| samocha_enrichment_background |
enrichment/samocha_background
|
0 |
4 |
1.38 MB |
## Samocha's Enrichment Background Model
From Samocha KE, et al. A framework for the interpretation of
de novo mutation in human disease. Nat Genet. 2014 Sep;46(9):944-50.
doi: 10.1038/ng.3050. Epub 2014 Aug 3. PMID: 25086666; PMCID: PMC4222185. |
| gene_score |
gene_properties/gene_scores/Iossifov_Wigler_PNAS_2015
|
0 |
6 |
7.8 MB |
|
| gene_score |
gene_properties/gene_scores/LGD
|
0 |
7 |
531.84 KB |
|
| gene_score |
gene_properties/gene_scores/RVIS
|
0 |
7 |
450.58 KB |
|
| gene_score |
gene_properties/gene_scores/SFARI_gene_score
|
0 |
6 |
124.6 KB |
|
| gene_score |
gene_properties/gene_scores/Satterstrom_Buxbaum_Cell_2020
|
0 |
6 |
613.37 KB |
|
| gene_score |
gene_properties/gene_scores/pLI
|
0 |
7 |
893.37 KB |
|
| gene_score |
gene_properties/gene_scores/pRec
|
0 |
7 |
895.21 KB |
|
| gene_set |
gene_properties/gene_sets/GO
|
0 |
4 |
12.07 MB |
|
| gene_set |
gene_properties/gene_sets/MSigDB_curated
|
0 |
3 |
3.12 MB |
|
| gene_set |
gene_properties/gene_sets/autism
|
0 |
7 |
4.37 KB |
|
| gene_set |
gene_properties/gene_sets/disease
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0 |
3 |
66.76 KB |
|
| gene_set |
gene_properties/gene_sets/domain
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0 |
3 |
391.19 KB |
|
| gene_set |
gene_properties/gene_sets/main
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0 |
17 |
103.89 KB |
|
| gene_set |
gene_properties/gene_sets/miRNA
|
0 |
4 |
1.6 MB |
|
| gene_set |
gene_properties/gene_sets/miRNA_Darnell
|
0 |
3 |
95.15 KB |
|
| gene_set |
gene_properties/gene_sets/relevant
|
0 |
15 |
101.75 KB |
|
| gene_set |
gene_properties/gene_sets/sfari
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0 |
11 |
11.53 KB |
|
| gene_set |
gene_properties/gene_sets/spark
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0 |
5 |
1.22 KB |
|
| gene_weights_enrichment_background |
hg19/enrichment/coding_length_in_target_ref_gene_v20190211
|
0 |
3 |
91.6 KB |
## Coding Length in Target Enrichment Background
Using refGene gene models for HG19 from 20190211. Target regions are from
the SSC WES study.
|
| gene_weights_enrichment_background |
hg19/enrichment/coding_length_ref_gene_v20190211
|
0 |
3 |
142.61 KB |
## Coding Length Enrichment Background
Using refGene gene models for HG19 from 20190211
|
| gene_models |
hg19/gene_models/ccds_v201309
|
0 |
5 |
2.56 MB |
|
| gene_models |
hg19/gene_models/knownGene_v201304
|
0 |
5 |
5.49 MB |
|
| gene_models |
hg19/gene_models/refGeneMito_v201309
|
0 |
5 |
3.98 MB |
|
| gene_models |
hg19/gene_models/refGene_v201309
|
0 |
5 |
3.97 MB |
|
| gene_models |
hg19/gene_models/refGene_v20190211
|
0 |
5 |
5.47 MB |
|
| genome |
hg19/genomes/GATK_ResourceBundle_5777_b37_phiX174
|
0 |
93 |
2.94 GB |
## HG19 Reference Genome
Default HG19 reference genome used by GPF
|
| np_score |
hg19/scores/CADD
|
0 |
10 |
79.37 GB |
## CADD
Downloaded from https://cadd.gs.washington.edu/download ;
Higher values of raw scores
have relative meaning that a variant is more likely to be simulated (or
"not observed") and therefore more likely to have deleterious effects.
