Protein production used to be the thinking back in the day of the term "junk DNA" but we've since learned that actually there are sequences that have non-protein generating functions. Promoters and alternative splicing are the ones that come to mind. There are viral gene inserts which were originally thought to have no function but seem to be amplified in some regions and is now hypothesized to be a source of accelerated evolution, such as, in neurons which may have contributed to how humans diverged from chimps. The epigenome is the methyl groups around the DNA which can open or close to prevent the genes from being expressed, which might be mainly driven by environmental conditions and change frequently. There are some portions of DNA which might fold on itself to prevent expression as well.

If you only look at the raw gene sequence and say only the protein producing ones count. You have no way of telling:

• how much
• how many kinds
• speed
• and whether the protein is currently being expressed

without taking all those things into account. Also there are so many of the above being discovered that there's really no way to calculate all that yet

Well… sort of. While encoding proteins is arguably the most important and certainly the most visible function of the genome, there are parts that code for RNA that does not get translated into protein. These and other non-coding segments actually make up the majority of the human genome, and many of them play important roles. Though it is true that almost all those roles support the expression or regulation of proteins in some indirect way.

Also, a gene moving to a different locus can actually make a big difference, because the way it is expressed and regulated can change, even if it codes for the same protein.

> So if a gene/allele gets moved to a different place, it still counts as no difference.

Definitely not. Translocation often leads to or implies different expression of genes. As an aside many, many translocations over large amounts of evolutionary time can lead to things like chromosome loss and/or speciation events. These are important forms of genetic change/mutation that do lead to important functional change. And they do make genomes quite different in ways that aren't measurable by simple percentages.

See, that's the problem though. Simply translocating a sequence, with no alteration, can diminish or amplify expression dramatically. So that could still be considered a difference.