Only 85% of the genome is accessible to accurate analysis with the short read technology used by the 1000 Genomes pilot project.  The remaining 15% is either repeats or segmental duplications.

The project created a "callability mask" to identify those regions that could not be assayed accurately.  More information about these files are available here:

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/release/2010_03/pilot1/supporting/README_callability_masks