Original Genotyping files can be downloaded from www.triticeaetoolbox.org.
Alias_CAPname_Xrefnames.txt: Alias for each sample in the data set. Alias represent the program to which each accession belong, and a numeric count of samples within a breeding program
samples_information.txt: Has the basic information for each sample, easy to use for analysis
Sample_information_FULL.csv: All samples' information downloaded from T3 website. I modified it by adding my new sample assigination (Alias) and changing the 29 BushAg Internation accessions' program assignation from "BA" to "BAI"
Barley_NorthAm_QC_AB_no_duplicates_or.txt (and Barley_NorthAm_QC_ACTG_no_duplicates_or.txt): Genotype file (for genotypes and nucleotides) after QC controling for >25% missingness, >6.25% heterozygosity, duplicated individuals and missing information (row type, growth habit) and removal of single samples representing a population. from this population. SNPs are sorted by their genetic map position according to Munoz et al 2011. Total individuals 3,613 x 2,542 SNPs
Barley_Annotations.txt : SNP annotations using SNP contextual sequences compared to a barley sequence to find their position, gene location, state of the variant (synonymous, non-synonymous, coding, non-coding). We used SNPmeta (Kono et al., 2014) to obtain this information.
Fang_et_al_TableS3.txt: From Fang et al 2014, we got H.Bulbosum states to be used as ancestral states.
GeneticMap_T3_020315.txt: BOPA SNPs genetic map (Munoz et. al., 2011) downloaded from T3 for 2,994 SNPs.
List_NIL_duplicates.txt: Accessions (using alias names) that are Near Isogenic Lines.
Lines_missing_sampleInfo.txt: Accessions missing row-type or growth habit information that were removed during QC, as indicated in the manuscript.