0ba33e96-67cb-4650-b2bd-6ee13fa7de97 English ISO/IEC 8859-1 (also known as Latin 1) dataset dataset NERC EDS Environmental Information Data Centre Lancaster Environment Centre, Library Avenue, Bailrigg Lancaster LA1 4AP UK info@eidc.ac.uk https://eidc.ac.uk/ EIDC website The Environmental Information Data Centre (EIDC) is the UK's national data centre for terrestrial and freshwater sciences. information pointOfContact 2025-11-21T10:07:59 UK GEMINI 2.3 WGS 84 Conversion rate, frequency and state of single nucleotide polymorphism loci for Scots pine Axiom microarray 2020-06-26 publication https://catalogue.ceh.ac.uk/id/0ba33e96-67cb-4650-b2bd-6ee13fa7de97 10.5285/0ba33e96-67cb-4650-b2bd-6ee13fa7de97 doi: 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 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 Cavers, S. UK Centre for Ecology & Hydrology enquiries@ceh.ac.uk https://orcid.org/0000-0003-2139-9236 ORCID record ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers. information author Wachowiak, W. Adam Mickiewicz University witwac@amu.edu.pl https://orcid.org/0000-0003-2898-3523 ORCID record ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers. information author Perry, A. UK Centre for Ecology & Hydrology enquiries@ceh.ac.uk https://orcid.org/0000-0002-7889-7597 ORCID record ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers. information author Cavers, S. UK Centre for Ecology & Hydrology enquiries@ceh.ac.uk pointOfContact UK Centre for Ecology & Hydrology enquiries@ceh.ac.uk owner NERC EDS Environmental Information Data Centre info@eidc.ac.uk custodian NERC Environmental Information Data Centre info@eidc.ac.uk publisher Environmental Monitoring Facilities theme GEMET - INSPIRE themes, version 1.0 2008-06-01 publication Pinus sylvestris Pinus mugo Pinus uliginosa Pinus uncinata Wikidata 2012-10-29 creation conifer GEMET - Concepts, version 4.1.3 2019-01-28 creation Genomics Microarray SNPs Polymorphism Divergence Natural selection Speciation otherRestrictions no limitations otherRestrictions This resource is available under the terms of the Open Government Licence otherRestrictions 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 textTable 1000 English utf8 biota -9.527 17.764 35.922 60.989 Text NERC EDS Environmental Information Data Centre info@eidc.ac.uk distributor https://data-package.ceh.ac.uk/data/0ba33e96-67cb-4650-b2bd-6ee13fa7de97 Download the data Download a copy of this data download https://data-package.ceh.ac.uk/sd/0ba33e96-67cb-4650-b2bd-6ee13fa7de97.zip Supporting information Supporting information available to assist in re-use of this dataset information dataset dataset 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 2010-12-08 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)).