Structural variation in the human genome has been underestimated

In todays issue of Science, a study concludes that the structural variation in our genome is probably larger than what has been though. They suggest that the variation surpass single nucleotide variation (as revealed by the HapMap project).

The study was conducted with massive paired-end sequencing on two individuals from the HapMap project, one European and one African, so the sample is somewhat small. On the other hand, we have not been thinking of variation between two random individuals as drastic as is shown here.

I am curious if this variation is also the actual cause behind the differences between the HPR assembly and the Celera assembly. Obviously, the challenge of putting together a genome assembly for a pool of individuals is now somewhat of an ill-posed problem! I think Celera pooled data from five people of different ethnic populations, and then they added data from the HPR sample: all in all a problematic task.