Both MILRET and MILRAA count only reads that completely span an IES and either contain an insert or do not. If inserts/IESs are too long, the mapping will have a clip instead of an insert. For short IESs this is negligible, but as IESs are longer, a greater proportion of mapped IES+ reads will have clips, but these are currently ignored in calculating the retention score.
Both MILRET and MILRAA count only reads that completely span an IES and either contain an insert or do not. If inserts/IESs are too long, the mapping will have a clip instead of an insert. For short IESs this is negligible, but as IESs are longer, a greater proportion of mapped IES+ reads will have clips, but these are currently ignored in calculating the retention score.