TB-Profiler result

Run: SRR6407487
Summary

Run ID: SRR6407487

Sample name:

Date: 2024-04-15T03:32:00.657491

Number of reads: 61849575

Percentage reads mapped: 79.09

Median coverage: 245.0

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
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
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 1473246 n.1401A>G non_coding_transcript_exon_variant 0.21 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
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 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.17 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.26 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.43 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.58 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.55 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 0.4 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472252 n.407G>A non_coding_transcript_exon_variant 0.4 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.4 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.4 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472572 n.727T>C non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin
amikacin Uncertain significance
rrs 1472574 n.729T>C non_coding_transcript_exon_variant 0.14 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472579 n.734_735delGCinsACGA non_coding_transcript_exon_variant 0.14 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472582 n.738_739delTA non_coding_transcript_exon_variant 0.17 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472594 n.749G>C non_coding_transcript_exon_variant 0.18 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.22 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.28 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.24 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.24 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.34 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.11 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1475538 n.1881T>C non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475550 n.1893A>C non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1475551 n.1894T>G non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1475555 n.1898T>G non_coding_transcript_exon_variant 0.11 capreomycin
linezolid
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.37 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.39 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.42 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.42 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 0.69 capreomycin
linezolid
rrl 1476420 n.2763G>A non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.74 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.71 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.71 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.67 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.68 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.69 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.71 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.56 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid