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

Published by Agricultural Research Service | Department of Agriculture | Metadata Last Checked: January 27, 2026 | Last Modified: 2025-06-30
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.txtResource Description: Defines sample id's used in the vcf filesResource Title: Chr01.AnLab_1.5K.gtf.gz. File Name: Chr01.AnLab1.5K.gtf.gzResource Description: Chromosome 1 SNP annotationResource Title: Chr01.AnLab_1.5K.vcf.gz. File Name: Chr01.AnLab1.5K.vcf.gzResource Description: Chromosome 1 sample genotypesResource Title: Chr02.AnLab_1.5K.gtf.gz. File Name: Chr02.AnLab1.5K.gtf.gzResource Description: Chromosome 2 SNP annotationResource Title: Chr02.AnLab_1.5K.vcf.gz. File Name: Chr02.AnLab1.5K.vcf.gzResource Description: Chromosome 2 sample genotypesResource Title: Chr03.AnLab_1.5K.gtf.gz. File Name: Chr03.AnLab1.5K.gtf.gzResource Description: Chromosome 3 SNP annotationResource Title: Chr03.AnLab_1.5K.vcf.gz. File Name: Chr03.AnLab1.5K.vcf.gzResource Description: Chromosome 3 sample genotypesResource Title: Chr04.AnLab_1.5K.gtf.gz. File Name: Chr04.AnLab1.5K.gtf.gzResource Description: Chromosome 4 SNP annotationResource Title: Chr04.AnLab_1.5K.vcf.gz. File Name: Chr04.AnLab1.5K.vcf.gzResource Description: Chromosome 4 sample genotypesResource Title: Chr05.AnLab_1.5K.gtf.gz. File Name: Chr05.AnLab1.5K.gtf.gzResource Description: Chromosome 5 SNP annotationResource Title: Chr05.AnLab_1.5K.vcf.gz. File Name: Chr05.AnLab1.5K.vcf.gzResource Description: Chromosome 5 sample genotypesResource Title: Chr06.AnLab_1.5K.gtf.gz. File Name: Chr06.AnLab1.5K.gtf.gzResource Description: Chromosome 6 SNP annotationResource Title: Chr06.AnLab_1.5K.vcf.gz. File Name: Chr06.AnLab1.5K.vcf.gzResource Description: Chromosome 6 sample genotypesResource Title: Chr07.AnLab_1.5K.gtf.gz. File Name: Chr07.AnLab1.5K.gtf.gzResource Description: Chromosome 7 SNP annotationResource Title: Chr07.AnLab_1.5K.vcf.gz. File Name: Chr07.AnLab1.5K.vcf.gzResource Description: Chromosome 7 sample genotypesResource Title: Chr08.AnLab_1.5K.gtf.gz. File Name: Chr08.AnLab1.5K.gtf.gzResource Description: Chromosome 8 SNP annotationResource Title: Chr08.AnLab_1.5K.vcf.gz. File Name: Chr08.AnLab1.5K.vcf.gzResource Description: Chromosome 8 sample genotypesResource Title: Chr09.AnLab_1.5K.gtf.gz. File Name: Chr09.AnLab1.5K.gtf.gzResource Description: Chromosome 9 SNP annotationResource Title: Chr09.AnLab_1.5K.vcf.gz. File Name: Chr09.AnLab1.5K.vcf.gzResource Description: Chromosome 9 sample genotypesResource Title: Chr10.AnLab_1.5K.gtf.gz. File Name: Chr10.AnLab1.5K.gtf.gzResource Description: Chromosome 10 SNP annotationResource Title: Chr10.AnLab_1.5K.vcf.gz. File Name: Chr10.AnLab1.5K.vcf.gzResource Description: Chromosome 10 sample genotypesResource Title: Chr11.AnLab_1.5K.gtf.gz. File Name: Chr11.AnLab1.5K.gtf.gzResource Description: Chromosome 11 SNP annotationResource Title: Chr11.AnLab_1.5K.vcf.gz. File Name: Chr11.AnLab1.5K.vcf.gzResource Description: Chromosome 11 sample genotypesResource Title: Chr12.AnLab_1.5K.gtf.gz. File Name: Chr12.AnLab1.5K.gtf.gzResource Description: Chromosome 12 SNP annotationResource Title: Chr12.AnLab_1.5K.vcf.gz. File Name: Chr12.AnLab1.5K.vcf.gzResource Description: Chromosome 12 sample genotypesResource Title: Chr13.AnLab_1.5K.gtf.gz. File Name: Chr13.AnLab1.5K.gtf.gzResource Description: Chromosome 13 SNP annotationResource Title: