Orientations and phases of gene overlap. Genes can overlap on the same strand and on the opposite strand. The reference gene in a pair of overlapping genes is called phase 0. Same-strand overlaps can be in two phases (1 and 2); opposite-strand overlaps can be in three phases (0, 1, and 2). First and second codon positions, in which ~5% and 0% of the changes are synonymous, are marked in red. Third codon positions, in which ~70% of the changes are synonymous, are marked in blue.