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 https://github.com/soybase/SoySNP-Names. SNP effects were predicted using SnpEff 3.0. Dataset also available at https://soybase.org/data/v2/Glycine/max/diversity/Wm82.gnm2.div.Valliyod... 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.