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    • Data from: Development of a versatile resource from 1500 diverse genomes for post-genomics research

    Metadata Updated: July 11, 2025

    This data set contains 32 million annotated SNPs having an average SNP density of 30 SNPs per kb and 12 non-synonymous SNPs per gene model. These SNPs were identified from a genetically diverse, worldwide, collection of soybean germplasm representing wild, landrace, and improved cultivars. A combination of new and publicly available re-sequencing data was used in this analysis. The accession genotypes and their annotations are described in the manuscript titled: "Analysis and characterization of 1500 diverse genome sequences as a versatile resource for post-genomics research".


    Resources in this dataset:


    • Resource Title: AnLab_1.5K.SampleIDs.txt.

      File Name: AnLab_1.5K.SampleIDs.txt

      Resource Description: Defines sample id's used in the vcf files


    • Resource Title: Chr01.AnLab_1.5K.gtf.gz.

      File Name: Chr01.AnLab1.5K.gtf.gz

      Resource Description: Chromosome 1 SNP annotation


    • Resource Title: Chr01.AnLab_1.5K.vcf.gz.

      File Name: Chr01.AnLab1.5K.vcf.gz

      Resource Description: Chromosome 1 sample genotypes


    • Resource Title: Chr02.AnLab_1.5K.gtf.gz.

      File Name: Chr02.AnLab1.5K.gtf.gz

      Resource Description: Chromosome 2 SNP annotation


    • Resource Title: Chr02.AnLab_1.5K.vcf.gz.

      File Name: Chr02.AnLab1.5K.vcf.gz

      Resource Description: Chromosome 2 sample genotypes


    • Resource Title: Chr03.AnLab_1.5K.gtf.gz.

      File Name: Chr03.AnLab1.5K.gtf.gz

      Resource Description: Chromosome 3 SNP annotation


    • Resource Title: Chr03.AnLab_1.5K.vcf.gz.

      File Name: Chr03.AnLab1.5K.vcf.gz

      Resource Description: Chromosome 3 sample genotypes


    • Resource Title: Chr04.AnLab_1.5K.gtf.gz.

      File Name: Chr04.AnLab1.5K.gtf.gz

      Resource Description: Chromosome 4 SNP annotation


    • Resource Title: Chr04.AnLab_1.5K.vcf.gz.

      File Name: Chr04.AnLab1.5K.vcf.gz

      Resource Description: Chromosome 4 sample genotypes


    • Resource Title: Chr05.AnLab_1.5K.gtf.gz.

      File Name: Chr05.AnLab1.5K.gtf.gz

      Resource Description: Chromosome 5 SNP annotation


    • Resource Title: Chr05.AnLab_1.5K.vcf.gz.

      File Name: Chr05.AnLab1.5K.vcf.gz

      Resource Description: Chromosome 5 sample genotypes


    • Resource Title: Chr06.AnLab_1.5K.gtf.gz.

      File Name: Chr06.AnLab1.5K.gtf.gz

      Resource Description: Chromosome 6 SNP annotation


    • Resource Title: Chr06.AnLab_1.5K.vcf.gz.

      File Name: Chr06.AnLab1.5K.vcf.gz

      Resource Description: Chromosome 6 sample genotypes


    • Resource Title: Chr07.AnLab_1.5K.gtf.gz.

      File Name: Chr07.AnLab1.5K.gtf.gz

      Resource Description: Chromosome 7 SNP annotation


    • Resource Title: Chr07.AnLab_1.5K.vcf.gz.

      File Name: Chr07.AnLab1.5K.vcf.gz

      Resource Description: Chromosome 7 sample genotypes


    • Resource Title: Chr08.AnLab_1.5K.gtf.gz.

      File Name: Chr08.AnLab1.5K.gtf.gz

      Resource Description: Chromosome 8 SNP annotation


    • Resource Title: Chr08.AnLab_1.5K.vcf.gz.

      File Name: Chr08.AnLab1.5K.vcf.gz

      Resource Description: Chromosome 8 sample genotypes


    • Resource Title: Chr09.AnLab_1.5K.gtf.gz.

      File Name: Chr09.AnLab1.5K.gtf.gz

      Resource Description: Chromosome 9 SNP annotation


    • Resource Title: Chr09.AnLab_1.5K.vcf.gz.

      File Name: Chr09.AnLab1.5K.vcf.gz

      Resource Description: Chromosome 9 sample genotypes


    • Resource Title: Chr10.AnLab_1.5K.gtf.gz.

      File Name: Chr10.AnLab1.5K.gtf.gz

      Resource Description: Chromosome 10 SNP annotation


    • Resource Title: Chr10.AnLab_1.5K.vcf.gz.

      File Name: Chr10.AnLab1.5K.vcf.gz

      Resource Description: Chromosome 10 sample genotypes


    • Resource Title: Chr11.AnLab_1.5K.gtf.gz.

      File Name: Chr11.AnLab1.5K.gtf.gz

      Resource Description: Chromosome 11 SNP annotation


    • Resource Title: Chr11.AnLab_1.5K.vcf.gz.

