Number of deletion calls covering the whole of true deletions. Solid lines and circles show the number of all deletion calls generated by each tool, whereas dashed lines and ‘+’ symbol s show the number of deletion calls covering the whole of true deletions. Most of the deletion calls of MoDIL, CNVnator (expanded by the window size), and Pindel covered the whole of true deletions. On the other hand, many CLEVER results did not always contain the whole of true deletions, while median of the distribution of predicted breakpoints was close to the true breakpoints as shown in Figure 10. BreakDancer results for high coverage data did not always contain true deletions either. Predicted breakpoints of BreakDancer approached true breakpoints as the depth of coverage increases, and sometimes intruded into true deletions when coverage was high.