Fig. 2a shows the rate of discovery of variants in the CEU samples of the low coverage project as assessed by comparison to external data sources: HapMap and the exon project for SNPs and array CGH data20 for large deletions. We estimate that while the low coverage project had only ~25% power to detect singleton SNPs, power to detect SNPs present five times in the 120 sampled chromosomes was ~90% (depending on the comparator), and power was essentially complete for those present 10 or more times. Similar results were seen in the YRI and CHB+JPT analysis panels at high allele counts, but slightly worse performance for variants present five times (~85% and 75% respectively at HapMap II sites; Supplementary Fig. 8). These results suggest that SNP discovery is less affected by the extent of LD (which is lowest in the YRI) than sequencing coverage (which was lowest in the CHB and JPT).
