Table 1 

Results of simulations indicating the reconstruction efficiency of PEMer for heterozygous deletions of different sizes 

SV size 
Single cutoff 
Multicutoff 
Simplified multicutoff 
Multicutoff* 
Simplified multicutoff* 


1000 
3 (4) 
3 (4) 
3 (4) 
3 (4) 
3 (4) 
2000 
12 (13) 
23 (26) 
21 (23) 
11 (13) 
6 (6) 
3000 
52 (57) 
61 (68) 
61 (68) 
49 (52) 
44 (46) 
4000 
84 (85) 
85 (86) 
85 (86) 
80 (82) 
80 (82) 
5000 
91 (93) 
91 (93) 
91 (93) 
91 (93) 
91 (93) 
6000 
92 (92) 
92 (92) 
92 (92) 
92 (92) 
92 (92) 
10000 
88 (91) 
88 (91) 
88 (91) 
88 (91) 
88 (91) 


Total 
422 (435) 
443 (460) 
441 (457) 
414 (427) 
404 (414) 
False positives (chromosome 2) 
31 (31) 
31 (31) 
26 (31) 
5 (4) 
2 (1) 


Each row displays statistics for reconstructed heterozygous deletions of a particular size, derived from simulations of 454/Roche based PEM data. Columns show numbers of identified SVs for each reconstruction strategy. Numbers in parentheses correspond to simulated SV reconstructions without sequencing error. All SVs were reconstructed at an effective span coverage λ = 5× (where, λ was assessed after optimal pairedend placement) of a simulated diploid chromosome 2. Note that for the single cutoff strategy events ≥ 5 kb were reconstructed at a level near the theoretical maximum of 95% derived from the Poisson approximation (see supplementary methods and notes in Additional data file 1). However, the multicutoff and simplified multicutoff strategies outperformed the single cutoff strategy in detecting SVs < 4 kb. *We also applied alternative  that is, optimal  cutoff parameters, for which the sensitivity is similar to the single cutoff, but for which a false positive rate of approximately 5% was observed. 

Korbel et al. Genome Biology 2009 10:R23 doi:10.1186/gb2009102r23 