Found a great write-up on the different mechanics, drawbacks, and benefits of the two different back squats. The low bar squat recruits more of the posterior chain (i.e. hamstrings) and you’ll more than like put up bigger numbers. However, the torso position of the low bar back squat does not translate well to olympic lifting (snatch, clean, overhead squats). Low bar will help with power cleans and power snatches since you recruit your hamstrings more, but not for true cleans and snatches. High bar squatting is what you want to focus on to improve your olympic lifting so you get used to keeping your torso upright while squatting out of the hole. Less hamstring recruitment is involved, so make sure you do extra work on your posterior chain with roman deadlifts and glute ham raises.
LOW BAR: The low bar is good for general strength training and powerlifting, yet it’s difficult to do well. It may have a place — much like the bench press — in beginner Olympic weightlifting training depending on the trainees weaknesses, but probably shouldn’t be used beyond the beginning stages.
HIGH BAR: The high bar squat is superior for Olympic weightlifting because it teaches proper clean/snatch receiving positioning. If there are problems with the low bar squat, then the high bar can be used to balance musculature or maintain squatting frequency. However, the high bar doesn’t utilize the hamstring’s stretch reflex nor does it develop the posterior chain.
For most of us it doesn’t matter which one we choose, as long as we squat. Fred Hartfield, aka Dr Squat, posits that high bar squats build strength and low bar squats demonstrate it, so try mixing it up and see what works best for you.
In the meantime, check out the 70s Big blog. Some smart and entertaining folks over there.