Fig. 3.

Precision and recall of MEIs, NUMTs, and VEIs called using existing algorithms. MEI (a, b), NUMT, and VEI (c, d) insertions were called using the indicated algorithms and simulated data (a, c) and the real data (b, d). NUMTs and VEIs were called using algorithms including modified versions of Mobster, MELT, and Tangram (Mobster-numt, Mobster-vei, MELT-numt, Tangram-numt, and Tangram-vei). For the real data, the mean values of the results obtained with the four NA12878 real datasets (data1 to data4) are indicated. VirusFinder and HGT-ID could not be applied to accomplish the runs for the real data due to unresolvable errors. The precision and recall percentages (or the number of true positives for the real data) determined for the respective call sets are indicated on the x-axis and y-axis, respectively. The data labeled with (+len) were determined considering insertion length in addition to breakpoints in (a). In this case, called sites were judged as true when the ratio of the called MEI lengths and the matched reference MEI length was ≧ 0.5 and ≦ 2.0. The algorithms without the label do not output the defined length of insertions