DOI: 10.5061/dryad.n8pk0p2x0
title: Most damaging CADD scores for hg19 human genome build (CADD scores generated with bStatistic removed)

description: Analyses of genetic variation in many taxa have established that neutral
 genetic diversity is shaped by natural selection at linked sites. Whether
 the mode of selection is primarily the fixation of strongly beneficial
 alleles (selective sweeps) or purifying selection on deleterious mutations
 (background selection) remains unknown, however. We address this question
 in humans by fitting a model of the joint effects of selective sweeps and
 background selection to autosomal polymorphism data from the 1000 Genomes
 Project. After controlling for variation in mutation rates along the
 genome, a model of background selection alone explains ~60% of the
 variance in diversity levels at the megabase scale. Adding the effects of
 selective sweeps driven by adaptive substitutions to the model does not
 improve the fit, and when both modes of selection are considered jointly,
 selective sweeps are estimated to have had little or no effect on linked
 neutral diversity. The regions under purifying selection are best
 predicted by phylogenetic conservation, with ~80% of the deleterious
 mutations affecting neutral diversity occurring in non-exonic regions.
 Thus, background selection is the dominant mode of linked selection in
 humans, with marked effects on diversity levels throughout autosomes.
description: This dataset contains CADD
 scores separated into each of the human autosomes in NumPy zipped files
 (.npz format). The scores are based on the most damaging CADD score for
 each site in the genome. These most damaging scores per site were based on
 a custom set of CADD scores generated by the Kircher Lab, which maintains
 and updates the CADD project. They removed the bStatistic input (based on
 McVicker's B) from the set of annotations used to generate CADD
 scores, since some of our work infers new B scores using CADD as an input,
 and we wanted to avoid the circularity of building new B scores using an
 annotation that includes the old B scores.
description: # Most damaging CADD scores for hg19 human genome build (CADD scores
 generated with bStatistic removed) *** This dataset contains CADD scores
 separated into each of the human autosomes in NumPy zipped files (.npz
 format). The scores are based on the most damaging CADD score for each
 site in the genome. These most damaging scores per site were based on a
 custom set of CADD scores generated by the Kircher Lab, which maintains
 and updates the CADD project. They removed the bStatistic input (based on
 McVicker's B) from the set of annotations used to generate CADD
 scores, since some of our work infers new B scores using CADD as an input,
 and we wanted to avoid the circularity of building new B scores using an
 annotation that includes the old B scores. Original CADD scores that these
 were derived from can be found at: https://cadd.gs.washington.edu/ These
 files must be opened using NumPy. They are formatted such that for each
 chromosome the most damaging CADD score is given for each chromosomal site
 (0 for missing data). Thus, for a chromosome 50M bp long, the file is an
 array of 50M scores. Note that these are not identical to raw CADD scores:
 as described in the appendix, we took the most damaging of the three
 possible single base substitutions for each site and kept that score
 (positions with no annotated score are given 0). These are formatted as
 zipped numpy arrays (.npz files). Each array is the length of the
 chromosome given in the filename with a score at each position (in hg19
 build). To unzip the scores, you use the key cadd. For each chromosome,
 the files contain one score per site in that chromosome, where the first
 position in the chromosome is at index 0, the last position at position
 (chromosome length)-1. NOTE: CADD scores were made using v1.6 with the
 bStatistic removed # how to open files: ``` import numpy as np ``` ``` a =
 np.load('/Users/MURPHYD/Downloads/chr22.cadd.scores.npz')['cadd'] ``` ``` len(a) ``` ``` 51304566 ```