At the risk of further confusing the issue (there are already 2 answers focusing on different aspects!!), I am going to focus on a somewhat different aspect of this question that I think we need to nail down before it can be addressed.
Going mostly off your question title, it would help to know what you mean by genotype vs. allele frequencies. These are ...
"Intergenic" is, well, an embarrassment, though it can be hard to avoid. Intergenic means, literally, between genes. Genes are, as you'd expect, genetically defined as regions of the chromosome with some genetic role. Between genes, we have, well, junk, spam, without meaning or significance, since otherwise, it would be a gene. In the 1990s ...
An intergenic region is just one of many types of non-coding sequence.
regulatory binding sites
ribosome entry sites
There's a lot of stuff that's part of genes besides the protein coding sequence.
A good way to get a picture of the sorts of things there are besides coding regions is ...
Obviously, there won't be a single number for this.
The phenomenon is fairly well understood in yeast. Unfortunately, most studies tend to focus on the rate of formation of specific well-understood rearrangements, and then use that as a baseline. I am having trouble finding a measurement of overall rearrangement rate, although the system is ideal for this.