I am trying to play with the conservation scores (as PhastCons score from UCSC) to prioritize the SNPs which are located in non-coding regions.
However, some of the values obtained from UCSC are quiet weak, or sometime no scores at all.
Additionally, I am working with the species (cattle) that the genome assemble is already quiet old on UCSC.
Any suggestions to get a accurate PhastCons score, or any other conservation scores may available for my situation.
Especially, how to compare the conservation only based on a SNP-id or position.