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.