      File Name: Chr11.AnLab1.5K.vcf.gz

      Resource Description: Chromosome 11 sample genotypes


    • Resource Title: Chr12.AnLab_1.5K.gtf.gz.

      File Name: Chr12.AnLab1.5K.gtf.gz

      Resource Description: Chromosome 12 SNP annotation


    • Resource Title: Chr12.AnLab_1.5K.vcf.gz.

      File Name: Chr12.AnLab1.5K.vcf.gz

      Resource Description: Chromosome 12 sample genotypes


    • Resource Title: Chr13.AnLab_1.5K.gtf.gz.

      File Name: Chr13.AnLab1.5K.gtf.gz

      Resource Description: Chromosome 13 SNP annotation


    • Resource Title: Chr13.AnLab_1.5K.vcf.gz.

      File Name: Chr13.AnLab1.5K.vcf.gz

      Resource Description: Chromosome 13 sample genotypes


    • Resource Title: Chr14.AnLab_1.5K.gtf.gz.

      File Name: Chr14.AnLab1.5K.gtf.gz

      Resource Description: Chromosome 14 SNP annotation


    • Resource Title: Chr14.AnLab_1.5K.vcf.gz.

      File Name: Chr14.AnLab1.5K.vcf.gz

      Resource Description: Chromosome 14 sample genotypes


    • Resource Title: Chr15.AnLab_1.5K.gtf.gz.

      File Name: Chr15.AnLab1.5K.gtf.gz

      Resource Description: Chromosome 15 SNP annotation


    • Resource Title: Chr15.AnLab_1.5K.vcf.gz.

      File Name: Chr15.AnLab1.5K.vcf.gz

      Resource Description: Chromosome 15 sample genotypes


    • Resource Title: Chr16.AnLab_1.5K.gtf.gz.

      File Name: Chr16.AnLab1.5K.gtf.gz

      Resource Description: Chromosome 16 SNP annotation


    • Resource Title: Chr16.AnLab_1.5K.vcf.gz.

      File Name: Chr16.AnLab1.5K.vcf.gz

      Resource Description: Chromosome 16 sample genotypes


    • Resource Title: Chr17.AnLab_1.5K.gtf.gz.

      File Name: Chr17.AnLab1.5K.gtf.gz

      Resource Description: Chromosome 17 SNP annotation


    • Resource Title: Chr17.AnLab_1.5K.vcf.gz.

      File Name: Chr17.AnLab1.5K.vcf.gz

      Resource Description: Chromosome 17 sample genotypes


    • Resource Title: Chr18.AnLab_1.5K.gtf.gz.

      File Name: Chr18.AnLab1.5K.gtf.gz

      Resource Description: Chromosome 18 SNP annotation


    • Resource Title: Chr18.AnLab_1.5K.vcf.gz.

      File Name: Chr18.AnLab1.5K.vcf.gz

      Resource Description: Chromosome 18 sample genotypes


    • Resource Title: Chr19.AnLab_1.5K.gtf.gz.

      File Name: Chr19.AnLab1.5K.gtf.gz

      Resource Description: Chromosome 19 SNP annotation


    • Resource Title: Chr19.AnLab_1.5K.vcf.gz.

      File Name: Chr19.AnLab1.5K.vcf.gz

      Resource Description: Chromosome 19 sample genotypes


    • Resource Title: Chr20.AnLab_1.5K.gtf.gz.

      File Name: Chr20.AnLab1.5K.gtf.gz

      Resource Description: Chromosome 20 SNP annotation


    • Resource Title: Chr20.AnLab_1.5K.vcf.gz.

      File Name: Chr20.AnLab1.5K.vcf.gz

      Resource Description: Chromosome 20 sample genotypes


    • Resource Title: Data_Directory.AnLab_1.5k.csv.

      File Name: Data_Directory.AnLab_1.5k.csv

      Resource Description: This is the data directory for this data set

    Access & Use Information

    Public: This dataset is intended for public access and use. License: us-pd

    Downloads & Resources

    Dates

    Metadata Created Date March 30, 2024
    Metadata Updated Date July 11, 2025

    Metadata Source

    Harvested from USDA JSON

    Other Data Resources

    Additional Metadata

    Resource Type Dataset
    Metadata Created Date March 30, 2024
    Metadata Updated Date July 11, 2025
    Publisher Agricultural Research Service
    Maintainer
    Identifier 10.15482/USDA.ADC/1519167
    Data Last Modified 2025-06-30
    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 479814a0-cbb6-4e56-9ea4-77689c73c7a0
    Harvest Source Id d3fafa34-0cb9-48f1-ab1d-5b5fdc783806
    Harvest Source Title USDA JSON
    License https://www.usa.gov/publicdomain/label/1.0/
    Program Code 005:040
    Source Datajson Identifier True
    Source Hash 46e0c4c8dd73ba3491bee03d82bad420e8b87c8035042175b67d42712c09b103
    Source Schema Version 1.1
    Temporal 2014-06-09/2018-08-21

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