Hello, Catarina,
I believe what you are seeing is the effect of the next nucleotide to the
right. If you read the text describing these tracks, phastCons uses a
window
scoring that is affected by nearby bases. The next nucleotide has quite a
bit of variability, which will affect the score.
If you turn on the phyloP for primates to full, you can see a more
individual
measure of single-nucleotide conservation. If you set your browser to
chr9:75,773,681-75,773,681
with both phyloP and phastCons turned to full visibility, then zoom out
by 3x several times you can see when you get to 81 bases window size
how the phastCons score drops at the edges of homology blocks. The
phyloP score drops markedly on the outside edges of these phastCons
blocks.
I hope this helps resolve your question. And thanks for specifying that
you are using hg19 assembly. That is always useful for us in looking at
you issue.
best wishes,
--b0b kuhn
ucsc genome bioinformatics group
On 2/14/2012 3:56 AM, Catarina Correia wrote:
> Hi
>
> I was looking phastcons score for some variants in the human genome
> and for the position chr9:75,773,681 (hg19) although the base is
> always the same in the aligments I got a very low score for Phastcons
> primates. Additionally, the phastcons acore for mammals and
> vertebrates is very high. How is this explained?
>
> Thanks for your help.
> Best
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