Scaled scores are PHRED-like (-10*log10(rank/total)) scaled C-score ranking
a variant relative to all possible substitutions of the
human genome (8.6x10^9).
|
| position_score |
hg19/scores/FitCons-i6-merged
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0 |
8 |
105.17 MB |
TODO
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| position_score |
hg19/scores/FitCons2_E035
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0 |
8 |
291.52 MB |
TODO
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| position_score |
hg19/scores/FitCons2_E067
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0 |
8 |
260.97 MB |
TODO
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| position_score |
hg19/scores/FitCons2_E068
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0 |
8 |
270.23 MB |
TODO
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| position_score |
hg19/scores/FitCons2_E069
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0 |
8 |
262.13 MB |
TODO
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| position_score |
hg19/scores/FitCons2_E070
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0 |
8 |
262.33 MB |
TODO
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| position_score |
hg19/scores/FitCons2_E071
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0 |
8 |
255.46 MB |
TODO
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| position_score |
hg19/scores/FitCons2_E072
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0 |
8 |
257.61 MB |
TODO
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| position_score |
hg19/scores/FitCons2_E073
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0 |
8 |
266.95 MB |
TODO
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| position_score |
hg19/scores/FitCons2_E074
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0 |
8 |
262.12 MB |
TODO
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| position_score |
hg19/scores/FitCons2_E081
|
0 |
8 |
276.04 MB |
TODO
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| position_score |
hg19/scores/FitCons2_E082
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0 |
8 |
278.89 MB |
TODO
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| position_score |
hg19/scores/Linsight
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0 |
8 |
1.35 GB |
TODO
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| np_score |
hg19/scores/MPC
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0 |
9 |
2.26 GB |
TODO
tabix -s 1 -b 2 -e 2 -f fordist_constraint_official_mpc_values_v2.txt.gz
|
| position_score |
hg19/scores/phastCons46_placentals
|
0 |
8 |
10.55 GB |
## phastCons46way placentals
This score is from:
http://hgdownload.soe.ucsc.edu/goldenPath/hg19/phastCons46way/README.txt
This directory contains compressed phastCons scores for multiple alignments
of 45 vertebrate genomes to the human genome, plus an alternate set of scores
for the primates subset of species in the alignments, and an alternate set of
scores for the placental mammal subset of species in the alignments.
For a description of the phastCons fixed step wiggle data file format, see:
http://genome.ucsc.edu/goldenPath/help/phastCons.html
The multiple alignments and methods description are at:
http://hgdownload.soe.ucsc.edu/goldenPath/hg19/multiz46way/
For a description of the phastCons data file format, see:
http://genome.ucsc.edu/goldenPath/help/phastCons.html
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
|
| position_score |
hg19/scores/phastCons46_primates
|
0 |
8 |
14.02 GB |
## phastCons46way primates
This score is from:
http://hgdownload.soe.ucsc.edu/goldenPath/hg19/phastCons46way/README.txt
This directory contains compressed phastCons scores for multiple alignments
of 45 vertebrate genomes to the human genome, plus an alternate set of scores
for the primates subset of species in the alignments, and an alternate set of
scores for the placental mammal subset of species in the alignments.
For a description of the phastCons fixed step wiggle data file format, see:
http://genome.ucsc.edu/goldenPath/help/phastCons.html
The multiple alignments and methods description are at:
http://hgdownload.soe.ucsc.edu/goldenPath/hg19/multiz46way/
For a description of the phastCons data file format, see:
http://genome.ucsc.edu/goldenPath/help/phastCons.html
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
|
| position_score |
hg19/scores/phastCons46_vertebrates
|
0 |
8 |
10.81 GB |
## phastCons46way vertebrates
This score is from:
http://hgdownload.soe.ucsc.edu/goldenPath/hg19/phastCons46way/README.txt
This directory contains compressed phastCons scores for multiple alignments
of 45 vertebrate genomes to the human genome, plus an alternate set of scores
for the primates subset of species in the alignments, and an alternate set of
scores for the placental mammal subset of species in the alignments.
