Filter: Output was filtered across the full population to maintain markers for which genotype calls were 50% or 80% complete,
heterozygosity was 10%, and minor allele frequency was 5%. Additional filters for Haplotag included a maximum base difference of three for aligning
tags, a maximum of nine tags per cluster, a maximum heterozygote frequency on a haplotype basis of 0.25, and a maximum tolerance
for tri-zygotes and multi-zygotes of 1% and 0%, respectively.
Filter: filtered SNPs to maximize predicted minor allele frequency (MAF), to minimize heterozygotes within varieties (which could signify miss-assemblies of orthologous and paralogous loci), and to eliminate SNPs that contained multiple variants within the 120- or 200-base context sequence used for assay design