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
2024-02-08T17:34:08
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
enquiries@ceh.ac.uk
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
Dr. Stephen Cavers
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
enquiries@ceh.ac.uk
custodian
NERC Environmental Information Data Centre
enquiries@ceh.ac.uk
publisher
Environmental Monitoring Facilities
theme
GEMET - INSPIRE themes, version 1.0
2008-06-01
publication
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
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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
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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)).