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

<p>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. </p> <p>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 (<a href="http://sift.jcvi.org/">http://sift.jcvi.org/</a>), PolyPhen2 (<a href="http://genetics.bwh.harvard.edu/pph2/">http://genetics.bwh.harvard.edu/pph2/</a>), 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 <a href="https://github.com/MorrellLAB/BAD_Mutations">https://github.com/MorrellLAB/BAD_Mutations</a>.</p> <p>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) </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Link to DRUM catalog record.</p> <p>File Name: Web Page, url: <a href="https://conservancy.umn.edu/handle/11299/181502">https://conservancy.umn.edu/handle/11299/181502</a> </p></li></ul><p></p>