TB-Profiler result

Run: ERR019872
Summary

Run ID: ERR019872

Sample name:

Date: 2024-04-15T18:13:52.968508

Number of reads: 1182927

Percentage reads mapped: 99.64

Median coverage: 14.0

Strain: lineage4.6.2.2;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
lineage4.6 Euro-American None 0.94
lineage4.6.2 Euro-American RD726 0.91
lineage4.6.2.2 Euro-American (Cameroon) RD726 0.95
lineage4 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) None 0.06
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 7362 p.Glu21Gln missense_variant 0.92 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.9 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mmpL5 778298 c.183G>A synonymous_variant 1.0 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472487 n.643dupT non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 0.92 capreomycin Not assoc w R
bacA 2063187 c.1542C>T synonymous_variant 0.83 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.85 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv3236c 3612910 p.Leu69Phe missense_variant 1.0 pyrazinamide Uncertain significance
whiB6 4338732 c.-211C>T upstream_gene_variant 0.64 capreomycin
amikacin
kanamycin