For a description of the phastCons fixed step wiggle data file format, see:
http://genome.ucsc.edu/goldenPath/help/phastCons.html
The multiple alignments and methods description are at:
http://hgdownload.soe.ucsc.edu/goldenPath/hg19/multiz46way/
For a description of the phastCons data file format, see:
http://genome.ucsc.edu/goldenPath/help/phastCons.html
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
|
| position_score |
hg19/scores/phyloP46_placentals
|
0 |
8 |
14.62 GB |
## phyloP46way placentals
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
|
| position_score |
hg19/scores/phyloP46_primates
|
0 |
8 |
10.81 GB |
## phyloP46way primates
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
|
| position_score |
hg19/scores/phyloP46_vertebrates
|
0 |
8 |
14.72 GB |
## 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
|
| allele_score |
hg19/variant_frequencies/gnomAD_v2.1.1/exomes
|
0 |
32 |
959.5 MB |
## gnomAD exomes v2.1.1
Original gnomAD exomes v2.1.1 is downloaded on October 19, 2020.
|
| allele_score |
hg19/variant_frequencies/gnomAD_v2.1.1/genomes
|
0 |
31 |
12.27 GB |
## gnomAD genomes v2.1.1 liftover
Original gnomAD genomes v2.1.1 liftover is downloaded on October 19, 2020
from https://gnomad.broadinstitute.org/.
tabix -s 1 -b 2 -e 2 -f gnomad..r2.1.1.extract.tsv.gz
|
| gene_weights_enrichment_background |
hg38/enrichment/coding_length_ref_gene_v20170601
|
0 |
3 |
139.34 KB |
## Coding Length Enrichment Background
Using refSeq gene models for HG38 from 20170601
|
| gene_models |
hg38/gene_models/refGene_v20170601
|
0 |
5 |
5.42 MB |
## refSeq gene models for HG38 from 20170601
|
| gene_models |
hg38/gene_models/refSeq_v20200330
|
0 |
5 |
4.15 MB |
## refSeq gene models for HG38 from 2020-03
Default gene models used by GPF for HG38.
|
| genome |
hg38/genomes/GRCh38-hg38
|
0 |
3375 |
3.04 GB |
## HG38 Reference Genome
Default HG38 reference genome used by GPF
|
| np_score |
hg38/scores/CADD_v1.4
|
0 |
18 |
79.42 GB |
## CADD GRCh38-v1.4
TODO
|
| np_score |
hg38/scores/CADD_v1.6
|
0 |
13 |
80.65 GB |
## CADD GRCh38-v1.6
TODO
|
| allele_score |
hg38/scores/clinvar_20221105
|
0 |
44 |
115.57 MB |
ClinVar resource downloaded on 2022-11-05. Chromosome names are
remapped to have `chr` prefix.
ClinVar is a freely accessible, public archive of reports of the
relationships among human variations and phenotypes, with supporting
evidence. ClinVar thus facilitates access to and communication about
the relationships asserted between human variation and observed health
status, and the history of that interpretation. ClinVar processes
submissions reporting variants found in patient samples, assertions
made regarding their clinical significance, information about the submitter,
and other supporting data. The alleles described in submissions are mapped
to reference sequences, and reported according to the HGVS standard.
ClinVar then presents the data for interactive users as well as those
wishing to use ClinVar in daily workflows and other local applications.
ClinVar works in collaboration with interested organizations to meet
the needs of the medical genetics community as efficiently and effectively
as possible
|
| position_score |
hg38/scores/phastCons100way
|
0 |
8 |
10.15 GB |
## phastConst100way
This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/hg38/phastCons100way/README.txt
This score contains compressed phastCons scores for multiple alignments
of 99 vertebrate genomes to the human genome.
