Download EGL Exome Coverage Tool

EGL Exome Coverage Tool
This tool can be used to view typical depth of sequence coverage obtained by exome sequencing
performed by our laboratory. These data were calculated based on approximately 30 samples
processed using our exome pipeline. An individual base is considered to have high coverage if the
coverage was 20X or greater for at least half of the samples analyzed. Depth of coverage of a region of
interest in a specific sample is not guaranteed. Please note, high coverage does not necessarily mean
high quality data, as the sequence in some regions are not unique (more information about
pseudogenes below).
Instructions:
The tool is available at: http://geneticslab.emory.edu/exome-coverage/.
To begin, please enter a gene or click on “Enter multiple genes” to provide a list of genes (one per line).
If searching for one gene, partial matches are allowed. If searching for a list of genes, only exact gene
symbol* matches will be listed. Click on “Search” to get the list of genes that match your criterion.
*Note: Gene names must follow official HGNC nomenclature (http://www.genenames.org/).
You will be presented with a list of genes/transcripts that we have analyzed matching your search term.
For example, searching for “ABC” returns 4 genes/transcripts in the following table:
Some genes/transcripts display a warning related to pseudogene issues. If your search returns more
than 15 genes, use the “Next” and “Previous” links to navigate through the whole list.
Clicking on a particular line will allow you to view detailed coverage information:
We currently use GRCh37/hg19 as the reference for our alignments. All coordinates are based on this
reference assembly.
For each coding exon, we also analyze 10 intronic bases on either side of the exon. Genomic coordinates
for the exon include these intronic bases.
The last 3 columns are related to pseudogene issues:
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Potential Pseudogene Region - determined computationally. Homology with another region of
the genome may or may not interfere with analysis.
Sanger Only - manually reviewed. This region cannot be assayed by NGS but Sanger sequencing
may be possible.
No Assay - sequence analysis of the region cannot be performed currently.
A checkmark in any of these 3 columns for any exon results in a warning in the initial gene/ transcript
page.