Data From: Development Of A Versatile Resource From 1500 Diverse Genomes For Post-genomics Research

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.AnLab 1.5K.gtf.gz

Resource Description: Chromosome 1 SNP annotation

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

File Name: Chr01.AnLab 1.5K.vcf.gz

Resource Description: Chromosome 1 sample genotypes

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

File Name: Chr02.AnLab 1.5K.gtf.gz

Resource Description: Chromosome 2 SNP annotation

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

File Name: Chr02.AnLab 1.5K.vcf.gz

Resource Description: Chromosome 2 sample genotypes

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

File Name: Chr03.AnLab 1.5K.gtf.gz

Resource Description: Chromosome 3 SNP annotation

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

File Name: Chr03.AnLab 1.5K.vcf.gz

Resource Description: Chromosome 3 sample genotypes

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

File Name: Chr04.AnLab 1.5K.gtf.gz

Resource Description: Chromosome 4 SNP annotation

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

File Name: Chr04.AnLab 1.5K.vcf.gz

Resource Description: Chromosome 4 sample genotypes

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

File Name: Chr05.AnLab 1.5K.gtf.gz

Resource Description: Chromosome 5 SNP annotation

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

File Name: Chr05.AnLab 1.5K.vcf.gz

Resource Description: Chromosome 5 sample genotypes

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

File Name: Chr06.AnLab 1.5K.gtf.gz

Resource Description: Chromosome 6 SNP annotation

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

File Name: Chr06.AnLab 1.5K.vcf.gz

Resource Description: Chromosome 6 sample genotypes

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

File Name: Chr07.AnLab 1.5K.gtf.gz

Resource Description: Chromosome 7 SNP annotation

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

File Name: Chr07.AnLab 1.5K.vcf.gz

Resource Description: Chromosome 7 sample genotypes

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

File Name: Chr08.AnLab 1.5K.gtf.gz

Resource Description: Chromosome 8 SNP annotation

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

File Name: Chr08.AnLab 1.5K.vcf.gz

Resource Description: Chromosome 8 sample genotypes

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

File Name: Chr09.AnLab 1.5K.gtf.gz

Resource Description: Chromosome 9 SNP annotation

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

File Name: Chr09.AnLab 1.5K.vcf.gz

Resource Description: Chromosome 9 sample genotypes

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

File Name: Chr10.AnLab 1.5K.gtf.gz

Resource Description: Chromosome 10 SNP annotation

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

File Name: Chr10.AnLab 1.5K.vcf.gz

Resource Description: Chromosome 10 sample genotypes

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

File Name: Chr11.AnLab 1.5K.gtf.gz

Resource Description: Chromosome 11 SNP annotation

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

File Name: Chr11.AnLab 1.5K.vcf.gz

Resource Description: Chromosome 11 sample genotypes

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

File Name: Chr12.AnLab 1.5K.gtf.gz

Resource Description: Chromosome 12 SNP annotation

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

File Name: Chr12.AnLab 1.5K.vcf.gz

Resource Description: Chromosome 12 sample genotypes

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

File Name: Chr13.AnLab 1.5K.gtf.gz

Resource Description: Chromosome 13 SNP annotation

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

File Name: Chr13.AnLab 1.5K.vcf.gz

Resource Description: Chromosome 13 sample genotypes

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

File Name: Chr14.AnLab 1.5K.gtf.gz

Resource Description: Chromosome 14 SNP annotation

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

File Name: Chr14.AnLab 1.5K.vcf.gz

Resource Description: Chromosome 14 sample genotypes

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

File Name: Chr15.AnLab 1.5K.gtf.gz

Resource Description: Chromosome 15 SNP annotation

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

File Name: Chr15.AnLab 1.5K.vcf.gz

Resource Description: Chromosome 15 sample genotypes

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

File Name: Chr16.AnLab 1.5K.gtf.gz

Resource Description: Chromosome 16 SNP annotation

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

File Name: Chr16.AnLab 1.5K.vcf.gz

Resource Description: Chromosome 16 sample genotypes

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

File Name: Chr17.AnLab 1.5K.gtf.gz

Resource Description: Chromosome 17 SNP annotation

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

File Name: Chr17.AnLab 1.5K.vcf.gz

Resource Description: Chromosome 17 sample genotypes

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

File Name: Chr18.AnLab 1.5K.gtf.gz

Resource Description: Chromosome 18 SNP annotation

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

File Name: Chr18.AnLab 1.5K.vcf.gz

Resource Description: Chromosome 18 sample genotypes

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

File Name: Chr19.AnLab 1.5K.gtf.gz

Resource Description: Chromosome 19 SNP annotation

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

File Name: Chr19.AnLab 1.5K.vcf.gz

Resource Description: Chromosome 19 sample genotypes

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

File Name: Chr20.AnLab 1.5K.gtf.gz

Resource Description: Chromosome 20 SNP annotation

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

File Name: Chr20.AnLab 1.5K.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
Organization: Department of Agriculture
Organization URL: https://catalog.data.gov/organization/usda
Last updated: 2025-06-30
Tags: ARS, GRIN, NP301, SNPs, data.gov, genetic diversity, genomics, linkage disequilibrium, soybean, whole genome resequencing