brilliant, this predicted 175 and I got 124.

although this is a very simple way of calculating the raw expected amount of SNPs on a region, it does not consider many factors that can modify the resulting figures. among others, exons are less prone to variability, so the SNP ratio depending only on their base length should be less than intronic regions, and even less than intergenic regions. for that reason I would say that the figure you are considering (124 versus 175) is definitely consistent.

good point. it only holds for randomly distributed snps. see @Eric's comment to @Istvan's answer as well.

good idea. it also depends on what's the actual coverage for exon vs. non-exon which will affect the ability to make the SNP calls. you might expect non-exon to have more simple sequence and therefore be less likely to have good enough coverage to do proper SNP calling.

I don't know if that overlap with your suggestion @brentp, but I would expect non-exons, under an assumption of relaxed selection pressures, to contain more variation than exons, thus boosting the proportion of SNPs in non-exon portions of the chromosome. Possible explanation for the less-than expected proportion of exon-SNPs?

@Istvan - are there any tools that will automatically calculate this for you? I would be especially interested in any tools that take into account factors mentioned by Eric about election pressure.

@Andrea_bio I am not aware of a tool that would compute this for you right away but it is likely that it exists in one form or another - I would imagine that this question is fairly common

I asked this question in another comment below but I hadn't seen your answer then. Is there any software for calculating SNP distribution that takes into account the factors you have mentioned such as mutation rate, population size, organism. I would be very interested in this.