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    • 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

    Metadata Updated: June 5, 2025

    Oat Landrace Diversity (OLD) Panel phenotypes, genotypes, and metadata from: Rahman et al. (2024) "A global assembly of landrace oat (Avena sativa L.) accessions is a discovery resource for adaptive variation, association mapping, and trait deployment". "File S1" and "File S2" include population metadata and phenotypic (environmental) data used in association mapping, of which mapping results are listed in "File S3". "Rahman_et_al_2024_Metadata.geojson" is geographical information of OLD Panel accessions surveyed in this study. "SBATCH_RUN_nsgc_deepvariant_glsnexus.sh" and "RUN_nsgc_deepvariant_glsnexus.sh" 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). "DeepVariantWGS.yml" is the config file for running GLNexus. "nsgc.gdv.gln.cohort.clean.maf01maxmiss75diploid.beagle_sorted_filt.gt.vcf" is the final genotype file described in the study.

    Access & Use Information

    Public: This dataset is intended for public access and use. License: Creative Commons Attribution

    Downloads & Resources

    Dates

    Metadata Created Date November 2, 2024
    Metadata Updated Date June 5, 2025

    Metadata Source

    Harvested from USDA JSON

    Other Data Resources

    Additional Metadata

    Resource Type Dataset
    Metadata Created Date November 2, 2024
    Metadata Updated Date June 5, 2025
    Publisher Agricultural Research Service
    Maintainer
    Identifier 10.15482/USDA.ADC/27095383.v1
    Data Last Modified 2025-05-08
    Category geospatial
    Public Access Level public
    Bureau Code 005:18
    Metadata Context https://project-open-data.cio.gov/v1.1/schema/catalog.jsonld
    Schema Version https://project-open-data.cio.gov/v1.1/schema
    Catalog Describedby https://project-open-data.cio.gov/v1.1/schema/catalog.json
    Harvest Object Id 3f55ddce-d207-4460-8555-98c7662a2c11
    Harvest Source Id d3fafa34-0cb9-48f1-ab1d-5b5fdc783806
    Harvest Source Title USDA JSON
    License https://creativecommons.org/licenses/by/4.0/
    Metadata Type geospatial
    Old Spatial {"type": "Polygon", "coordinates": -153.0, -42.65, 174.88571, -42.65, 174.88571, 65.0, -153.0, 65.0, -153.0, -42.65}
    Program Code 005:040
    Source Datajson Identifier True
    Source Hash c050e8236f07c4ed8eb541c64660ed4d8b374702d60d8b10c43591af60cefb35
    Source Schema Version 1.1
    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

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