Data from: Genetic variation among 481 diverse soybean accessions

Metadata Updated: November 10, 2021

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. Dataset also available at https://soybase.org/data/v2/Glycine/max/diversity/Wm82.gnm2.div.Valliyod... 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, 2021

Metadata Source

Harvested from USDA JSON

Additional Metadata

Resource Type Dataset
Metadata Created Date November 10, 2020
Metadata Updated Date November 10, 2021
Publisher Agricultural Research Service
Unique Identifier Unknown
Maintainer
Identifier c816b299-60fd-47a4-8a6a-4ad1e7285daf
Data Last Modified 2021-10-27
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
Harvest Object Id 4ed57e6c-64ff-40f6-a2d0-170cd826b590
Harvest Source Id d3fafa34-0cb9-48f1-ab1d-5b5fdc783806
Harvest Source Title USDA JSON
License https://creativecommons.org/publicdomain/zero/1.0/
Program Code 005:040
Source Datajson Identifier True
Source Hash 67e9397de2ac95e74466855df877b04c6711fa4d
Source Schema Version 1.1

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