Effect of different thresholds on SV identification. Different sets of indels are called at combinations of different values for thresholds tr, tn, and tc. Each bar shows the percentages of the true positives, the false negatives, and the false positives of each call set, which are represented by the colored, the white, and the gray portions, respectively. The bars in different shades of green and red are used for the true positive calls of deletion and insertion of different length. (A-B) The alignment score ratio threshold, tr. SV are calls for a set of simulated reads using different tr while tn = 5 and tc = 0.1 are kept unchanged. (C-D) The number of supportive read threshold, tn. SV are calls for the same set of simulated reads using different tn while tr = 1 and tc = 0.1 are kept unchanged. (E-F) The maximum centeredness threshold, tc. SV are calls for the same set of simulated reads using different tc while tn = 5 and tr = 1 are kept unchanged.