Genomic Scores
Field |
Description |
|---|---|
phyloP100 |
Link: http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP100way/. Conservation scoring by phyloP (phylogenetic p-values) from the PHAST package (http://compgen.bscb.cornell.edu/phast/) for multiple alignments of 99 vertebrate genomes to the human genome. 
|
phyloP46_vertebrates |
Link: http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/. 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. 
|
phyloP46_placentals |
Alternate set of phyloP46_vertebrates scores for the placental mammal subset of species in the alignments. 
|
phyloP46_primates |
Alternate set of phyloP46_vertebrates scores for the primates subset species in the alignments. 
|
phastCons100 |
Link: http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons100way/. Compressed phastCons scores for multiple alignments of 99 vertebrate genomes to the human genome. PhastCons is a program for identifying evolutionarily conserved elements in a multiple alignment, given a phylogenetic tree. 
|
phastCons46_vertebrates |
Link: http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/. 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. PhastCons is a program for identifying evolutionarily conserved elements in a multiple alignment, given a phylogenetic tree. 
|
phastCons46_placentals |
Alternate set of phastCons46_vertebrates scores for the placental mammal subset of species in the alignments. 
|
phastCons46_primates |
Alternate set of phastCons46_vertebrates scores for the primates subset of species in the alignments. 
|
CADD_raw |
Link: 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). 
|
CADD_phred |
Link: 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). 
|
Linsight |
Linsight scores for prediction of deleterious noncoding variants 
|
FitCons i6 merged |
Link: http://compgen.cshl.edu/fitCons/0downloads/tracks/i6/scores/. Indicates the fraction of genomic positions evincing a particular pattern (or “fingerprint”) of functional assay results, that are under selective pressure. Score ranges from 0.0 to 1.0. A lower score indicates higher confidence. 
|
Brain Angular Gyrus |
FitCons2 Scores for E067-Brain Angular Gyrus score-Roadmap Epigenomics DHS regions 
|
Brain Anterior Caudate |
Scores for E068-Brain Anterior Caudate score-Roadmap Epigenomics DHS regions 
|
Brain Cingulate Gyrus |
Scores for E069-Brain Cingulate Gyrus score-Roadmap Epigenomics DHS regions 
|
Brain Germinal Matrix |
Scores for E070-Brain Germinal Matrix score-Roadmap Epigenomics DHS regions 
|
Brain Hippocampus Middle |
Scores for E071-Brain Hippocampus Middle score-Roadmap Epigenomics DHS regions 
|
Brain Inferior Temporal Lobe |
Scores for E072-Brain Inferior Temporal Lobe score-Roadmap Epigenomics DHS regions 
|
Brain Dorsolateral Prefrontal Cortex |
Scores for E073-Brain Dorsolateral Prefrontal Cortex score-Roadmap Epigenomics DHS regions 
|
Brain Substantia Nigra |
Scores for E074-Brain Substantia Nigra score-Roadmap Epigenomics DHS regions 
|
Fetal Brain Male |
Scores for E081-Fetal Brain Male score-Roadmap Epigenomics DHS regions 
|
Fetal Brain Female |
Scores for E082-Fetal Brain Female score-Roadmap Epigenomics DHS regions 
|
SSC Frequency |
SSC Frequency 
|
genome gnomAD AC |
Allele counts for the genome-only subset of gnomAD v2.1. |
genome gnomAD AN |
Allele numbers for the genome-only subset of gnomAD v2.1. |
genome gnomAD AF |
Allele frequencies for the genome-only subset of gnomAD v2.1. gnomAD v2.1 comprises a total of 16mln SNVs and 1.2mln indels from 125,748 exomes, and 229mln SNVs and 33mln indels from 15,708 genomes. (Cited from https://macarthurlab.org/2018/10/17/gnomad-v2-1/) “The raw counts (ac and an) refer to the total number of chromosomes with this allele, and total that were able to be called (whether reference or alternate), respectively. Thus, the allele frequency is ac/an.” (Cited from https://macarthurlab.org/2016/03/17/reproduce-all-the-figures-a-users-guide-to-exac-part-2/) “Deleterious variants are expected to have lower allele frequencies than neutral ones, due to negative selection.” (Cited from the ExAC paper, p.10, ‘Inferring variant deleteriousness and gene constraint’) A total of 15,708 genomes. (Cited from https://gnomad.broadinstitute.org/faq) 
|
genome gnomAD AF percent |
Allele frequencies for the genome-only subset of gnomAD v2.1, as a percentage. (i.e. multiplied by 100.0) 
|
genome gnomAD controls AC |
Controls-only allele counts for the genome-only subset of gnomAD v2.1. (Only samples from individuals who were not selected as a case in a case/control study of common disease.) |
genome gnomAD controls AN |
Controls-only allele numbers for the genome-only subset of gnomAD v2.1. (Only samples from individuals who were not selected as a case in a case/control study of common disease.) |
genome gnomAD controls AF |
Controls-only allele frequencies for the genome-only subset of gnomAD v2.1. (Only samples from individuals who were not selected as a case in a case/control study of common disease.) 
