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)
Gzipped variant calling of barley SNPs
Gzipped variant calling of soybean SNPs
Format and Info lines from header of Barley variant calls file
Format and Info lines from header of Soybean variant calls file
|Release Date|| |
University of Minnesota
|Temporal Coverage|| |
January 1, 2013 to December 31, 2014
|Contact Name|| |
Kono, Thomas J.Y.
|Public Access Level|| |