BGS Hosted Metadata
Conversion rate, frequency and state of single nucleotide polymorphism loci for Scots pine Axiom microarray
The data comprise summary statistics for performance of a genotyping microarray for a test set of 87 samples for four pine species. The summary statistics comprise state (polymorphic, monomorphic), mean allele frequency and conversion rate, estimated for each locus as a mean across 87 sample genotypes. The array comprised 49,829 SNPs (single nucleotide polymorphisms) from several sources. The majority (N = 49,052) were obtained from transcriptome sequencing of four pine species: Pinus sylvestris, Pinus mugo, Pinus uncinata and Pinus uliginosa. The SNP set was filtered by the array manufacturer (Thermo Fisher) based on p-convert values signifying the SNP array quality, and a list of recommended and non-recommended SNP probes (avoiding SNPs with polymorphisms within 35 bp) was provided to the authors. These included SNPs that were common to all species and also SNPs fixed in one species and polymorphic within and among others. A further set of SNPs (N = 578) were included from candidate genes (N = 279), which had been resequenced in previous population genetic studies of the pine species. Variation in mitochondrial DNA (mtDNA) was targeted by inclusion of a set of mtDNA- specific SNPs (N = 14). Finally, a set of SNPs putatively associated with susceptibility to Dothistroma needle blight (discovered in Pinus radiata, European Nucleotide Archive accession numbers ERS1034542-53) were also included (N = 185). Full details about this dataset can be found at https://doi.org/10.5285/0ba33e96-67cb-4650-b2bd-6ee13fa7de97
Simple
- Date (Publication)
- 2020-06-26
- Citation identifier
- https://catalogue.ceh.ac.uk/id/0ba33e96-67cb-4650-b2bd-6ee13fa7de97
- Citation identifier
- doi: / 10.5285/0ba33e96-67cb-4650-b2bd-6ee13fa7de97
- Other citation details
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Cavers, S., Wachowiak, W., Perry, A. (2020). Conversion rate, frequency and state of single nucleotide polymorphism loci for Scots pine Axiom microarray. NERC Environmental Information Data Centre 10.5285/0ba33e96-67cb-4650-b2bd-6ee13fa7de97
- Point of contact
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Organisation name Individual name Electronic mail address Role UK Centre for Ecology & Hydrology Cavers, S. Author Adam Mickiewicz University
Wachowiak, W. Author UK Centre for Ecology & Hydrology Perry, A. Author UK Centre for Ecology & Hydrology Cavers, S.
Point of contact UK Centre for Ecology & Hydrology Owner NERC EDS Environmental Information Data Centre Custodian NERC Environmental Information Data Centre Publisher
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GEMET - INSPIRE themes, version 1.0
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Environmental Monitoring Facilities
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- Access constraints
- Other restrictions
- Other constraints
- no limitations
- Use constraints
- Other restrictions
- Use constraints
- Other restrictions
- Other constraints
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If you reuse this data, you should cite: Cavers, S., Wachowiak, W., Perry, A. (2020). Conversion rate, frequency and state of single nucleotide polymorphism loci for Scots pine Axiom microarray. NERC Environmental Information Data Centre https://doi.org/10.5285/0ba33e96-67cb-4650-b2bd-6ee13fa7de97
- Spatial representation type
- Text, table
- Distance
- 1000 urn:ogc:def:uom:EPSG::9001
- Language
- English
- Character set
- UTF8
- Topic category
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- Biota
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- Unique resource identifier
- WGS 84
- Distribution format
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Name Version Text
- Distributor contact
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Organisation name Individual name Electronic mail address Role NERC EDS Environmental Information Data Centre
Distributor
- OnLine resource
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Protocol Linkage Name https://data-package.ceh.ac.uk/data/0ba33e96-67cb-4650-b2bd-6ee13fa7de97 Download the data
- OnLine resource
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Protocol Linkage Name https://data-package.ceh.ac.uk/sd/0ba33e96-67cb-4650-b2bd-6ee13fa7de97.zip Supporting information
- Hierarchy level
- Dataset
- Other
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dataset
Conformance result
- Title
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Commission Regulation (EU) No 1089/2010 of 23 November 2010 implementing Directive 2007/2/EC of the European Parliament and of the Council as regards interoperability of spatial data sets and services
- Date (Publication)
- 2010-12-08
- Statement
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The dataset is a list of 49,829 SNP loci, identified by individual code with accompanying columns of basic information and statistics (Conversion type (Poly - polymorphic, Mono-monomorphic), mean allelic frequency (MAF), and call rate (CR)).
Metadata
- File identifier
- 0ba33e96-67cb-4650-b2bd-6ee13fa7de97 XML
- Metadata language
- English
- Character set
- 8859 Part 1
- Hierarchy level
- Dataset
- Hierarchy level name
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dataset
- Date stamp
- 2025-03-21T13:20:46
- Metadata standard name
- UK GEMINI
- Metadata standard version
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2.3
- Metadata author
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Organisation name Individual name Electronic mail address Role NERC EDS Environmental Information Data Centre Point of contact
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