Figure 2

Coverage achieved by the GENCODE exome. (a) Cumulative fold coverage plot for HapMap samples captured with Agilent SureSelect Human All Exon Kit (CCDS), the GENCODE exome, and the regions covered by the GENCODE exome only. Similar data are presented for the clinical samples and the GENCODE exome only in Supplementary Figure 1. In all cases, the thin red vertical line indicates a fold coverage of eightfold, the preferred coverage required for variant calling. (b and c) Detailed view of the average sequence depth of the seven clinical samples across the entire gene region post sequence capture of two example genes that are unique to the GENCODE exome: (b) ABCB11 and (c) XPC. In the upper part of each panel, the positions of the baits from the GENCODE exome are given as dark grey boxes above the exon structure (adapted from the Ensembl genome browser) of each gene in red. The increased sequencing depth of the eights exon of XPC is caused by good coverage of this larger exon with eight different bait sequences, whereas the other smaller exons are covered by one or two baits.