TB-Profiler result

Run: ERR551721
Summary

Run ID: ERR551721

Sample name:

Date: 2024-10-03T22:14:06.505950

Number of reads: 243052

Percentage reads mapped: 99.27

Median coverage: 9.0

Strain: lineage2.2.1;lineage4

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.3
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.42
lineage2.2 East-Asian (Beijing) RD105;RD207 0.37
lineage4 Euro-American None 0.78
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 pncA p.Leu85Arg Assoc w R
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Gly88Ala Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Gly88Ala Assoc w R - Interim
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
gyrA 7564 p.Gly88Ala missense_variant 1.0 levofloxacin Assoc w R - Interim
moxifloxacin Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
pncA 2288988 p.Leu85Arg missense_variant 1.0 pyrazinamide 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoC 764714 p.Leu449Val missense_variant 1.0 rifampicin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
ethA 4326533 p.Thr314Ile missense_variant 1.0 ethionamide Uncertain significance
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R