TB-Profiler result

Run: SRR23961529
Summary

Run ID: SRR23961529

Sample name:

Date: 2024-03-26T20:01:16.023951

Number of reads: 209237

Percentage reads mapped: 80.75

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.462C>T 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 1472307 n.462C>T non_coding_transcript_exon_variant 1.0 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
rpoC 766765 c.3396A>C synonymous_variant 0.9 rifampicin Not assoc w R - Interim
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474291 n.634_649delTTTCCTCTCCGGAGGAinsC non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.93 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833928 c.387G>C synonymous_variant 1.0 pyrazinamide
rpsA 1833940 c.399C>G synonymous_variant 1.0 pyrazinamide
rpoA 3877638 c.870T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
clpC1 4038671 c.2034T>C synonymous_variant 1.0 pyrazinamide
clpC1 4038683 c.2022T>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4038695 c.2010C>G synonymous_variant 1.0 pyrazinamide
clpC1 4038701 c.2004G>C synonymous_variant 1.0 pyrazinamide
clpC1 4038704 c.2001T>C synonymous_variant 1.0 pyrazinamide
clpC1 4038707 c.1998C>G synonymous_variant 1.0 pyrazinamide
clpC1 4038710 c.1995G>C synonymous_variant 1.0 pyrazinamide
clpC1 4038713 c.1992T>C synonymous_variant 1.0 pyrazinamide
clpC1 4038740 c.1965G>C synonymous_variant 1.0 pyrazinamide
clpC1 4038755 c.1950G>C synonymous_variant 1.0 pyrazinamide
clpC1 4038767 c.1938G>C synonymous_variant 1.0 pyrazinamide
clpC1 4038773 c.1932T>C synonymous_variant 1.0 pyrazinamide
clpC1 4038782 c.1923G>C synonymous_variant 0.9 pyrazinamide
clpC1 4038878 c.1827A>G synonymous_variant 0.9 pyrazinamide Not assoc w R - Interim
clpC1 4038908 c.1797C>G synonymous_variant 0.83 pyrazinamide
clpC1 4038914 c.1791G>C synonymous_variant 0.77 pyrazinamide
clpC1 4038923 c.1782A>G synonymous_variant 0.71 pyrazinamide
clpC1 4038932 c.1773G>C synonymous_variant 0.77 pyrazinamide
clpC1 4038953 c.1752A>G synonymous_variant 0.7 pyrazinamide
clpC1 4038956 c.1749T>C synonymous_variant 0.7 pyrazinamide
clpC1 4038965 c.1740T>C synonymous_variant 0.7 pyrazinamide