PhyloP
Clarissa Torresan
Can anyone explain to me what’s the difference between PhyloP (as I find in GnomAD and genome browser, for exemple) and PhyloP 100 (as in Varsome)??
As far as I could find, the 100 means that 100 species were used to do the statistics.
Does it means that the PhyloP (not 100) analyses more species? Or less?? Or… they are the same, some are just naming it differently?
Thanks for your attention!!
Clarissa Torresan
Luis Nassar
Hi, Clarissa.
As you suspect, PhyloP 100 represents a PhyloP conservation score using 100 assemblies/species. If you click on any of our conservation tracks you will see details on how they were made and which assemblies were used, for example here is our PhyloP 100 track description page for hg38 (https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=cons100way).
We cannot speak conclusively for Varsome or gnomAD. Looking at both, it appears the data may have been downloaded from us, but you would have to ask them for a conclusive answer. For example, the gnomAD data doesn't appear to be our 100-way conservation data, but instead our 241-way placental mammal data (https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&c=chr1&g=cons241way). PhyloP just refers to the conservation algorithm, so scores can vary depending on the species used. It is possible they have different names for the same data but you would have to contact them to confirm.
I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.
Lou Nassar
UCSC Genomics Institute
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