Coverage assessment

[Seq84]

Hi,

We are making a target resequencing experiment in 6 differents regions. During coverage assessment with DepthOfCoverage walker in GATK we noticed that regions rich in GC (high %GC) were characterize by lower coverage values compare to ones in low-normal %GC regions.

How the % in GC can affect coverage in a target resequencing experiment?

Thanks in advance

[visivas]

We found similar distribution of coverage for targeted resequencing experiment with %GC compared to whole genome. We had peak coverage in regions that had between 30%-70% GC content.