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

# README_PhastCons_CanFam4_241MAMMALSv4 # Author: Michael X. Dong ([e-mail]) Uppsala Universitet # Date of generation : 2022-12-22 # Description: This dataset contains the PhastCons scores calculated on a domestic dog alignment (Canis_lupus_familiaris) Alignment was updated by Hickey et al. using cactus-update to integrate CanFam4 on the same branch than canFam3 and village dog. (https://cgl.gi.ucsc.edu/data/cactus/) Four more assemblies were added. 241 Mammals MAF-formatted alignment, with alignment duplicates filtered out by mafTools. Autosomes and chrX were processed using different neutral models generated independently from "ancestral" repeat coordinates. chrX model were generated from random positions after converting ancestral repeat coordinates to canFam4 then selecting random positions on chromosome X for modelling. For this release, CanFam3 (GCF_000002285.3) and Village Dog (GCA_004027395.1) were left in the calculations, with negligeable impact on the mammalian constraint scoring due to the proximity with canFam4 in the tree (they were removed for the scoring). Single base pair PhasCons conservation scores and predicted PhastCons conserved regions were generated for the autosomes and chromsome X following the method for 43 primates from the 2023 publication from Sullivan et al. , in line with other similar tracks from UCSC. For details, see section, "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/ There are two files: - the individual PhastCons scores, in wig format, compressed : PhastConsScores_dog_v4_mdong_241MAMMALS.wig.gz - and the list of predicted PhastCons regions, in BED format, compressed : regions.PhastCons.dog_v4_mdong_241MAMMALS.bed.gz Alignment version used: 241-mammalian-2020v2.1.hal (https://cgl.gi.ucsc.edu/data/cactus/) Version: v4 Reference: 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, chrX Species selected: All (244) Nb of files: 2 Split: merged into one BED after process Tree used: 241-mammalian-2020v2.1.nh (https://cgl.gi.ucsc.edu/data/cactus/241-mammalian-2020v2.1.nh) Models used: Anc239_allARs_100kb_lessGC40_241species_30Consensus.newCanFam4Tree.nocf3.mod, dog_100kb_chrX_lessGC40_241species_30Consensus.newCanFam4Tree.nocf3.mod Parameters (PhastCons): --msa-format MAF --target-coverage 0.3 --expected-length 45 --rho 0.3 --viterbi --score