[Genome] [Question] discrepancy of multiz17way score between the database and the browser

[Archana Thakkapallayil]

Hello Mousheng Xu,

There are 2 different scores associated with the Conservation track: the 
multiple alignment score associated with the multiz* tables and the 
phastCons conservation score associated with the phastCons*way tables, 
which draws the blue wiggle Conservation on the top. The conservation 
scores are displayed as a "wiggle" (histogram), where the height 
reflects the size of the score.

You can obtain these scores from the conservation scores downloads for 
the Human assembly. However, if you want to retrieve the scores 
associated with specific chromosomal ranges, it's easiest to use the 
Table Browser. To do this:

1. Set the clade, genome, and assembly to the appropriate genome.
2. Set group=Comparative Genomics, track=Conservation, 
table=phastCons*way, and region=the chromosomal position in which you're 
interested.
3. Set output format=data points, then click "get output".

This will return the conservation scores associated with each base 
position within your range.

You can read more about the methods used for our Conservation track in 
the description page here:
http://www.genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=multiz17way

See this help page from our website for more details about the phastCons 
file format:  http://genome.ucsc.edu/goldenPath/help/phastCons.html

Please see this answer to a previously answered mailing list question 
that explains how to get the conservation score from rs numbers: 
http://www.soe.ucsc.edu/pipermail/genome/2006-February/009806.html

I hope this helps to answer your question. If you have any further 
questions please don't hesitate to contact us again.

Regards,

Archana
UCSC Genome Bioinformatics Group

mousheng xu wrote:
> Dear Genome Help,
>
> If you do a ""select * from multiz17way where chrom='chr6' and chromStart =
> 31647790", you will get the following return:
>
>  826     chr6    31647790        31649567        2389798 430695879
> 0.698777
>
> Which means that the multiz17way score for the region chr6:31647790-31649567
> (total 1778 bps) is 0.698777. But if you take this region into the browser,
> the "17-Way Cons" track shown on the top as "Conservation" shows a lot of
> variation (not a constant value of 0.698777) with peaks and dips.
>
> Does the browser combine other information to compute the "Conservation"? If
> I am interested in getting the conservation of a SNP rs909253, how can I get
> it?
>
> Thanks a lot!
>
> Mousheng Xu
>
> Research Fellow,
> BWH, Harvard Medical School
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>