For a description of the phastCons fixed step wiggle data file format, see:
http://genome.ucsc.edu/goldenPath/help/phastCons.html
Assemblies used in these alignments:
== Primate subset ==
Human Homo sapiens Dec 2013 GRCh38/hg38 Reference species
Chimp Pan troglodytes Feb 2011 CSAC 2.1.4/panTro4 Syntenic net
Gorilla Gorilla gorilla gorilla May 2011 gorGor3.1/gorGor3 Reciprocal best net
Orangutan Pongo pygmaeus abelii July 2007 WUGSC 2.0.2/ponAbe2 Reciprocal best net
Gibbon Nomascus leucogenys Oct 2012 GGSC Nleu3.0/nomLeu3 Syntenic net
Rhesus Macaca mulatta Oct 2010 BGI CR_1.0/rheMac3 Syntenic net
Crab-eating macaque Macaca fascicularis Jun 2013 Macaca_fascicularis_5.0/macFas5 Syntenic net
Baboon Papio hamadryas Mar 2012 Baylor Panu_2.0/papAnu2 Reciprocal best net
Green monkey Chlorocebus sabaeus Mar 2014 Chlorocebus_sabeus 1.1/chlSab2 Syntenic net
Marmoset Callithrix jacchus Mar 2009 WUGSC 3.2/calJac3 Syntenic net
Squirrel monkey Saimiri boliviensis Oct 2011 Broad/saiBol1 Syntenic net
Bushbaby Otolemur garnettii Mar 2011 Broad/otoGar3 Syntenic net
== Euarchontoglires subset ==
Chinese tree shrew Tupaia chinensis Jan 2013 TupChi_1.0/tupChi1 Syntenic net
Squirrel Spermophilus tridecemlineatus Nov 2011 Broad/speTri2 Syntenic net
Lesser Egyptian jerboa Jaculus jaculus May 2012 JacJac1.0/jacJac1 Syntenic net
Prairie vole Microtus ochrogaster Oct 2012 MicOch1.0/micOch1 Syntenic net
Chinese hamster Cricetulus griseus Jul 2013 C_griseus_v1.0/criGri1 Syntenic net
Golden hamster Mesocricetus auratus Mar 2013 MesAur1.0/mesAur1 Syntenic net
Mouse Mus musculus Dec 2011 GRCm38/mm10 Syntenic net
Rat Rattus norvegicus Jul 2014 RGSC 6.0/rn6 Syntenic net
Naked mole-rat Heterocephalus glaber Jan 2012 Broad HetGla_female_1.0/hetGla2 Syntenic net
Guinea pig Cavia porcellus Feb 2008 Broad/cavPor3 Syntenic net
Chinchilla Chinchilla lanigera May 2012 ChiLan1.0/chiLan1 Syntenic net
Brush-tailed rat Octodon degus Apr 2012 OctDeg1.0/octDeg1 Syntenic net
Rabbit Oryctolagus cuniculus Apr 2009 Broad/oryCun2 Syntenic net
Pika Ochotona princeps May 2012 OchPri3.0/ochPri3 Syntenic net
== Laurasiatheria subset ==
Pig Sus scrofa Aug 2011 SGSC Sscrofa10.2/susScr3 Syntenic net
Alpaca Vicugna pacos Mar 2013 Vicugna_pacos-2.0.1/vicPac2 Syntenic net
Bactrian camel Camelus ferus Dec 2011 CB1/camFer1 Syntenic net
Dolphin Tursiops truncatus Oct 2011 Baylor Ttru_1.4/turTru2 Reciprocal best net
Killer whale Orcinus orca Jan 2013 Oorc_1.1/orcOrc1 Syntenic net
Tibetan antelope Pantholops hodgsonii May 2013 PHO1.0/panHod1 Syntenic net
Cow Bos taurus Jun 2014 UMD_3.1.1/bosTau8 Syntenic net
Sheep Ovis aries Aug 2012 ISGC Oar_v3.1/oviAri3 Syntenic net
Domestic goat Capra hircus May 2012 CHIR_1.0/capHir1 Syntenic net
Horse Equus caballus Sep 2007 Broad/equCab2 Syntenic net
White rhinoceros Ceratotherium simum May 2012 CerSimSim1.0/cerSim1 Syntenic net
Cat Felis catus Nov 2014 ICGSC Felis_catus 8.0/felCat8 Syntenic net
Dog Canis lupus familiaris Sep 2011 Broad CanFam3.1/canFam3 Syntenic net
Ferret Mustela putorius furo Apr 2011 MusPutFur1.0/musFur1 Syntenic net
Panda Ailuropoda melanoleuca Dec 2009 BGI-Shenzhen 1.0/ailMel1 Syntenic net
Pacific walrus Odobenus rosmarus divergens Jan 2013 Oros_1.0/odoRosDiv1 Syntenic net
Weddell seal Leptonychotes weddellii Mar 2013 LepWed1.0/lepWed1 Reciprocal best net
