Request of Information on Conservation data analisys

[Davide Barbagallo]

To whom it may concern,

I used the track "conservation" within the "Group Comparative Genomics" to find if there was conservation within a defined region of the genome, by specifically using the table "Cons 100 Verts (phastcons100way)",

Please, find attached the results of the output to my query: can you kindly tell me how I can interpret those results? What do these numbers beside each position mean and how can I use that to estimate a score of conservation?

Thank you for your attention and kind reply.

Best,

Davide Barbagallo

[Matthew Speir]

Hi Davide,

Thank you for your question about obtaining conservation scores from the UCSC Genome Browser.

I recommend reading the "Conservation" track description page, https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=cons100way#TRACK_HTML, in particular, the sections titled "PhastCons Conservation" and "PhyloP Conservation". These sections of track description page contain a short explanation of how we generate the phastCons and phyloP conservation scores using the "PHAST" software package. The page also briefly discusses what these scores represent. If you want more detail about how these scores are calculated, I would recommend reading the papers listed on the PHAST website: http://compgen.cshl.edu/phast/background.php.

You may also want to search our mailing list archives for similar questions about PhastCons scores and what they represent: https://groups.google.com/a/soe.ucsc.edu/forum/#!searchin/genome/PhastCons$20interpret.

I hope this is helpful. 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 Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

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