BSA and Exon Capture HTS. (a) Schematic of Exon Capture HTS with BSA. Two pools of embryos are sequenced, one mutant and one WT from a mapcross. The WT pool is sequenced and SNPs identified based on allele counts where the major allele fraction (MAF) is approximately 50%. These positions are examined in the mutant pools for LOH. (b,d) Graph of homozygosity ratio to scaffold number using genome v4.1 for ruby (b) and grinch (d). (c,e) same as b,d but version 7.1 of the genome. In (b-e), scaffolds or scaffold intervals with <20 SNPs have been excluded. The peaks with the highest homozygosity ratios are labeled.