Quality scores are not phred-scaled.

[reedacartwright]

Quality scores are log10(likelihood of ref/likelihood of nonref) (right?).

To prevent misinterpretations, the documentation should make it clear that a quality score of 1 is equivalent to the ref being having 10 times the likelihood of nonref, and a quality score of 4 means 10000 times.

This is different from the standard quality score scalings in which these situations would result in scores of 10 and 40.

[gwct]

I've added the following page to the website which should hopefully clear things up:

https://gwct.github.io/referee/scores.html

[reedacartwright]

That's clear. Thanks.