Figure 6

For one of the HapMap - HapMap CNVs (CNV38 from Additional File 3), depicted are the performances of all four platforms. In this case the variant is not obvious (or even apparent) in three of the platforms due to poor coverage of the region. Nimblegen has no coverage, and Agilent and Affymetrix have relatively low coverage. However, these last two platforms do show the copy number variation with what probes they have. Illumina is less convincing on a probe-by-probe basis, but successfully demonstrates the CNV through sheer number of probes in the region.