How To Obtain An Accurate Conservation Scores (E.G. Phastcons Score)

Question

[Draco]

Hey, all:

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.

Many thanks.