Black flying-fox Pteropus alecto Aug 2012 ASM32557v1/pteAle1 Syntenic net
Megabat Pteropus vampyrus Jul 2008 Broad/pteVam1 Reciprocal best net
David's myotis bat Myotis davidii Aug 2012 ASM32734v1/myoDav1 Syntenic net
Microbat Myotis lucifugus Jul 2010 Broad Institute Myoluc2.0/myoLuc2 Syntenic net
Big brown bat Eptesicus fuscus Jul 2012 EptFus1.0/eptFus1 Syntenic net
Hedgehog Erinaceus europaeus May 2012 EriEur2.0/eriEur2 Syntenic net
Shrew Sorex araneus Aug 2008 Broad/sorAra2 Syntenic net
Star-nosed mole Condylura cristata Mar 2012 ConCri1.0/conCri1 Syntenic net
== Afrotheria subset ==
Elephant Loxodonta africana Jul 2009 Broad/loxAfr3 Syntenic net
Cape elephant shrew Elephantulus edwardii Aug 2012 EleEdw1.0/eleEdw1 Syntenic net
Manatee Trichechus manatus latirostris Oct 2011 Broad v1.0/triMan1 Syntenic net
Cape golden mole Chrysochloris asiatica Aug 2012 ChrAsi1.0/chrAsi1 Syntenic net
Tenrec Echinops telfairi Nov 2012 Broad/echTel2 Syntenic net
Aardvark Orycteropus afer afer May 2012 OryAfe1.0/oryAfe1 Syntenic net
== Mammal subset ==
Armadillo Dasypus novemcinctus Dec 2011 Baylor/dasNov3 Syntenic net
Opossum Monodelphis domestica Oct 2006 Broad/monDom5 Net
Tasmanian devil Sarcophilus harrisii Feb 2011 WTSI Devil_ref v7.0/sarHar1 Net
Wallaby Macropus eugenii Sep 2009 TWGS Meug_1.1/macEug2 Reciprocal best net
Platypus Ornithorhynchus anatinus Mar 2007 WUGSC 5.0.1/ornAna1 Reciprocal best net
== Aves subset ==
Saker falcon Falco cherrug Feb 2013 F_cherrug_v1.0/falChe1 Net
Peregrine falcon Falco peregrinus Feb 2013 F_peregrinus_v1.0/falPer1 Net
Collared flycatcher Ficedula albicollis Jun 2013 FicAlb1.5/ficAlb2 Net
White-throated sparrow Zonotrichia albicollis Apr 2013 ASM38545v1/zonAlb1 Net
Medium ground finch Geospiza fortis Apr 2012 GeoFor_1.0/geoFor1 Net
Zebra finch Taeniopygia guttata Feb 2013 WashU taeGut324/taeGut2 Net
Tibetan ground jay Pseudopodoces humilis Jan 2013 PseHum1.0/pseHum1 Net
Budgerigar Melopsittacus undulatus Sep 2011 WUSTL v6.3/melUnd1 Net
Parrot Amazona vittata Jan 2013 AV1/amaVit1 Net
Scarlet macaw Ara macao Jun 2013 SMACv1.1/araMac1 Net
Rock pigeon Columba livia Feb 2013 Cliv_1.0/colLiv1 Net
Mallard duck Anas platyrhynchos Apr 2013 BGI_duck_1.0/anaPla1 Net
Chicken Gallus gallus Nov 2011 ICGSC Gallus_gallus-4.0/galGal4 Net
Turkey Meleagris gallopavo Dec 2009 TGC Turkey_2.01/melGal1 Net
== Sarcopterygii subset ==
American alligator Alligator mississippiensis Aug 2012 allMis0.2/allMis1 Net
Green seaturtle Chelonia mydas Mar 2013 CheMyd_1.0/cheMyd1 Net
Painted turtle Chrysemys picta bellii Mar 2014 v3.0.3/chrPic2 Net
Chinese softshell turtle Pelodiscus sinensis Oct 2011 PelSin_1.0/pelSin1 Net
Spiny softshell turtle Apalone spinifera May 2013 ASM38561v1/apaSpi1 Net
Lizard Anolis carolinensis May 2010 Broad AnoCar2.0/anoCar2 Net
X. tropicalis Xenopus tropicalis Sep 2012 JGI 7.0/xenTro7 Net
Coelacanth Latimeria chalumnae Aug 2011 Broad/latCha1 Net
== Fish subset ==
Tetraodon Tetraodon nigroviridis Mar 2007 Genoscope 8.0/tetNig2 Net
Fugu Takifugu rubripes Oct 2011 FUGU5/fr3 Net
Yellowbelly pufferfish Takifugu flavidus May 2013 version 1 of Takifugu flavidus genome/takFla1 Net
Nile tilapia Oreochromis niloticus Jan 2011 Broad oreNil1.1/oreNil2 Net
Princess of Burundi Neolamprologus brichardi May 2011 NeoBri1.0/neoBri1 Net