Chr13.AnLab_1.5K.vcf.gz. File Name: Chr13.AnLab1.5K.vcf.gzResource Description: Chromosome 13 sample genotypesResource Title: Chr14.AnLab_1.5K.gtf.gz. File Name: Chr14.AnLab1.5K.gtf.gzResource Description: Chromosome 14 SNP annotationResource Title: Chr14.AnLab_1.5K.vcf.gz. File Name: Chr14.AnLab1.5K.vcf.gzResource Description: Chromosome 14 sample genotypesResource Title: Chr15.AnLab_1.5K.gtf.gz. File Name: Chr15.AnLab1.5K.gtf.gzResource Description: Chromosome 15 SNP annotationResource Title: Chr15.AnLab_1.5K.vcf.gz. File Name: Chr15.AnLab1.5K.vcf.gzResource Description: Chromosome 15 sample genotypesResource Title: Chr16.AnLab_1.5K.gtf.gz. File Name: Chr16.AnLab1.5K.gtf.gzResource Description: Chromosome 16 SNP annotationResource Title: Chr16.AnLab_1.5K.vcf.gz. File Name: Chr16.AnLab1.5K.vcf.gzResource Description: Chromosome 16 sample genotypesResource Title: Chr17.AnLab_1.5K.gtf.gz. File Name: Chr17.AnLab1.5K.gtf.gzResource Description: Chromosome 17 SNP annotationResource Title: Chr17.AnLab_1.5K.vcf.gz. File Name: Chr17.AnLab1.5K.vcf.gzResource Description: Chromosome 17 sample genotypesResource Title: Chr18.AnLab_1.5K.gtf.gz. File Name: Chr18.AnLab1.5K.gtf.gzResource Description: Chromosome 18 SNP annotationResource Title: Chr18.AnLab_1.5K.vcf.gz. File Name: Chr18.AnLab1.5K.vcf.gzResource Description: Chromosome 18 sample genotypesResource Title: Chr19.AnLab_1.5K.gtf.gz. File Name: Chr19.AnLab1.5K.gtf.gzResource Description: Chromosome 19 SNP annotationResource Title: Chr19.AnLab_1.5K.vcf.gz. File Name: Chr19.AnLab1.5K.vcf.gzResource Description: Chromosome 19 sample genotypesResource Title: Chr20.AnLab_1.5K.gtf.gz. File Name: Chr20.AnLab1.5K.gtf.gzResource Description: Chromosome 20 SNP annotationResource Title: Chr20.AnLab_1.5K.vcf.gz. File Name: Chr20.AnLab1.5K.vcf.gzResource Description: Chromosome 20 sample genotypesResource Title: Data_Directory.AnLab_1.5k.csv. File Name: Data_Directory.AnLab_1.5k.csvResource Description: This is the data directory for this data set

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Complete Metadata
@type dcat:Dataset
accessLevel public
bureauCode 
                                            [
  "005:18"
]
contactPoint 
                                            {
  "fn": "An, Yong-Qiang (Charles)",
  "hasEmail": "mailto:yong-qiang.an@usda.gov"
}
description <p>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". </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: AnLab_1.5K.SampleIDs.txt.</p> <p>File Name: AnLab_1.5K.SampleIDs.txt</p><p>Resource Description: Defines sample id's used in the vcf files</p></li><br><li><p>Resource Title: Chr01.AnLab_1.5K.gtf.gz.</p> <p>File Name: Chr01.AnLab<em>1.5K.gtf</em>.gz</p><p>Resource Description: Chromosome 1 SNP annotation</p></li><br><li><p>Resource Title: Chr01.AnLab_1.5K.vcf.gz.</p> <p>File Name: Chr01.AnLab<em>1.5K.vcf</em>.gz</p><p>Resource Description: Chromosome 1 sample genotypes</p></li><br><li><p>Resource Title: Chr02.AnLab_1.5K.gtf.gz.</p> <p>File Name: Chr02.AnLab<em>1.5K.gtf</em>.gz</p><p>Resource Description: Chromosome 2 SNP annotation</p></li><br><li><p>Resource Title: Chr02.AnLab_1.5K.vcf.gz.</p> <p>File Name: Chr02.AnLab<em>1.5K.vcf</em>.gz</p><p>Resource Description: Chromosome 2 sample genotypes</p></li><br><li><p>Resource Title: Chr03.AnLab_1.5K.gtf.gz.</p> <p>File Name: Chr03.AnLab<em>1.5K.gtf</em>.gz</p><p>Resource Description: Chromosome 3 SNP annotation</p></li><br><li><p>Resource Title: Chr03.AnLab_1.5K.vcf.gz.