Ag Data Commons
42 files

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

posted on 2023-12-19, 14:30 authored by Yong-Qiang (Charles) An, Hengyou Zhang, Rick J. Meyer

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


USDA-ARS: 5070-21000-042-00-D

United Soybean Board: USB #2020-162-0202

Bayer CropScience: Appl. No


Data contact name

An, Yong-Qiang (Charles)

Data contact email


Ag Data Commons

Intended use

This data set maybe used to explore the genetic diversity found within soybean germplasm and to look directly at points of annotation within any given gene model

Use limitations

SNP calls and annotations are based on the soybean reference genome (G. max cv. Williams 82.a2 v1) from Phytozome v10

Temporal Extent Start Date


Temporal Extent End Date



  • Not specified

Geographic location - description

This data set derives from a genetically diverse, worldwide, collection of soybean accessions.

ISO Topic Category

  • biota
  • economy
  • farming

National Agricultural Library Thesaurus terms

nucleotide sequences; single nucleotide polymorphism; genes; models; soybeans; germplasm; landraces; cultivars; genotype

OMB Bureau Code

  • 005:18 - Agricultural Research Service

OMB Program Code

  • 005:040 - National Research

ARS National Program Number

  • 301

Pending citation

  • No

Public Access Level

  • Public

Preferred dataset citation

An, Yong-Qiang (Charles); Zhang, Hengyou; Meyer, Rick J. (2020). Data from: Development of a versatile resource from 1500 diverse genomes for post-genomics research. Ag Data Commons.

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