Burton's mouthbreeder Haplochromis burtoni Oct 2011 AstBur1.0/hapBur1 Net
Zebra mbuna Maylandia zebra Mar 2012 MetZeb1.1/mayZeb1 Net
Pundamilia nyererei Pundamilia nyererei Oct 2011 PunNye1.0/punNye1 Net
Medaka Oryzias latipes Oct 2005 NIG/UT MEDAKA1/oryLat2 Net
Southern platyfish Xiphophorus maculatus Jan 2012 Xiphophorus_maculatus-4.4.2/xipMac1 Net
Stickleback Gasterosteus aculeatus Feb 2006 Broad/gasAcu1 Net
Atlantic cod Gadus morhua May 2010 Genofisk GadMor_May2010/gadMor1 Net
Zebrafish Danio rerio Sep 2014 Zv10/danRer10 Net
Mexican tetra (cavefish) Astyanax mexicanus Apr 2013 Astyanax_mexicanus-1.0.2/astMex1 Net
Spotted gar Lepisosteus oculatus Dec 2011 LepOcu1/lepOcu1 Net
Lamprey Petromyzon marinus Sep 2010 WUGSC 7.0/petMar2 Net
|
| position_score |
hg38/scores/phastCons20way
|
0 |
8 |
13.6 GB |
## phastCons20way
This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/hg38/phastCons20way/README.txt
This score contains compressed phastCons scores for multiple alignments
of 19 genome sequences to the human genome.
For a description of the phastCons fixed step wiggle data file format, see:
http://genome.ucsc.edu/goldenPath/help/phastCons.html
The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/hg38/multiz20way/
For more information about this data, see the track
description for the Conservation track:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=tarSyr2&g=cons20way
Assemblies used in these alignments: (alignment
type)
Human - Homo sapiens Dec. 2013 (GRCh38/hg38) reference
Baboon - Papio anubis Mar. 2012 (Baylor Panu_2.0/papAnu2) syntenic
Bushbaby - Otolemur garnettii Mar. 2011 (Broad/otoGar3) reciprocal best
Bonobo - Pan paniscus May. 2012 (Max-Planck/panPan1) reciprocal best
Chimp - Pan troglodytes Feb. 2011 (CSAC 2.1.4/panTro4) syntenic
Crab-eating macaque - Macaca fascicularis
Jun 2013 (Macaca_fascicularis_5.0/macFas5) syntenic
Gibbon - Nomascus leucogenys Oct. 2012 (GGSC Nleu3.0/nomLeu3) syntenic
Golden snub-nosed monkey - Rhinopithecus roxellana
Oct. 2014 (Rrox_v1/rhiRox1) reciprocal best
Gorilla - Gorilla gorilla gorilla May 2011 (gorGor3.1/gorGor3) reciprocal best
Green monkey - Chlorocebus sabaeus
Mar. 2014 (Chlorocebus_sabeus 1.1/chlSab2) syntenic
Marmoset - Callithrix jacchus Mar. 2009 (WUGSC 3.2/calJac3) syntenic
Mouse lemur - Microcebus murinus Jul. 2007 (Broad/micMur1) reciprocal best
Orangutan - Pongo pygmaeus abelii Jul. 2007 (WUGSC 2.0.2/ponAbe2) syntenic
Proboscis monkey - Nasalis larvatus
Nov. 2014 (Charlie1.0/nasLar1) reciprocal best
Rhesus - Macaca mulatta Oct. 2010 (BGI CR_1.0/rheMac3) syntenic
Squirrel monkey - Saimiri boliviensis Oct. 2011 (Broad/saiBol1) reciprocal best
Tarsier - Tarsius syrichta
Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2) reciprocal best
Tree shrew - Tupaia belangeri Dec. 2006 (Broad/tupBel1) reciprocal best
Mouse - Mus musculus Dec. 2011 (GRCm38/mm10) syntenic
Dog - Canis lupus familiaris Sep. 2011 (Broad CanFam3.1/canFam3) syntenic
|
| position_score |
hg38/scores/phastCons30way
|
0 |
8 |
12.97 GB |
## phastCons30way
This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/hg38/phastCons30way/README.txt
This score contains compressed phastCons scores for multiple alignments
of 29 genome sequences to the human genome.
