{"@type": "dcat:Dataset", "accessLevel": "public", "bureauCode": ["005:18"], "contactPoint": {"fn": "Carlson, Craig, H.", "hasEmail": "mailto:craig.h.carlson@usda.gov"}, "description": "<p>Oat Landrace Diversity (OLD) Panel phenotypes, genotypes, and metadata from: Rahman et al. (2024) \"A global assembly of landrace oat (<em>Avena sativa</em> L.) accessions is a discovery resource for adaptive variation, association mapping, and trait deployment\".</p>\n<p><strong>\"File S1\"</strong> and <strong>\"File S2\"</strong> include population metadata and phenotypic (environmental) data used in association mapping, of which mapping results are listed in <strong>\"File S3\"</strong>.</p>\n<p><strong>\"Rahman_et_al_2024_Metadata.geojson\"</strong> is geographical information of OLD Panel accessions surveyed in this study.</p>\n<p><strong>\"SBATCH_RUN_nsgc_deepvariant_glsnexus.sh\"</strong> and <strong>\"RUN_nsgc_deepvariant_glsnexus.sh\"</strong> are scripts for variant calling and filtering in SciNet clusters from GBS alignments. IMPORTANT: Do not pull containers in $HOME directory - put them in the main path (for use in SciNet clusters). Google DeepVariant - generates \"deepvariant_1.6.0.sif\" (RUN: singularity pull docker://google/deepvariant:1.6.0); GLNexus - generates \"glnexus_v1.4.1.sif\" (RUN: singularity pull docker://google/glnexus:1.4.1). <strong>\"DeepVariantWGS.yml\"</strong> is the config file for running GLNexus.</p>\n<p><strong>\"nsgc.gdv.gln.cohort.clean.maf01maxmiss75diploid.beagle_sorted_filt.gt.vcf\"</strong> is the final genotype file described in the study.</p>", "distribution": [{"@type": "dcat:Distribution", "accessURL": "https://geodata.nal.usda.gov/geonetwork/srv/api/records/510fbd89-b712-4adb-96a8-4877f35f3619/formatters/xml", "conformsTo": "https://www.isotc211.org/2005/gmd", "format": "xml", "mediaType": "text/xml", "title": "Geodata ISO 19139 metadata"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/49384138", "format": "xlsx", "mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet", "title": "File S1.xlsx"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/49384195", "format": "vcf", "mediaType": "text/plain", "title": "nsgc.gdv.gln.cohort.clean.maf01maxmiss75diploid.beagle_sorted_filt.gt.vcf"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/49384273", "format": "xlsx", "mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet", "title": "File S2.xlsx"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/49384339", "format": "geojson", "mediaType": "application/json", "title": "Rahman_et_al_2024_Metadata.geojson"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/49384381", "format": "xlsx", "mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet", "title": "File S3.xlsx"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/49384528", "format": "sh", "mediaType": "text/x-shellscript", "title": "SBATCH_RUN_nsgc_deepvariant_glsnexus.sh"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/49384531", "format": "sh", "mediaType": "text/x-shellscript", "title": "RUN_nsgc_deepvariant_glsnexus.sh"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/49384543", "format": "yml", "mediaType": "text/plain", "title": "DeepVariantWGS.yml"}], "identifier": "10.15482/USDA.ADC/27095383.v1", "keyword": ["Adaptation", "Climate change", "Founder population", "Functional traits", "GWAS", "Landrace", "Oats", "QTL"], "license": "https://creativecommons.org/licenses/by/4.0/", "modified": "2025-11-21", "programCode": ["005:040"], "publisher": {"@type": "org:Organization", "name": "Agricultural Research Service"}, "spatial": "{\"type\": \"Polygon\", \"coordinates\": [[[-153.0, -42.65], [174.88571, -42.65], [174.88571, 65.0], [-153.0, 65.0], [-153.0, -42.65]]]}", "temporal": "2024-09-24/2024-09-24", "theme": ["geospatial"], "title": "Data from: A global assembly of landrace oat (<i>Avena sativa</i> L.) accessions is a discovery resource for adaptive variation, association mapping, and trait deployment"}