(a) Representative example of a germline IGE insertion event that was found in each of the 6 individual flies and that is absent in the simulated Drosophila melanogaster reference genome (DMsim). Putative somatic insertion events of the same IGE occurred at loci which are approximately 10 kb up- and downstream of the original germline insertion site. Dark purple diamonds represent the original germline insertion site, which, as expected, was present in each of the 12 samples (αβ-KCs and the rest of the brain). Light purple diamonds represent putative somatic IGE insertions in each of the samples. (b) Plot showing the number of putative new insertions in WGS data from oocytes (Khurana et al., 2011). Samples were normalized to a depth of 18.3-fold (as in Khurana et al., 2011) and the bars represent the putative insertions that were not detected in the parental strains. In addition, the number of IGE ‘mobilizations’ is shown. Note that the number of false positive IGE insertions is highest in the sample obtained from 21 day old dysgenic ovaries, and decreases in the F2 generation. (c) Graph illustrating the penetrance of a small selection of simulated IGE insertions. The actual penetrance for each locus should be 1. However, due to variations in local sequencing coverage, the analysis pipeline assigns varying frequencies to each IGE insertion. The penetrance of each IGE insertion shown apparently increases with age. (d) The average number of putative de novo insertions present in the three samples from oocytes (Khurana et al., 2011) correlates with the theoretical number of sequencing reads that map onto each transposon sequence in the Drosophila reference genome. The number of reads was based on the sequencing coverage (18.3-fold) and the number of 76nt fragments that overlap with each transposon reference sequence. Note, for example, Roo, R1 and FW the three endogenous transposons that contribute most frequently to ‘insertions’ are also the most abundant elements in the reference genome.