Heterozygote frequencies in Juglans and Pistacia P1+P2
datasets are 0.003 and 0.002 respectively, 20-50X lower than in their
corresponding P1 and P2 datasets (Table 1). The proportion of
heterozygous genotypes in P1 and P2 datasets increases strongly with
increasing read depth, whereas the proportion in P1+P2 datasets is not
affected by read depth (Figure 2). Most heterozygous genotypes in P1+P2
datasets are concentrated in a few individuals, probably due to
cross-contamination during DNA extraction or library preparation (Figure
2). Therefore, the dual alignment strategy for interspecific hybrids
results in effectively haploid datasets and enables simple detection and
removal of cross-contaminated samples.