For a description of the phastCons fixed step wiggle data file format, see:
http://genome.ucsc.edu/goldenPath/help/phastCons.html
For more information about this data, see the track
description for the Conservation track:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=tarSyr2&g=cons30way
-----------------------------------------------------------------------------
Assemblies used in these alignments: (alignment type)
Human - Homo sapiens
Dec. 2013 (GRCh38/hg38) (reference)
Angolan colobus - Colobus angolensis palliatus
Mar. 2015 (Cang.pa_1.0/colAng1) (syntenic)
Armadillo - Dasypus novemcinctus
Dec. 2011 (Baylor/dasNov3) (syntenic)
Baboon - Papio anubis
Feb. 2013 (Baylor Panu_2.0/papAnu3) (reciprocal best)
Black lemur - Eulemur macaco
Aug. 2015 (Emacaco_refEf_BWA_oneround/eulMac1) (reciprocal best)
Black snub-nosed monkey - Rhinopithecus bieti
Aug. 2016 (ASM169854v1/rhiBie1) (reciprocal best)
Bonobo - Pan paniscus
Aug. 2015 (MPI-EVA panpan1.1/panPan2) (syntenic)
Bushbaby - Otolemur garnettii
Mar. 2011 (Broad/otoGar3) (syntenic)
Chimp - Pan troglodytes
May 2016 (Pan_tro 3.0/panTro5) (syntenic)
Coquerel's sifaka - Propithecus coquereli
Mar. 2015 (Pcoq_1.0/proCoq1) (syntenic)
Crab-eating macaque - Macaca fascicularis
Jun. 2013 (Macaca_fascicularis_5.0/macFas5) (syntenic)
Dog - Canis lupus familiaris
Sep. 2011 (Broad CanFam3.1/canFam3) (syntenic)
Drill - Mandrillus leucophaeus
Mar. 2015 (Mleu.le_1.0/manLeu1) (syntenic)
Gibbon - Nomascus leucogenys
Oct. 2012 (GGSC Nleu3.0/nomLeu3) (syntenic)
Golden snub-nosed monkey - Rhinopithecus roxellana
Oct. 2014 (Rrox_v1/rhiRox1) (reciprocal best)
Gorilla - Gorilla gorilla gorilla
Mar. 2016 (GSMRT3/gorGor5) (syntenic)
Green monkey - Chlorocebus sabaeus
Mar. 2014 (Chlorocebus_sabeus 1.1/chlSab2) (syntenic)
Ma's night monkey - Aotus nancymaae
Jun. 2017 (Anan_2.0/aotNan1) (syntenic)
Marmoset - Callithrix jacchus
March 2009 (WUGSC 3.2/calJac3) (syntenic)
Mouse - Mus musculus
Dec. 2011 (GRCm38/mm10) (syntenic)
Mouse lemur - Microcebus murinus
Feb. 2017 (Mmur_3.0/micMur3) (syntenic)
Orangutan - Pongo pygmaeus abelii
July 2007 (WUGSC 2.0.2/ponAbe2) (reciprocal best)
Pig-tailed macaque - Macaca nemestrina
Mar. 2015 (Mnem_1.0/macNem1) (syntenic)
Proboscis monkey - Nasalis larvatus
Nov. 2014 (Charlie1.0/nasLar1) (reciprocal best)
Rhesus - Macaca mulatta
Nov. 2015 (BCM Mmul_8.0.1/rheMac8) (syntenic)
Sclater's lemur - Eulemur flavifrons
Aug. 2015 (Eflavifronsk33QCA/eulFla1) (reciprocal best)
Sooty mangabey - Cercocebus atys
Mar. 2015 (Caty_1.0/cerAty1) (syntenic)
