Ag Data Commons

File(s) stored somewhere else

Please note: Linked content is NOT stored on Ag Data Commons and we can't guarantee its availability, quality, security or accept any liability.

Variants from "The role of deleterious substitutions in crop genomes"

posted on 2024-02-13, 13:06 authored by Thomas J.Y. Kono, Fengli Fu, Mohsen Mohammadi, Paul J. Hoffman, Chaochih Liu, Robert M. Stupar, Kevin P. Smith, Peter Tiffin, Justin C. Fay, Peter L. Morrell

SNP calls in protein coding regions were obtained from 15 barley and 8 soybean lines. Non synonymous SNPs were predicted to be deleterious or not using three approaches.

There are two gzipped VCF (variant call format) files with variant calls for barley and soybean. A total of 652,797 SNPs were identified in the barley lines, which consisted of 13 cultivars and 2 wild accessions. For soybean, 7 cultivars and 1 wild accession were used, and 586,102 SNPs were called. Whether a variant is deleterious or not was determined using SIFT (, PolyPhen2 (, and a likelihood ratio test of sequence conservation. Raw reads are available through the SRA accession numbers in Table S1 of Kono et al. 2016. The code used for this research, BAD_Mutations, is open source and freely available at

Sponsorship: USDA NIFA National Needs Fellowship (Appropriation No. 5430-21000-006-00D); MnDrive 2014 Food Security Fellowship; Minnesota Agricultural Experiment Station Variety Development fund; United Soybean Board; U.S. NSF Plant Genome Program (BDI-1339393)

Resources in this dataset:


USDA-NIFA: 5430-21000-006-00D

National Science Foundation: BDI-1339393


Data contact name

Kono, Thomas J.Y.

Data contact email


University of Minnesota

Temporal Extent Start Date


Temporal Extent End Date



  • Not specified

Geographic Coverage


ISO Topic Category

  • biota
  • farming

National Agricultural Library Thesaurus terms

single nucleotide polymorphism; open reading frames; barley; soybeans; cultivars; germplasm conservation; mutation; bioinformatics

Pending citation

  • No

Public Access Level

  • Public

Preferred dataset citation

Kono, Thomas J Y; Fu, Fengli; Mohammadi, Mohsen; Hoffman, Paul J; Liu, Chaochih; Stupar, Robert M; Smith, Kevin P; Tiffin, Peter; Fay, Justin C; Morrell, Peter L. (2016). Variants from "The role of deleterious substitutions in crop genomes". Retrieved from the Data Repository for the University of Minnesota,

Usage metrics




    Ref. manager