For deletions larger than 500 bp, power was approximately 40% for singletons and reached 90% for variants present ten times or more in the sample set. Our use of different algorithms for SV discovery ensured that all major mechanistic subclasses of deletions were found in our analyses (Supplementary Fig. 9). The lack of appropriate comparator datasets for short indels and larger structural variants other than deletions prevented a detailed assessment of the power to detect these types of variants. However, power to detect short indels was approximately 70% for variants present at least 5 times in the sample, based on the rediscovery of indels in samples overlapping with the SeattleSNPs project25. Extrapolating from comparisons to Alu insertions discovered in the Venter genome26 suggested an average sensitivity for common mobile element insertions of about 75%. Analysis of a set of duplications20 suggested only 30-40% of common duplications were discovered here, mostly as deletions with respect to the reference. Methods capable of discovering inversions and novel sequence insertions in low coverage data with comparable specificity remain to be developed.