Squirrel monkey - Saimiri boliviensis
Oct. 2011 (Broad/saiBol1) (syntenic)
Tarsier - Tarsius syrichta
Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2) (reciprocal best)
White-faced sapajou - Cebus capucinus imitator
Apr. 2016 (Cebus_imitator-1.0/cebCap1) (syntenic)
|
| position_score |
hg38/scores/phastCons7way
|
0 |
11 |
14.64 GB |
## phastConst7way
Downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/hg38/phastCons7way/
```
Assemblies used in these alignments: (alignment
type)
Human - Homo sapiens Dec. 2013 (GRCh38/hg38) reference
Chimp - Pan troglodytes Feb. 2011 (GSAC 2.1.4/panTro4) syntenic
Rhesus - Macaca mulatta Oct. 2010 (BGI CR_1.0/rheMac3) syntenic
Dog - Canis lupus familiaris Sep. 2011 (Broad/canFam3) syntenic
Mouse - Mus musculus Dec. 2011 (GRCm38/mm10) syntenic
Rat - Rattus norvegicus Mar. 2012 (RGSC Rnor 5.0/rn5) syntenic
Opossum - Monodelphis domestica Oct. 2006 (Broad/monDom5) net
```
|
| position_score |
hg38/scores/phyloP100way
|
0 |
8 |
16.1 GB |
phyloP (phylogenetic p-values) conservation score based on the
multiple alignments of 100 vertebrate genomes (including human).
|
| position_score |
hg38/scores/phyloP20way
|
0 |
8 |
14.56 GB |
## phyloP20way
TODO
|
| position_score |
hg38/scores/phyloP30way
|
0 |
8 |
14.72 GB |
## phyloP30way
TODO
|
| position_score |
hg38/scores/phyloP7way
|
0 |
8 |
12.54 GB |
## phyloP7way
TODO
|
| allele_score |
hg38/variant_frequencies/SSC_WG38_CSHL_2380
|
0 |
12 |
783.72 MB |
TODO
exported from SFARI_SSC_WGS_CSHL using
`gpf_validation_data/data_hg38/exports/SFARI_SSC_WGS_CSHL_frequency` scripts
|
| allele_score |
hg38/variant_frequencies/gnomAD_v2.1.1_liftover/exomes
|
0 |
35 |
928.31 MB |
## gnomAD exomes v2.1.1 liftover
Original gnomAD exomes v2.1.1 liftover is downloaded on October 19, 2020.
|
| allele_score |
hg38/variant_frequencies/gnomAD_v2.1.1_liftover/genomes
|
0 |
35 |
11.53 GB |
## gnomAD genomes v2.1.1 liftover
Original gnomAD genomes v2.1.1 liftover is downloaded on October 19, 2020
from https://gnomad.broadinstitute.org/.
tabix -s 1 -b 2 -e 2 -f gnomad..r2.1.1.extract.tsv.gz
|
| allele_score |
hg38/variant_frequencies/gnomAD_v3/genomes
|
0 |
18 |
17.64 GB |
## gnomAD genomes v3.0
Original gnomAD genomes v3.0 is downloaded on October 17, 2020
from https://gnomad.broadinstitute.org/.
tabix -s 1 -b 2 -e 2 -f gnomad.genomes.r3.0.extract.tsv.gz
|
| liftover_chain |
liftover/hg19ToHg38
|
0 |
6 |
450.19 KB |
## Liftover Chain Hg19 to Hg38
|
| liftover_chain |
liftover/hg38ToHg19
|
0 |
6 |
2.4 MB |
|