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Data from: Genetic variation among 481 diverse soybean accessions

posted on 2024-02-21, 22:10 authored by Babu Valliyodan, Anne V. Brown, Steven B. Cannon, Henry Nguyen

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 SNP effects were predicted using SnpEff 3.0.

Dataset also available at

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.

Resources in this dataset:

  • Resource Title: Data Dictionary.File Name: Data_Dictionary_USB481.csvResource Description: Provides the name of Data file with details of Data type, Description of data content, Correspondence to SoyBase Data Store File, and Size of file.

  • Resource Title: List_of_Accessions.txt.gz.File Name: glyma.Wm82.gnm2_.div_.Valliyodan_Brown_2021.USB481_list.txt.gzResource Description: Table containing the list of all the accessions that were re-sequenced and the metadata associated with each accession.

  • Resource Title: Alignment_used_for_Phylogenetic_trees.fna.gz.File Name: glyma.Wm82.gnm2_.div_.Valliyodan_Brown_2021.sampled_25Kpos.fna_.gzResource Description: Aligned SNP data for USB481 accessions, based on SNPs sampled at one SNP per 25kb

  • Resource Title: Phylogenetic_tree.nh.txt.gz.File Name: glyma.Wm82.gnm2_.div_.Valliyodan_Brown_2021.sampled_25Kpos.nh_.txt.gzResource Description: Phylogenetic tree (newick format) of SNP data for USB481 data, based on SNPs sampled at one SNP per 25kb

  • Resource Title: Phylogenetic_tree.pxml.txt.gz.File Name: glyma.Wm82.gnm2_.div_.Valliyodan_Brown_2021.sampled_25Kpos.pxml_.txt.gzResource Description: Phylogenetic tree (phyloxml format; colored) of SNP data for USB481 data, based on SNPs sampled at one SNP per 25kb

  • Resource Title: SNP_Effect_predictions.gff3.gz.File Name: glyma.Wm82.gnm2_.div_.Valliyodan_Brown_2021.snpEff.gff3_.gzResource Description: Output from snpEff program using the SNPs from the full USB481.vcf file as input.

  • Resource Title: Soja_SNP_calls.vcf.gz.File Name: glyma.Wm82.gnm2_.div_.Valliyodan_Brown_2021.Soja_.vcf.gzResource Description: Genotype information in vcf format for 45 Soja lines from USB-funded project.

  • Resource Title: Soy106.vcf.gz.File Name: glyma.Wm82.gnm2_.div_.Valliyodan_Brown_2021.Soy106.vcf.gzResource Description: Genotype information in VCF format for 106 accessions from USB-funded project; from Valliyodan et al Sci Rep 2016.

  • Resource Title: USB481_index.vcf.gz.tbi.File Name: glyma.Wm82.gnm2_.div_.Valliyodan_Brown_2021.USB481_list.txt.gzResource Description: Binary indexed USB481.vcf.gz produced using tabix.

  • Resource Title: USB-40x.vcf.gz.File Name: glyma.Wm82.gnm2_.div_.Valliyodan_Brown_2021.USB-40x.vcf.gzResource Description: Genotype information in VCF format for 46 accessions sequenced at 40x coverage from USB-funded project.

  • Resource Title: SnpEff_predictions_Gmax_Accessions.gff.gz.File Name: glyma.Wm82.gnm2_.div_.Valliyodan_Brown_2021.snpEff_Gmax.gff_.gzResource Description: SnpEff results in GFF format using the USB481_nosoja.vcf file as input.

  • Resource Title: SnpEff_predictions_Gsoja_Accessions.gff.gz.File Name: glyma.Wm82.gnm2_.div_.Valliyodan_Brown_2021.snpEff_Gsoja.gff_.gzResource Description: SnpEff output in GFF format using Soja_SNP_Calls.vcf.gz as an input.

  • Resource Title: USB-15x.vcf.gz.File Name: glyma.Wm82.gnm2_.div_.Valliyodan_Brown_2021.USB-15x.vcf.gzResource Description: Genotype information in VCF format for 284 accessions sequenced at 15x coverage from USB-funded project.

  • Resource Title: USB481.vcf.gz.File Name: glyma.Wm82.gnm2_.div_.Valliyodan_Brown_2021.USB481.vcf.gzResource Description: Genotype information in VCF format for all 481 accessions from USB-funded project
  • Title: USB481_nosoja.vcf.gz.File Name: glyma.Wm82.gnm2_.div_.Valliyodan_Brown_2021.USB481_nosoja.vcf.gzResource Description: Combined genotype information, in VCF format, for all USB lines excluding the Sjoa lines from USB funded project.


United Soybean Board: 1320-532-5615

Bayer CropScience

USDA-ARS: 5030-21000-069-00-D


Data contact name

Brown, Anne V.

Data contact email


Ag Data Commons

Intended use

To study genetic variation in diverse soybean accessions and can be used in future genome wide association studies.


  • Not specified

ISO Topic Category

  • biota
  • farming

National Agricultural Library Thesaurus terms

genetic variation; soybeans; genomics; single nucleotide polymorphism; data collection; haplotypes; algorithms; sequence analysis; Glycine max; Glycine soja

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

Valliyodan, Babu; Brown, Anne V.; Cannon, Steven B.; Nguyen, Henry (2020). Data from: Genetic variation among 481 diverse soybean accessions. Ag Data Commons.

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