</p> <p>File Name: Chr03.AnLab<em>1.5K.vcf</em>.gz</p><p>Resource Description: Chromosome 3 sample genotypes</p></li><br><li><p>Resource Title: Chr04.AnLab_1.5K.gtf.gz.</p> <p>File Name: Chr04.AnLab<em>1.5K.gtf</em>.gz</p><p>Resource Description: Chromosome 4 SNP annotation</p></li><br><li><p>Resource Title: Chr04.AnLab_1.5K.vcf.gz.</p> <p>File Name: Chr04.AnLab<em>1.5K.vcf</em>.gz</p><p>Resource Description: Chromosome 4 sample genotypes</p></li><br><li><p>Resource Title: Chr05.AnLab_1.5K.gtf.gz.</p> <p>File Name: Chr05.AnLab<em>1.5K.gtf</em>.gz</p><p>Resource Description: Chromosome 5 SNP annotation</p></li><br><li><p>Resource Title: Chr05.AnLab_1.5K.vcf.gz.</p> <p>File Name: Chr05.AnLab<em>1.5K.vcf</em>.gz</p><p>Resource Description: Chromosome 5 sample genotypes</p></li><br><li><p>Resource Title: Chr06.AnLab_1.5K.gtf.gz.</p> <p>File Name: Chr06.AnLab<em>1.5K.gtf</em>.gz</p><p>Resource Description: Chromosome 6 SNP annotation</p></li><br><li><p>Resource Title: Chr06.AnLab_1.5K.vcf.gz.</p> <p>File Name: Chr06.AnLab<em>1.5K.vcf</em>.gz</p><p>Resource Description: Chromosome 6 sample genotypes</p></li><br><li><p>Resource Title: Chr07.AnLab_1.5K.gtf.gz.</p> <p>File Name: Chr07.AnLab<em>1.5K.gtf</em>.gz</p><p>Resource Description: Chromosome 7 SNP annotation</p></li><br><li><p>Resource Title: Chr07.AnLab_1.5K.vcf.gz.</p> <p>File Name: Chr07.AnLab<em>1.5K.vcf</em>.gz</p><p>Resource Description: Chromosome 7 sample genotypes</p></li><br><li><p>Resource Title: Chr08.AnLab_1.5K.gtf.gz.</p> <p>File Name: Chr08.AnLab<em>1.5K.gtf</em>.gz</p><p>Resource Description: Chromosome 8 SNP annotation</p></li><br><li><p>Resource Title: Chr08.AnLab_1.5K.vcf.gz.</p> <p>File Name: Chr08.AnLab<em>1.5K.vcf</em>.gz</p><p>Resource Description: Chromosome 8 sample genotypes</p></li><br><li><p>Resource Title: Chr09.AnLab_1.5K.gtf.gz.</p> <p>File Name: Chr09.AnLab<em>1.5K.gtf</em>.gz</p><p>Resource Description: Chromosome 9 SNP annotation</p></li><br><li><p>Resource Title: Chr09.AnLab_1.5K.vcf.gz.</p> <p>File Name: Chr09.AnLab<em>1.5K.vcf</em>.gz</p><p>Resource Description: Chromosome 9 sample genotypes</p></li><br><li><p>Resource Title: Chr10.AnLab_1.5K.gtf.gz.</p> <p>File Name: Chr10.AnLab<em>1.5K.gtf</em>.gz</p><p>Resource Description: Chromosome 10 SNP annotation</p></li><br><li><p>Resource Title: Chr10.AnLab_1.5K.vcf.gz.</p> <p>File Name: Chr10.AnLab<em>1.5K.vcf</em>.gz</p><p>Resource Description: Chromosome 10 sample genotypes</p></li><br><li><p>Resource Title: Chr11.AnLab_1.5K.gtf.gz.</p> <p>File Name: Chr11.AnLab<em>1.5K.gtf</em>.gz</p><p>Resource Description: Chromosome 11 SNP annotation</p></li><br><li><p>Resource Title: Chr11.AnLab_1.5K.vcf.gz.</p> <p>File Name: Chr11.AnLab<em>1.5K.vcf</em>.gz</p><p>Resource Description: Chromosome 11 sample genotypes</p></li><br><li><p>Resource Title: Chr12.AnLab_1.5K.gtf.gz.</p> <p>File Name: Chr12.AnLab<em>1.5K.gtf</em>.gz</p><p>Resource Description: Chromosome 12 SNP annotation</p></li><br><li><p>Resource Title: Chr12.AnLab_1.5K.vcf.gz.</p> <p>File Name: Chr12.AnLab<em>1.5K.vcf</em>.gz</p><p>Resource Description: Chromosome 12 sample genotypes</p></li><br><li><p>Resource Title: Chr13.AnLab_1.5K.gtf.gz.</p> <p>File Name: Chr13.AnLab<em>1.5K.gtf</em>.gz</p><p>Resource Description: Chromosome 13 SNP annotation</p></li><br><li><p>Resource Title: Chr13.AnLab_1.5K.vcf.gz.