Reads were mapped to the reference human genome (UCSC hg18), initially with ELAND (Illumina) for quality recalibration, and then again with Maq30. Sequence calls were also performed by Maq, and filtered to coordinates with >= 8x coverage and a phred-like30 consensus quality >= 20. Indels affecting coding sequence were identified as described previously2. Sequence calls were compared against 8 HapMap individuals for whom we had previously reported exome data2. Annotations of variants were based on NCBI and UCSC databases, supplemented with PolyPhen Grid Gateway predictions generated for nearly all nonsynonymous SNPs. Any non-synonymous variant that was not assigned a “benign” PolyPhen prediction was considered to be damaging, as were all splice acceptor and donor site mutations and all coding indels.
