Differences between premature stop enriched–common genes (PSE-Cs) and phenotype-associated genes (PAGs). (A) Gene models in the B73 reference genome contain alternate alleles that introduce premature stop codons, totaling 713 models. A threshold of 0.25 alternate allele frequency defined 162 PSE-Cs, which were used as a second comparator category of gene models in this study. (B) Principal component analysis (PCA) of PSE-Cs (n = 162) and PAGs (n = 272). The first two principal components explain 28.62% of the variance. Data included in the PCA included a set of 2675 previously published features that were downloaded from the MaizeGDB (Sen et al. 2023). (C) Difference in the number of exons per gene model between PSE-Cs and PAGs. (D) Difference in the length of the three prime untranslated regions (3′ UTRs) of gene models between PSE-Cs and PAGs. (E) Difference in the number of isoforms per gene model between PSE-Cs and PAGs. (F) Difference in the proportion of GC content between PSE-Cs and PAGs. (**) P-value < 0.01, (***) P-value < 0.001, (n.s) nonsignificant (two-tailed Mann–Whitney U test).