|
genome gnomAD controls AF percent |
Controls-only allele frequencies for the genome-only subset of gnomAD v2.1, as a percentage. (i.e. multiplied by 100.0) (Only samples from individuals who were not selected as a case in a case/control study of common disease.) 
|
genome gnomAD non-neuro AC |
Non-neuro allele counts for the genome-only subset of gnomAD v2.1. (Only samples from individuals who were not ascertained for having a neurological condition in a neurological case/control study) |
genome gnomAD non-neuro AN |
Non-neuro allele numbers for the genome-only subset of gnomAD v2.1. (Only samples from individuals who were not ascertained for having a neurological condition in a neurological case/control study) |
genome gnomAD non-neuro AF |
Non-neuro allele frequencies for the genome-only subset of gnomAD v2.1. (Only samples from individuals who were not ascertained for having a neurological condition in a neurological case/control study) 
|
genome gnomAD non-neuro AF percent |
Non-neuro allele frequencies for the genome-only subset of gnomAD v2.1, as a percentage. (i.e. multiplied by 100.0) (Only samples from individuals who were not ascertained for having a neurological condition in a neurological case/control study) 
|
exome gnomAD AC |
Allele counts for the exome-only subset of gnomAD v2.1. |
exome gnomAD AN |
Allele numbers for the exome-only subset of gnomAD v2.1. |
exome gnomAD AF |
Allele frequencies for the exome-only subset of gnomAD v2.1. A total of 125,748 exomes. (Cited from https://gnomad.broadinstitute.org/faq) 
|
exome gnomAD AF percent |
Allele frequencies for the exome-only subset of gnomAD v2.1, as a percentage. (i.e. multiplied by 100.0) 
|
exome gnomAD controls AC |
Controls-only allele counts for the exome-only subset of gnomAD v2.1. (Only samples from individuals who were not selected as a case in a case/control study of common disease.) |
exome gnomAD controls AN |
Controls-only allele numbers for the exome-only subset of gnomAD v2.1. (Only samples from individuals who were not selected as a case in a case/control study of common disease.) |
exome gnomAD controls AF |
Controls-only allele frequencies for the exome-only subset of gnomAD v2.1. (Only samples from individuals who were not selected as a case in a case/control study of common disease.) 
|
exome gnomAD controls AF percent |
Controls-only allele frequencies for the exome-only subset of gnomAD v2.1, as a percentage. (i.e. multiplied by 100.0) (Only samples from individuals who were not selected as a case in a case/control study of common disease.) 
|
exome gnomAD non-neuro AC |
Non-neuro allele counts for the exome-only subset of gnomAD v2.1. (Only samples from individuals who were not ascertained for having a neurological condition in a neurological case/control study) |
exome gnomAD non-neuro AN |
Non-neuro allele numbers for the exome-only subset of gnomAD v2.1. (Only samples from individuals who were not ascertained for having a neurological condition in a neurological case/control study) |
exome gnomAD non-neuro AF |
Non-neuro allele frequencies for the exome-only subset of gnomAD v2.1. (Only samples from individuals who were not ascertained for having a neurological condition in a neurological case/control study) 
|
exome gnomAD non-neuro AF percent |
Non-neuro allele frequencies for the exome-only subset of gnomAD v2.1, as a percentage. (i.e. multiplied by 100.0) (Only samples from individuals who were not ascertained for having a neurological condition in a neurological case/control study) 
|
MPC |
MPC - Missense badness, PolyPhen-2, and Constraint Downloaded from: MPC download link 
|