PhyloP

Overview

PhyloP (phylogenetic p-values) conservation scores are obtained from the [PHAST package] (http://compgen.bscb.cornell.edu/phast/) for multiple alignments of vertebrate genomes to the human genome. For GRCh38, the multiple alignments are against 19 mammals and for GRCh37, it is against 45 vertebrate genomes.

Publication

Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 Aug;15(8):1034-50. (http://www.genome.org/cgi/doi/10.1101/gr.3715005)

WigFix File

The data is provided in WigFix files which is a text file that provides conservation scores for contiguous intervals in the following format:

fixedStep chrom=chr1 start=10918 step=1
0.064
0.058
0.064
0.058
0.064
0.064
fixedStep chrom=chr1 start=34045 step=1
0.111
0.100
0.111
0.111
0.100
0.111
0.111
0.111
0.100
0.111
-1.636

We convert them to binary files with indexes for fast query. Note that these are scores for genomic positions and are reported only for SNVs.

Download URL

GRCh37: http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate/

GRCh38: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/phyloP20way/

JSON Output

Unlike other supplemetary datasources, phyloP scores are reported in the variants section.

"variants":[
   {
      "vid":"2:48010488:A",
      "chromosome":"chr2",
      "begin":48010488,
      "end":48010488,
      "refAllele":"G",
      "altAllele":"A",
      "variantType":"SNV",
      "phylopScore":0.459
  }
]  

Field	Type	Notes
phylopScore	float	range: -14.08 to 6.424