Despite being the most comprehensive population-based CNV map so far, still to be well-characterized are CNVs <500 bp, insertions of new sequences relative to the reference sequence, subtle changes in the total number of copies of high-copy number dispersed repeats such as Alu elements and LINEs, and CNVs on the Y chromosome and heterochromatic regions. Notwithstanding, we estimate that in this study we have discovered about 80–90% of common CNVs (MAF > 5%) greater than 1 kb in length, and have been able to genotype approximately 40% of these (Supplementary Methods). The remaining CNVs will probably be best captured by genome sequencing experiments.
