CanFam4-referenced PhyloP scores, estimated from Zoonomia 241 Mammals (v2.1) alignment

File: PhyloPScores.CanFam4_v4_mdong_241MAMMALS.bed.gz Date of generation : 2022-12-22 This dataset contains the PhyloP scores calculated on a dog-referenced alignment (Canis_lupus_familiaris, assembly: CanFam4 / UU_Cfam_GSD_1.0) Alignment was processed by Hickey et al. using cactus-update to integrate CanFam4 (UU_Cfam_GSD_1.0, GCA_011100685.1) on the same branch than canFam3 and village dog.Furthermore, four more Canine species plus one Cat assembly were added:- Canis lupus orion (Greenland wolf, GCA_905319855.2) - Canis lupus dingo (desert dingo, GCA_003254725.2)- Nyctereutes procyonoides (Raccoon Dog, GCA_905146905)- Otocyon megalotis megalotis (Southern bat-eared fox, GCA_017311455.1)- and Felis catus (Domestic cat - felCat_126, GCA_018350175.1)The resulting alignment was versioned as v2.1 :https://cgl.gi.ucsc.edu/data/cactus/241-mammalian-2020v2.1.hal HAL alignment was then MAF-formatted, with CanFam4 as reference, and alignment duplicates filtered out by mafTools. Autosomes and chrX were processed using different neutral models generated independently from "ancestral" repeat coordinates. Neutral models used are the same than the Zoonomia project. CanFam3 (GCF_000002285.3), Village Dog (GCA_004027395.1) and felCat_126 (GCA_018350175.1) were excluded from calculations. Single base pair phyloP scores were generated for the autosomes and chromsome X as described in the 2023 publications. - Christmas, Matthew J., et al. "Evolutionary constraint and innovation across hundreds of placental mammals." Science 380.6643 (2023): eabn3943. - Sullivan, Patrick F., et al. "Leveraging base-pair mammalian constraint to understand genetic variation and human disease." Science 380.6643 (2023): eabn2937. For details, see "Deriving Mammalian and Primate Constraint Measures for the Human Genome", in the supplement of Sullivan et al., Science380, eabn2937(2023).DOI:10.1126/science.abn2937 The full list of genomes included in the alignement can be found via the track settings, or via the Zoonomia homepage, zoonomiaproject.org/ Alignment version: 241-mammalian-2020v2.1.hal (v2.1)Version: v4Reference: Canis_lupus_familiaris (CanFam4/UU_Cfam_GSD_1.0, https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_011100685.1)Chromosomes : from chr1 to chr38, chrXSpecies selected: All (244), CanFam3, village dog and FelCat126 excludedNb of files: 1 (23.13 Gb total, BED.gz format)Split: 6, using "split -b 4096m". (merge back by using cat)Tree used: 241-mammalian-2020v2.1.nh (http://cgl.gi.ucsc.edu/data/cactus/241-mammalian-2020v2.phast-242.nh)Models used: Anc239.AncRep.bed.vshalLiftOverCanFam4.autosomes.random100kb.MTDF.nocf3.noVD.nofca126.mod, Anc239.AncRep.bed.vshalLiftOverCanFam4.chrX.random100kb.MTDF.nocf3.noVD.nofca126.mod