Barley Exome Diversity

These are the data sets produced and analyzed by P. Civáň, K. Drosou, D. Armisen-Gimenez, W. Duchemin, J. Salse and T.A. Brown as part of the ADAPT project (European Research Council grant 339941 awarded to T.A. Brown). 320 exome-capture libraries from wild and cultivated barley were mapped onto the pseudomolecule-level assembly of the cultivar Morex. Variants within annotated genes were scored by GATK.
Manuscript under preparation (Oct. 2019).
Contents:
(i) base.vcf.gz
produced from the complete data set by removing indels, removing sites with ExcessHet>3, removing sites with >10% missing data
(ii) core.vcf.gz
produced from the base data set by LD pruning (which also removed multiallelic SNPs)
(iii) base_annotated.csv
produced from the base data set by adding 9 additional columns:
Feature (UTR5, UTR3, CDS, Intron)
REFCOD (reference codon)
ALTCOD (alternative codon[s])
REFAA (reference amino acid)
ALTAA (alternative amino acid[s])
SYNONYMOUS (S, N)
IEJ (intron-exon junction - [1, 2, 3, 4 - the four sites surrounding an intron-exon junction; 5 - other])
TRANSCRIPT (160517 annotation)