Think more closely about what to do with bases where we have data on deletions

[petercombs]

At least in the Kircher data, there are SNPs where we know what effect a deletion has. In theory, we could use this, though the data may be somewhat biased (for instance, for HBG1 we have 85 of the 274 bases with a deletion measured).

Also, I should double check that I'm not counting these in the possible up, down, and neutral mutations, since at the moment I don't count them in the actual up, down, and neutral.