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

image of barley

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 (http://sift.jcvi.org/), PolyPhen2 (http://genetics.bwh.harvard.edu/pph2/), 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 https://github.com/MorrellLAB/BAD_Mutations.

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)

Dataset Info

These fields are compatible with DCAT, an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web.
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.
Product Type
Genome/Genetics Data
Temporal Coverage
University of Minnesota
Contact Name
Kono, Thomas J.Y.
Contact Email
Public Access Level
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, http://doi.org/10.13020/D65C7D.
Primary Article

Kono, T., Fu, F., Mohammadi, M., Hoffman, P., Liu, C., & Stupar, R. et al. (2016). The Role of Deleterious Substitutions in Crop Genomes. Molecular Biology And Evolution, 33(9), 2307-2317.

Methods Citation

Mascher, M., Richmond, T., Gerhardt, D., Himmelbach, A., Clissold, L., & Sampath, D. et al. (2013). Barley whole exome capture: a tool for genomic research in the genusHordeumand beyond. The Plant Journal, 76(3), 494-505.

Funding Source(s)
National Institute of Food and Agriculture
National Science Foundation
Dataset DOI (digital object identifier)
Modified Date
Release Date
Ag Data Commons Keywords: 
  • Genomics & Genetics
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