Relieve pain, prevent injury, and increase performance. Get customized mobility coaching developed by Dr. Kelly Starrett.
I’d say you’re on the right track in considering that right ankle being more mobile. In the deep ranges of squatting, the mobility demand on the ankles is pretty high, and a little more range there might mean a lot in terms of the overall squat position.
Do as David said, and test/retest the squat position before and after each mobility drill. I would even take a joint-by-joint approach to this. We’re all about the systems approach to mobility around here, of course, and you might find that, say, smashing the calf doesn’t create any more ankle mobility for your squat, but doing a banded ankle mobilization will. Go through a few different mobility drills for each aspect of the squat (ankle dorsiflexion, hip flexion, hip external rotation, hip abduction), retesting after each.
Chances are, anyway, that it isn’t just one thing, but the contribution of all kinds of things. Just try to find the biggest culprit and take it out of the picture first.
Also, try a high hamstring smash and floss on the left side if mobilizing that left ankle doesn’t level things out enough.