Resource

Id:hg19/scores/phyloP46_vertebrates
Type:position_score
Summary: ## phyloP46way vertebrates This file is from: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/phyloP46way/README.txt This directory contains conservation scoring by phyloP (phylogenetic p-values) from the PHAST package (http://compgen.bscb.cornell.edu/phast/) for multiple alignments of 45 vertebrate genomes to the human genome, plus alternate sets of scores for the primate species and the placental mammal species in the alignments. The phastCons data can be found at: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/phastCons46way/ The multiple alignments and methods description are at: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/multiz46way/ For more information about this data, see the track description for the Conservation track: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cons46way Assemblies used in these alignments: - Human Homo sapiens Feb. 2009 hg19/GRCh37 - Chimp Pan troglodytes Mar. 2006 panTro2 - Gorilla Gorilla gorilla gorilla Oct. 2008 gorGor1 - Orangutan Pongo pygmaeus abelii July 2007 ponAbe2 - Rhesus Macaca mulatta Jan. 2006 rheMac2 - Baboon Papio hamadryas Nov. 2008 papHam1 - Marmoset Callithrix jacchus June 2007 calJac1 - Tarsier Tarsius syrichta Aug. 2008 tarSyr1 - Mouse lemur Microcebus murinus Jul. 2007 micMur1 - Bushbaby Otolemur garnettii Dec. 2006 otoGar1 - Tree shrew Tupaia belangeri Dec. 2006 tupBel1 - Mouse Mus musculus July 2007 mm9 - Rat Rattus norvegicus Nov. 2004 rn4 - Kangaroo rat Dipodomys ordii Jul. 2008 dipOrd1 - Guinea Pig Cavia porcellus Feb. 2008 cavPor3 - Squirrel Spermophilus tridecemlineatus Feb. 2008 speTri1 - Rabbit Oryctolagus cuniculus Apr. 2009 oryCun2 - Pika Ochotona princeps Jul. 2008 ochPri2 - Alpaca Vicugna pacos Jul. 2008 vicPac1 - Dolphin Tursiops truncatus Feb. 2008 turTru1 - Cow Bos taurus Oct. 2007 bosTau4 - Horse Equus caballus Sep. 2007 equCab2 - Cat Felis catus Mar. 2006 felCat3 - Dog Canis lupus familiaris May 2005 canFam2 - Microbat Myotis lucifugus Mar. 2006 myoLuc1 - Megabat Pteropus vampyrus Jul. 2008 pteVam1 - Hedgehog Erinaceus europaeus June 2006 eriEur1 - Shrew Sorex araneus June 2006 sorAra1 - Elephant Loxodonta africana Jul. 2009 loxAfr3 - Rock hyrax Procavia capensis Jul. 2008 proCap1 - Tenrec Echinops telfairi July 2005 echTel1 - Armadillo Dasypus novemcinctus Jul. 2008 dasNov2 - Sloth Choloepus hoffmanni Jul. 2008 choHof1 - Wallaby Macropus eugenii Nov. 2007 macEug1 - Opossum Monodelphis domestica Oct. 2006 monDom5 - Platypus Ornithorhynchus anatinus Mar. 2007 ornAna1 - Chicken Gallus gallus May 2006 galGal3 - Zebra finch Taeniopygia guttata Jul. 2008 taeGut1 - Lizard Anolis carolinensis Feb. 2007 anoCar1 - X. tropicalis Xenopus tropicalis Aug. 2005 xenTro2 - Tetraodon Tetraodon nigroviridis Mar. 2007 tetNig2 - Fugu Takifugu rubripes Oct. 2004 fr2 - Stickleback Gasterosteus aculeatus Feb. 2006 gasAcu1 - Medaka Oryzias latipes Oct. 2005 oryLat2 - Zebrafish Danio rerio Dec. 2008 danRer6 - Lamprey Petromyzon marinus Mar. 2007 petMar1
Description:

phyloP46way vertebrates

This file is from:

http://hgdownload.soe.ucsc.edu/goldenPath/hg19/phyloP46way/README.txt

This directory contains conservation scoring by phyloP (phylogenetic p-values) from the PHAST package (http://compgen.bscb.cornell.edu/phast/) for multiple alignments of 45 vertebrate genomes to the human genome, plus alternate sets of scores for the primate species and the placental mammal species in the alignments.

