TB-Profiler result

Run: SRR8692825
Summary

Run ID: SRR8692825

Sample name:

Date: 2024-10-05T07:54:25.029209

Number of reads: 788969

Percentage reads mapped: 14.22

Median coverage: 17.0

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 0.97
lineage4.9 Euro-American (H37Rv-like) None 0.96
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 rplC p.Cys154Arg Assoc w R
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
rplC 801268 p.Cys154Arg missense_variant 0.44 linezolid 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
mmpL5 776100 p.Thr794Ile missense_variant 0.38 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1258c 1406686 p.Val219Ile missense_variant 1.0 streptomycin
pyrazinamide
isoniazid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472847 n.1002G>C non_coding_transcript_exon_variant 0.37 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472848 n.1003T>G non_coding_transcript_exon_variant 0.37 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472849 n.1004C>G non_coding_transcript_exon_variant 0.37 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472850 n.1005T>C non_coding_transcript_exon_variant 0.37 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472857 n.1012A>G non_coding_transcript_exon_variant 0.39 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472858 n.1013G>T non_coding_transcript_exon_variant 0.39 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472859 n.1014G>C non_coding_transcript_exon_variant 0.39 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472860 n.1015C>G non_coding_transcript_exon_variant 0.39 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.67 capreomycin Uncertain significance
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.69 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.69 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.67 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.43 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1475991 n.2334T>C non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid
rrl 1475995 n.2338G>A non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid
rrl 1476030 n.2373A>G non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid
rrl 1476032 n.2375C>A non_coding_transcript_exon_variant 0.38 capreomycin
linezolid
rrl 1476034 n.2377C>G non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid
rrl 1476035 n.2378G>C non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid
rrl 1476044 n.2387T>G non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid
rrl 1476045 n.2388G>T non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid
rrl 1476047 n.2390G>T non_coding_transcript_exon_variant 0.4 capreomycin
linezolid
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.47 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476529 n.2872A>G non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid
rrl 1476583 n.2926G>C non_coding_transcript_exon_variant 0.69 capreomycin
linezolid
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid