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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)

FieldValue
Tags
Modified
2019-08-05
Release Date
2018-06-06
Identifier
cf8a26e4-5b21-4b3d-8430-c191ded06cf9
Publisher
University of Minnesota
Temporal Coverage
January 1, 2013 to December 31, 2014
License
Contact Name
Kono, Thomas J.Y.
Contact Email
Public Access Level
Public