The phastCons data can be found at: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/phastCons46way/

The multiple alignments and methods description are at: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/multiz46way/

For more information about this data, see the track description for the Conservation track: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cons46way

Assemblies used in these alignments:

  • Human Homo sapiens Feb. 2009 hg19/GRCh37
  • Chimp Pan troglodytes Mar. 2006 panTro2
  • Gorilla Gorilla gorilla gorilla Oct. 2008 gorGor1
  • Orangutan Pongo pygmaeus abelii July 2007 ponAbe2
  • Rhesus Macaca mulatta Jan. 2006 rheMac2
  • Baboon Papio hamadryas Nov. 2008 papHam1
  • Marmoset Callithrix jacchus June 2007 calJac1
  • Tarsier Tarsius syrichta Aug. 2008 tarSyr1
  • Mouse lemur Microcebus murinus Jul. 2007 micMur1
  • Bushbaby Otolemur garnettii Dec. 2006 otoGar1
  • Tree shrew Tupaia belangeri Dec. 2006 tupBel1
  • Mouse Mus musculus July 2007 mm9
  • Rat Rattus norvegicus Nov. 2004 rn4
  • Kangaroo rat Dipodomys ordii Jul. 2008 dipOrd1
  • Guinea Pig Cavia porcellus Feb. 2008 cavPor3
  • Squirrel Spermophilus tridecemlineatus Feb. 2008 speTri1
  • Rabbit Oryctolagus cuniculus Apr. 2009 oryCun2
  • Pika Ochotona princeps Jul. 2008 ochPri2
  • Alpaca Vicugna pacos Jul. 2008 vicPac1
  • Dolphin Tursiops truncatus Feb. 2008 turTru1
  • Cow Bos taurus Oct. 2007 bosTau4
  • Horse Equus caballus Sep. 2007 equCab2
  • Cat Felis catus Mar. 2006 felCat3
  • Dog Canis lupus familiaris May 2005 canFam2
  • Microbat Myotis lucifugus Mar. 2006 myoLuc1
  • Megabat Pteropus vampyrus Jul. 2008 pteVam1
  • Hedgehog Erinaceus europaeus June 2006 eriEur1
  • Shrew Sorex araneus June 2006 sorAra1
  • Elephant Loxodonta africana Jul. 2009 loxAfr3
  • Rock hyrax Procavia capensis Jul. 2008 proCap1
  • Tenrec Echinops telfairi July 2005 echTel1
  • Armadillo Dasypus novemcinctus Jul. 2008 dasNov2
  • Sloth Choloepus hoffmanni Jul. 2008 choHof1
  • Wallaby Macropus eugenii Nov. 2007 macEug1
  • Opossum Monodelphis domestica Oct. 2006 monDom5
  • Platypus Ornithorhynchus anatinus Mar. 2007 ornAna1
  • Chicken Gallus gallus May 2006 galGal3
  • Zebra finch Taeniopygia guttata Jul. 2008 taeGut1
  • Lizard Anolis carolinensis Feb. 2007 anoCar1
  • X. tropicalis Xenopus tropicalis Aug. 2005 xenTro2
  • Tetraodon Tetraodon nigroviridis Mar. 2007 tetNig2
  • Fugu Takifugu rubripes Oct. 2004 fr2
  • Stickleback Gasterosteus aculeatus Feb. 2006 gasAcu1
  • Medaka Oryzias latipes Oct. 2005 oryLat2
  • Zebrafish Danio rerio Dec. 2008 danRer6
  • Lamprey Petromyzon marinus Mar. 2007 petMar1
Labels:
  • reference_genome: hg19/genomes/GATK_ResourceBundle_5777_b37_phiX174

Scores

id type default annotation description histogram range
phyloP46_vertebrates float

phylop46_vertebrates

 phyloP46_vertebrates HISTOGRAM FOR phyloP46_vertebrates [-14.080, 6.424]

Files

Filename Size md5
genomic_resource.yaml 4.79 KB db8b7fd242fbaec2a37b9d2c83b2fa31
phyloP46_vertebrates.bedGraph.gz 14.71 GB 4384ba92e608ae7c822476105124a8fc
phyloP46_vertebrates.bedGraph.gz.dvc 107.0 B 07937e4cf38c5821f991c2e0956bfb1f
phyloP46_vertebrates.bedGraph.gz.tbi 2.78 MB 8aaed3280ae4cb0b017c9573a2e12782
phyloP46_vertebrates.bedGraph.gz.tbi.dvc 107.0 B bd48cc48cdce70bcdd13d584e1aa6c88
statistics/