GC content of the reference around the given site
The GC content is the number of GC bases relative to the total number of bases (# GC bases / # all bases) around this site on the reference.
The window size used to calculate the GC content around the site is set by the tool used for annotation (currently UnifiedGenotyper, HaplotypeCaller or VariantAnnotator). See the Technical Document for each tool to find out what window size they use.
GATK version 2.8-1-g2a26ec9 built at 2013/12/06 16:54:02.