Read alignments compared to digest sites predicted in silico . An in silico digest of the maize and rice reference genomes identified predicted restriction sites for each enzyme. Following alignment to the genome, sequencing reads from each GBS dataset were categorized as “predicted” (blue) when the ends aligned to proximal restriction sites, “mispaired” (red) when the ends aligned to non-proximal restriction sites, “singlet” (purple) when only one end of a read aligned to a restriction site, and “null” (orange) when neither end of a read aligned to an in silico predicted restriction site. The number of each type of site with coverage (mapping quality (MQ) ≥20) was determined for both A) maize and B) rice. The mean coverage per site type (MQ ≥20) was also calculated in C) maize and D) rice for all enzymes.