n.383G>C non_coding_transcript_exon_variant 0.62 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.72 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472338 n.493A>C non_coding_transcript_exon_variant 0.76 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.86 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.46 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.67 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472396 n.551A>T non_coding_transcript_exon_variant 0.56 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472544 n.699C>T non_coding_transcript_exon_variant 0.9 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.68 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472579 n.734G>A non_coding_transcript_exon_variant 0.84 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.71 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.86 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.55 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472719 n.874G>A non_coding_transcript_exon_variant 0.68 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.73 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.53 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.72 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.65 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.92 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.96 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.89 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.95 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.5 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrl 1474199 n.542G>C non_coding_transcript_exon_variant 0.62 capreomycin
linezolid
rrl 1474200 n.545delT non_coding_transcript_exon_variant 0.91 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474208 n.551C>T non_coding_transcript_exon_variant 0.67 capreomycin
linezolid
rrl 1474213 n.556G>A non_coding_transcript_exon_variant 0.69 capreomycin
linezolid
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474228 n.571T>G non_coding_transcript_exon_variant 0.94 capreomycin
linezolid
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474584 n.927C>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474586 n.929T>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474594 n.937G>C non_coding_transcript_exon_variant 0.48 capreomycin
linezolid
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.65 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>A non_coding_transcript_exon_variant 0.55 capreomycin
linezolid
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.38 capreomycin
linezolid
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Uncertain significance