---
identifier: Wm82.gnm2.div.Liu_Shi_2025

provenance: "Data in this directory derives from the publication Liu, Shi et al., 2025, referenced below. Files in this present directory are derived, and may have changes, as noted below. The files here are held as part of the SoyBase and LegumeInfo projects, and are made available here for the purpose of reproducibility of analyses at these sites (e.g. gene family alignments and phylogenies, genome browsers, etc.) and for further use by researchers, as that research extends other analyses at the SoyBase and projects. If you are conducting research on large-scale data sets for this species, please consider retrieving the data from the primary repositories. If you use the data in the present directory, please 1) please cite the data appropriately - generally referring to the original publications for this data; and if you make use of any significant modifications in the files (noted below under Transformations where applicable), then please also cite the respective database project(s) related to this directory."

synopsis: Predicted SNP effects relative to genes in Williams 82 gnm2 (Wm82.a2.v1). 

scientific_name: Glycine max

taxid: 3847

scientific_name_abbrev: glyma

genotype:
  - Wm82 and 1,556 soybean whole-genome sequences

description: "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)."

original_file_creation_date: "2024-09-01"

local_file_creation_date: "2024-11-07"

dataset_release_date: "2024-11-07"

publication_title: Landscape of rare allelic variants in cultivated and wild soybean genomes

contributors: Liu Z, Shi XL, Yang Q, Li Y, Yang CY, Zhang MC, An YQ, Yan L. Song QJ

data_curators: Steven Cannon

public_access_level: private

license: Open

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)"