Effects of alignment strategy on heterozygosity and minor allele frequency
Three genotypic datasets each were generated for both Pistaciaand Juglans , by aligning reads to the maternal genome only (P1), to the paternal genome only (P2), or to both maternal and paternal genomes simultaneously (P1+P2). Dual alignment to both parental genomes resulted in a higher proportion of reads aligning for hybrids of both genera (Table 1). SNPs with low coverage and excess heterozygosity were filtered from each dataset, and a depth threshold of 5 was applied to P1 and P2 datasets prior to imputation to minimize undercalling of heterozygotes. Results are summarized in Table 1. Note thatJuglans and Pistacia have basic chromosome numbers of 16 and 15, and that dual alignment (P1+P2) results in alignment to 32 and 30 chromosomes respectively.