PhyloP

Overview

Publication

Kuderna, L.F.K., Ulirsch, J.C., Rashid, S. et al. Identification of constrained sequence elements across 239 primate genomes. Nature 2023. (https://doi.org/10.1038/s41586-023-06798-8)

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)

PhyloP Primate

PhyloP primate analyzes 239 primate species and identifies 111,318 hypersensitivity sites and 267,410 binding sites constrained specifically in primates. It enriches that with human genetic variants, these elements influence gene expression and impact complex traits and diseases.

PhyloP Primate is only available for GRCh38 assembly.

BigWig File

The original file is primates_msa.phylop.conacc.lrt.bw which is a bigwig file. This file was converted to wig file using: (https://genome.ucsc.edu/goldenPath/help/bigWig.html) After conversion the wig file provides the scores in the following format:

0.14
0.074
-2.487
0.073
0.052
0.073
fixedStep chrom=chr1 start=10558 step=1 span=1
-1.991
0.052
-2.047
0.052
0.052
0.074
-1.992
0.074
0.052
0.073
0.074
0.052
0.074
-2.05
-2.059
0.074
0.074
0.074

JSON Output

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

 "variants": [
    {
        "vid": "1-64927-G-T",
        "chromosome": "chr1",
        "begin": 64927,
        "end": 64927,
        "refAllele": "G",
        "altAllele": "T",
        "variantType": "SNV",
        "hgvsg": "NC_000001.11:g.64927G>T",
        "phyloPPrimateScore": 0.151
    }
]

Field	Type	Notes
phyloPPrimateScore	float	range: -20 to 1.951

PhyloP

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.

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