SNP Functional Annotation Dataset Description

A total of 1,556 soybean whole-genome sequences mostly deposited
in SRA NCBI and generated by the Soybean Genome Improvement Laboratory
at USDA-ARS, Beltsville, MD, USA were analyzed, and SNPs were
identified (Zhang, H., Jiang, H., Hu, Z., Song, Q., & An, Y.C.
(2022) BMC Genomics, 23, 250). We converted the SNP VCF files to
SNP allele files and eliminated SNPs with missing and heterozygosity
greater than 30%, with one or tri-alleles only. To reduce false SNP
calling, SNPs with the number of accessions containing minor alleles
less than or equal to 2 across 1,556 cultivated and wild soybeans
were eliminated. SNP functional annotation was performed using
Annovar based on the whole-genome sequence assembly Wm82a2v1 and
its gene IDs. The input variant file included the following columns:
variant chromosome IDs, variant physical positions, reference genome
variant allele, alternate variant allele. The annotation file
contains the following columns: chromosome, SNP position, reference
allele, alternative allele, G. max minor allele, G. soja minor
allele, mutation type, gene ID in Wm82a2v1, and the position and
function of SNPs in the gene (see HGVS (Human Genome Variant Society)
site https://hgvs-nomenclature.org/stable/recommendations/general/
for the nomenclature describing genetic variants).

For details, please refer to the following citation:

Liu Z, Shi XL, Yang Q, Li Y, Yang CY, Zhang MC, An YQ, Yan L. Song
QJ. 2025. Landscape of rare allelic variants in cultivated and wild
soybean genomes (in review)