For the low coverage analysis, the accessible genome contains approximately 85% of the reference sequence and 93% of the coding sequences. Over 99% of sites genotyped in the second generation haplotype map (HapMap II)4 are included. Of inaccessible sites, over 97% are annotated as high copy repeats or segmental duplications. However, only one quarter of previously discovered repeats and segmental duplications were inaccessible (Supplementary Table 2). Much of the data for the trio project was collected prior to technical improvements in our ability to map sequence reads robustly to some of the repeated regions of the genome (primarily longer, paired reads). For these reasons, stringent alignment was more difficult and a smaller portion of the genome was “accessible” in the trio project: 80% of the reference, 85% of coding sequence and 97% of HapMap II sites (Table 1).
