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)
Format and Info lines from header of Soybean variant calls file
Format and Info lines from header of Barley variant calls file
Gzipped variant calling of soybean SNPs
Gzipped variant calling of barley SNPs
Dataset InfoThese fields are compatible with DCAT, an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web.
University of Minnesota
Kono, Thomas J.Y.
|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.
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.
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.
National Institute of Food and Agriculture
National Science Foundation
|Dataset DOI (digital object identifier)|
- Genomics & Genetics