</p> <p>File Name: Chr13.AnLab<em>1.5K.vcf</em>.gz</p><p>Resource Description: Chromosome 13 sample genotypes</p></li><br><li><p>Resource Title: Chr14.AnLab_1.5K.gtf.gz.</p> <p>File Name: Chr14.AnLab<em>1.5K.gtf</em>.gz</p><p>Resource Description: Chromosome 14 SNP annotation</p></li><br><li><p>Resource Title: Chr14.AnLab_1.5K.vcf.gz.</p> <p>File Name: Chr14.AnLab<em>1.5K.vcf</em>.gz</p><p>Resource Description: Chromosome 14 sample genotypes</p></li><br><li><p>Resource Title: Chr15.AnLab_1.5K.gtf.gz.</p> <p>File Name: Chr15.AnLab<em>1.5K.gtf</em>.gz</p><p>Resource Description: Chromosome 15 SNP annotation</p></li><br><li><p>Resource Title: Chr15.AnLab_1.5K.vcf.gz.</p> <p>File Name: Chr15.AnLab<em>1.5K.vcf</em>.gz</p><p>Resource Description: Chromosome 15 sample genotypes</p></li><br><li><p>Resource Title: Chr16.AnLab_1.5K.gtf.gz.</p> <p>File Name: Chr16.AnLab<em>1.5K.gtf</em>.gz</p><p>Resource Description: Chromosome 16 SNP annotation</p></li><br><li><p>Resource Title: Chr16.AnLab_1.5K.vcf.gz.</p> <p>File Name: Chr16.AnLab<em>1.5K.vcf</em>.gz</p><p>Resource Description: Chromosome 16 sample genotypes</p></li><br><li><p>Resource Title: Chr17.AnLab_1.5K.gtf.gz.</p> <p>File Name: Chr17.AnLab<em>1.5K.gtf</em>.gz</p><p>Resource Description: Chromosome 17 SNP annotation</p></li><br><li><p>Resource Title: Chr17.AnLab_1.5K.vcf.gz.</p> <p>File Name: Chr17.AnLab<em>1.5K.vcf</em>.gz</p><p>Resource Description: Chromosome 17 sample genotypes</p></li><br><li><p>Resource Title: Chr18.AnLab_1.5K.gtf.gz.</p> <p>File Name: Chr18.AnLab<em>1.5K.gtf</em>.gz</p><p>Resource Description: Chromosome 18 SNP annotation</p></li><br><li><p>Resource Title: Chr18.AnLab_1.5K.vcf.gz.</p> <p>File Name: Chr18.AnLab<em>1.5K.vcf</em>.gz</p><p>Resource Description: Chromosome 18 sample genotypes</p></li><br><li><p>Resource Title: Chr19.AnLab_1.5K.gtf.gz.</p> <p>File Name: Chr19.AnLab<em>1.5K.gtf</em>.gz</p><p>Resource Description: Chromosome 19 SNP annotation</p></li><br><li><p>Resource Title: Chr19.AnLab_1.5K.vcf.gz.</p> <p>File Name: Chr19.AnLab<em>1.5K.vcf</em>.gz</p><p>Resource Description: Chromosome 19 sample genotypes</p></li><br><li><p>Resource Title: Chr20.AnLab_1.5K.gtf.gz.</p> <p>File Name: Chr20.AnLab<em>1.5K.gtf</em>.gz</p><p>Resource Description: Chromosome 20 SNP annotation</p></li><br><li><p>Resource Title: Chr20.AnLab_1.5K.vcf.gz.</p> <p>File Name: Chr20.AnLab<em>1.5K.vcf</em>.gz</p><p>Resource Description: Chromosome 20 sample genotypes</p></li><br><li><p>Resource Title: Data_Directory.AnLab_1.5k.csv.</p> <p>File Name: Data_Directory.AnLab_1.5k.csv</p><p>Resource Description: This is the data directory for this data set</p></li></ul><p></p>
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identifier 10.15482/USDA.ADC/1519167
keyword 
                                            [
  "ARS",
  "GRIN",
  "NP301",
  "SNPs",
  "data.gov",
  "genetic diversity",
  "genomics",
  "linkage disequilibrium",
  "soybean",
  "whole genome resequencing"
]
license https://www.usa.gov/publicdomain/label/1.0/
modified 2025-06-30
programCode 
                                            [
  "005:040"
]
publisher 
                                            {
  "name": "Agricultural Research Service",
  "@type": "org:Organization"
}
temporal 2014-06-09/2018-08-21
title Data from: Development of a versatile resource from 1500 diverse genomes for post-genomics research

data.gov

An official website of the GSA's Technology Transformation Services

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