Exome coverage, based on RefSeq sequences, was incomplete with exome capture but nearly complete with whole genome resequencing. (a) Since the CCDS only includes very well annotated protein-coding regions, we assessed exome kit coverage of the more comprehensive RefSeq sequences, which include protein-coding exons, non-coding exons, 3' and 5' UTRs, and non-coding RNAs, and encompass 65,545,985 bp of genomic space. Coverage of RefSeq sequences by the exome kits was clearly incomplete, with at most 50% of RefSeq covered at 1× depth or greater. (b) In contrast, coverage of RefSeq by whole genome data from the trio pilot of the 1000 Genomes Project was nearly complete, with approximately 98% of RefSeq covered at 1× or greater and approximately 94% covered at 20× or greater from the more deeply sequenced daughter samples. This plot uses an identical format to the one used in Figure 2; see the caption of Figure 2 for detailed description.
Parla et al. Genome Biology 2011 12:R97 doi:10.1186/gb-2011-12-9-r97