How to understand the conservation score about "0"

[王孝娟]

Dear UCSC team，

I am very sorry to bother you. Could you tell me how to understand the “0” score when I used the Cons 100 Verts (phast Cons 100way) to annotate the conservation of my variants dataset (GRCh/hg37). Such as “chr7:5540343-5540343”, “chr17: 5461874-5461874”?  because there are too many “0” score in our results.

Thank you very much, I am looking forward to hearing from you.

 

Best Regards,

Xiaojuan Wang

 

Institute of Health Sciences， Anhui University

Building C, 111 Jiulong Road, Hefei, China

 

[Christopher Lee]

Hi Xiaojuan,

Thank you for your question about a '0' in the phastCons score. A '0'
score for phastCons indicates that there is no conservation in that
location.

In your first example, if you turn codon translation on for the Multiz
100 Way track, you can see that the base is in the third codon
position, and has no effect on the codon if it changes, and thus is
not expected to be conserved:
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=chmalee&hgS_otherUserSessionName=hg19_genetic_drift

For your second example, your position appears to be at the end of a
mildly non-conserved stretch of bases, judging by the negative phyloP
score:
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=chmalee&hgS_otherUserSessionName=hg19_mildy_non_conserved

Both the phastCons and phyloP scores are described in the Conservation
track description page:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cons100way#TRACK_HTML

Thank you again for your inquiry and using the UCSC Genome Browser. If
you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a
publicly-accessible forum. If your question includes sensitive data,
you may send it instead to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute

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