Barley Exome Diversity

Published: 28 October 2019| Version 1 | DOI: 10.17632/bbv2mdxwcr.1
Contributors:
Peter Civan,
Konstantina Drosou

Description

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)

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