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  • Data from: Genetic variation among 481 diverse soybean accessions

    Metadata Updated: November 10, 2020

    This data is from the manuscript titled: "Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing". SNP calls were obtained from resequencing 481 diverse soybean lines comprising 52 wild (Glycine soja) and 429 cultivated (Glycine max). This dataset contains 6 gzipped VCF (Variant Call Format) files with variant calls for all 481 USB accessions, all G. max accessions, G. soja accessions, accessions sequenced at 15x coverage, accessions sequenced at 40x coverage, and 106 accessions re-sequenced from a previous study (Valliyodan et al. 2016). SNPs were called using the Haplotype caller algorithm from the Genome Analysis Toolkit (GATK) version gatk-2.5-2-gf57256b. A total of 7.8 million SNPs were identified between the 481 re-sequenced accessions. SNPs were assigned IDs using the script "assign_name.awk" available at https://github.com/soybase/SoySNP-Names. SNP effects were predicted using SnpEff 3.0. Funding support provided by the United Soybean Board for the large-scale sequencing of soybean genomes (project #1320-532-5615), Bayer (previously Monsanto and Bayer), and Corteva (previously Dow AgroSciences), with in-kind support for analysis from USDA Agricultural Research Service project 5030-21000-069-00-D.

    Access & Use Information

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

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    Dates

    Metadata Created Date November 10, 2020
    Metadata Updated Date November 10, 2020

    Metadata Source

    Harvested from USDA JSON

    Additional Metadata

    Resource Type Dataset
    Metadata Created Date November 10, 2020
    Metadata Updated Date November 10, 2020
    Publisher Agricultural Research Service
    Unique Identifier Unknown
    Maintainer
    Identifier c816b299-60fd-47a4-8a6a-4ad1e7285daf
    Data Last Modified 2020-09-03
    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
    Data Dictionary https://data.nal.usda.gov/dataset/data-genetic-variation-among-481-diverse-soybean-accessions/resource/dcd60c82-ae7d-4514-9d79-66fdaa7e5a57
    License https://creativecommons.org/publicdomain/zero/1.0/
    Program Code 005:040
    Source Datajson Identifier True
    Source Hash 85f4f399ae82d7f67794c402843e5a55b44ccef4
    Source Schema Version 1.1

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