Aren't the reads emitting a set of size greater than 4 bases per position, with a wildcard or "?" perhaps one option? (As in GATTACA might be read as is, but m

Aren't the reads emitting a set of size greater than 4 bases per position, with a wildcard or "?" perhaps one option? (As in GATTACA might be read as is, but might be read as GAT?ACA.) Still that's a minimal of 3 bits versus much longer. [Edit : i see another commenter with the same observation, more thoroughly explained! ]