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quinlan-lab / ccrhtml

A small repo for storing the code for making the files and html for CCRs.
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A map of constrained coding regions (CCRs) in the human genome.

If you use CCRs in any way, please cite the paper:

Havrilla, J.M., Pedersen, B.S., Layer, R.M. & Quinlan, A.R. A map of constrained coding regions in the human genome. Nature Genetics (2018). doi:10.1038/s41588-018-0294-6

Note that currently, all files use the hg19/GRCh37 human reference.

CCR Bed File | CCR Tabix Index File | CCR BigWig File

X-CCR Bed File | X-CCR Tabix Index File | X-CCR BigWig File

CCR Browser

So the browser is accessible at www.rebrand.ly/ccrregions (the link shown above) or the hard link at https://s3.us-east-2.amazonaws.com/ccrs/ccr.html. You can use either link to get to the browser, and after either link you can submit a locus as a query to the browser at the end of the URL like so:

Additionally you can do multi-locus search in the URL (or separated by spaces in the search bar of IGV) like so:

Browser Screenshot

BED file columns

Column Description
chrom Chromosome ID
start Start coordinate (may be part of a multi-exon CCR)
end End coordinate (may be part of a multi-exon CCR)
ccr_pct CCR percentile. 0 represents ExAC variants and is total non-constraint. 100 represents complete constraint, the highest constrained region in the model.
gene HGNC gene name.
ranges The range of coordinates that represent the CCR. For multi-exon spanning CCRs, this will be a comma-separated list of ranges.
varflag VARTRUE = 0th percentile CCR, and thus an ExAC variant coordinate (or several ExAC deletions merged into one CCR). VARFALSE = Anything that is not a 0th percentile CCR.
syn_density A calculation of the synonymous variant density of the CCR region. Used variants that were SNPs and did not change amino acids or stop/start codons. Allowed multiple alleles at same bp.
cpg CpG dinucleotide density of the whole CCR region.
cov_score The score of length scaled by coverage proportion at 10x for each base pair.
resid Raw residual value from the linear regression model.
resid_pctile Raw residual percentile, not weighted by proportion of exome represented.
unique_key A unique key ID for each CCR.