With enough raw data, whole genome sequencing could achieve almost complete coverage of the CCDS (intended target of the exome capture kits). Approximately 98% of CCDS was covered at 1× or greater and approximately 94% covered at 20× or greater from the more deeply sequenced daughter samples. To generate this plot depicting the relationship between CCDS coverage depth and raw sequence data input, we imposed a coverage model based on two assumptions: that CCDS coverage depth should match genome coverage depth, and that genome size (3 Gb) times the desired coverage depth is the amount of raw sequence data (in gigabases) necessary to achieve such depth. Illumina Only, only the alignment files from Illumina sequence data were used; All, alignment files from Illumina, 454, and SOLiD sequence data were used.
Parla et al. Genome Biology 2011 12:R97 doi:10.1186/gb-2011-12-9-r97