GC contents comparison between gap regions and non-gap regions. The gap regions (GR) have a comparative lower GC content compared with non-gap (NGR) regions. Contigs from SOLiD platform are most sensitive to the GC content. Here the gap region means the some continuous bases existing in the reference were not covered by the contigs from any platform when they were aligned to the reference.
Wang et al. BMC Systems Biology 2012 6(Suppl 3):S21 doi:10.1186/1752-0509-6-S3-S21