Performance of structural variant prediction on simulated 454 data sets. Read data sets with different average read lengths and coverage depths were generated according to a 454 error model with a 10% standard deviation in read length from simulated E. coli reference sequences with many examples of a single type of mutation causing structural variation randomly introduced. Results in terms of the sensitivity (or recall) for recovering true-positives (top panels) and the precision, equal to the number of true-positive predictions over the total number of predictions (bottom panels), are graphed as a function of junction skew scores accepted for making predictions. Results are shown for simulated genomes containing only a) deletions with breakpoints in non-repetitive reference genome sequences, b) new insertions of bacterial transposable sequences (IS elements), and c) deletions with one boundary ending on a repetitive IS element. The default junction skew score cutoff used by breseq is 3.0.