Bridges Singletons Annotated With Local Genomic Features

This dataset consists of a tarball archive containing 8,192 tab-delimited files (one per 7-mer sequence motif). Each file contains information about the status or value of 15 different genomic features at every possible site in hg19, centered at the 7-mer sequence motif indicated in the filename (or the reverse complement of that motif; e.g. <code>ACGATGC_annotated.txt</code> includes information for sites at 5’-ACG<strong>A</strong>TGC-3’ <em>and</em> sites at 5’-GCA<strong>T</strong>CGT-3’ motifs).

Each file contains the following columns:

<strong>AT_CG</strong> [indicator if site carries an A&gt;C or T&gt;G singleton (1) or not (0) in the BRIDGES data]

<strong>AT_GC</strong> [indicator if site carries an A&gt;G or T&gt;C singleton (1) or not (0) in the BRIDGES data]

<strong>AT_TA</strong> [indicator if site carries an A&gt;T or T&gt;A singleton (1) or not (0) in the BRIDGES data]

<strong>GC_AT</strong> [indicator if site carries a G&gt;A or C&gt;T singleton (1) or not (0) in the BRIDGES data]

<strong>GC_CG</strong> [indicator if site carries a G&gt;C or C&gt;G singleton (1) or not (0) in the BRIDGES data]

<strong>GC_TA</strong> [indicator if site carries a G&gt;T or C&gt;A singleton (1) or not (0) in the BRIDGES data]

<strong>DP</strong> [average depth of coverage at site]

<strong>H3K4me1</strong> [indicator if site is within a H3K4me1 broad peak (1) or not (0)]

<strong>H3K4me3</strong> [indicator if site is within a H3K4me3 broad peak (1) or not (0)]

<strong>H3K9ac</strong> [indicator if site is within a H3K9ac broad peak (1) or not (0)]

<strong>H3K9me3</strong> [indicator if site is within a H3K9me3 broad peak (1) or not (0)]

<strong>H3K27ac</strong> [indicator if site is within a H3K27ac broad peak (1) or not (0)]

<strong>H3K27me3</strong> [indicator if site is within a H3K27me3 broad peak (1) or not (0)]

<strong>H3K36me3</strong> [indicator if site is within a H3K36me3 broad peak (1) or not (0)]

<strong>EXON</strong> [indicator if site is within an exon (1) or not (0)]

<strong>CpGI</strong> [indicator if site is within a CpG island (1) or not (0)]

<strong>RR</strong> [average recombination rate in the 10kb window centered at the site]

<strong>LAMIN</strong> [indicator if site is within an Lamin-Associated Domain (1) or not (0)]

<strong>DHS</strong> [indicator if site is within a DNase Hypersensitive region (1) or not (0)]

<strong>TIME</strong> [average recombination rate in the 10kb window centered at the site]

<strong>GC</strong> [average GC content in the 10kb window centered at the site]

Note that the chromosome and position of each site has been removed to protect sample privacy.

Each file is then passed to an R script (available at https://github.com/carjed/smaug-genetics) to estimate the effects each feature on the relative mutation rate using a logistic regression model (e.g., <code>AT_GC ~ DP + ... + GC</code>). Each of the features used is available from data in the public domain; the provenance of these features is described in the associated paper, and additional scripts for processing the feature data can be found at at https://github.com/carjed/smaug-genetics.

The BRIDGES whole-genome sequencing study is described at https://doi.org/10.1101/108290