I've been looking at using conservation scores, obtained from the UCSC Genome database, as a means to prioritize some SNPs we're looking at that are in non-coding regions.
The PhastCons score is a probability that each nucleotide belongs to a conserved element, whereas abs(phyloP) is the -log(p-value) under a null hypothesis of neutral evolution, and a negative sign indicates faster-than expected evolution, while positive values imply conservation.
In eyeballing the data a bit, I was a little surprised that there appears to be only weak (0.397) correlation between the phyloP and and PhastCons values at each site. (I was looking at PhastCons vs. 1- exp(-phyloP) for only sites with positive phyloP). While I realize that they're different statistics and measuring slightly different things, I would have still expected them to be quite highly correlated.
Any experiences or thoughts about using these scores?