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snp matrix (single-nucleotide polymorphism)  (National Reference Center for Legionella)

 
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    National Reference Center for Legionella snp matrix (single-nucleotide polymorphism)
    Snp Matrix (Single Nucleotide Polymorphism), supplied by National Reference Center for Legionella, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/snp+matrix/snp+matrix++single+nucleotide+polymorphism+/pmc10588306__23___00095_DORTET_Supplement-14-2-17
    Average 90 stars, based on 1 article reviews
    snp matrix (single-nucleotide polymorphism) - by Bioz Stars, 2026-09
    90/100 stars

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    other:

    Article Title: Emergence and rapid dissemination of highly resistant NDM-14-producing Klebsiella pneumoniae ST147, France, 2022
    Article Snippet: SUPPLEMENTARY DATA Figure S1: SNP matrix (Single-Nucleotide Polymorphism) for the 37 NDM-14-producing Klebsiella pneumoniae ST-147 received at the French National Reference Center for Carbapenem-resistant Enterobacterales from 1st January 2014 to 30th June 2022.



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    Characteristics of the 1,728 clinical isolates. A A histogram showing the number of pairwise <t>SNP</t> differences. B A histogram showing the number of isolates that carry each of the 6,976 pangenome genes. C Geography of the phylogenetic neighborhood of the clinical clade. The SNP-based maximum <t>likelihood</t> <t>phylogeny</t> contains all environmental isolates identified in the NCBI Pathogen Detection database within 1000 cgMLST alleles of the clinical clade. Only select bootstrap values that highlight the separation between the clinical and environmental isolates are shown for clarity. The clinical clade (blue), which is only represented by ten isolates here, is nested within a larger clade (magenta) of ten isolates collected from California and one isolate from Washington, collected between 2010 and 2017. The sister clade (orange) contains isolates from California, New Mexico, and Mexico collected between 2014 and 2020. The phylogeny was inferred using GARLI (with 1,000 bootstraps) with the SNP matrix generated by the CFSAN SNP Pipeline
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    Characteristics of the 1,728 clinical isolates. A A histogram showing the number of pairwise SNP differences. B A histogram showing the number of isolates that carry each of the 6,976 pangenome genes. C Geography of the phylogenetic neighborhood of the clinical clade. The SNP-based maximum likelihood phylogeny contains all environmental isolates identified in the NCBI Pathogen Detection database within 1000 cgMLST alleles of the clinical clade. Only select bootstrap values that highlight the separation between the clinical and environmental isolates are shown for clarity. The clinical clade (blue), which is only represented by ten isolates here, is nested within a larger clade (magenta) of ten isolates collected from California and one isolate from Washington, collected between 2010 and 2017. The sister clade (orange) contains isolates from California, New Mexico, and Mexico collected between 2014 and 2020. The phylogeny was inferred using GARLI (with 1,000 bootstraps) with the SNP matrix generated by the CFSAN SNP Pipeline

    Journal: BMC Genomics

    Article Title: Assessment of plasmids for relating the 2020 Salmonella enterica serovar Newport onion outbreak to farms implicated by the outbreak investigation

    doi: 10.1186/s12864-023-09245-0

    Figure Lengend Snippet: Characteristics of the 1,728 clinical isolates. A A histogram showing the number of pairwise SNP differences. B A histogram showing the number of isolates that carry each of the 6,976 pangenome genes. C Geography of the phylogenetic neighborhood of the clinical clade. The SNP-based maximum likelihood phylogeny contains all environmental isolates identified in the NCBI Pathogen Detection database within 1000 cgMLST alleles of the clinical clade. Only select bootstrap values that highlight the separation between the clinical and environmental isolates are shown for clarity. The clinical clade (blue), which is only represented by ten isolates here, is nested within a larger clade (magenta) of ten isolates collected from California and one isolate from Washington, collected between 2010 and 2017. The sister clade (orange) contains isolates from California, New Mexico, and Mexico collected between 2014 and 2020. The phylogeny was inferred using GARLI (with 1,000 bootstraps) with the SNP matrix generated by the CFSAN SNP Pipeline

    Article Snippet: The phylogeny was inferred using GARLI (with 1,000 bootstraps) with the SNP matrix generated by the CFSAN SNP Pipeline To assess if the clinical clade was associated with a geographical location, the previous SNP analysis was extended to include all closely related (within 1,000 cgMLST alleles of the clinical isolates) environmental isolates from the National Center for Biotechnology Information (NCBI) Pathogen Detection database (Fig. C).

    Techniques: Generated