SV reconstruction efficiency in relation to the span coverage λ. We used simulations to generate heterozygous deletions 1-10 kb in size (median PEM insert size 2.5 kb; 454/Roche platform). Paired-end data were simulated with different span coverages λ; only optimally (uniquely) placed paired ends were considered when estimating λ. (a) Reconstruction efficiency for values of λ from 1× to 5×. (b) Reconstruction efficiency for values of λ from 5× to 25×.