Method ρ λ L p T+ F− T+ F− T+ F− QuEST − 0.15(0.03) 0.10(0.01) 998(115) 887(80) 0.74(0.09) 0.77(0.09) MACS 0.01 0.15(0.03) 0.12(0.02) 1002(114) 926(118) 0.74(0.08) 0.70(0.09) PICS 0.01 0.15(0.03) 0.15(0.03) 977(112) 1064(99) 0.72(0.08) 0.82(0.05) CCAT 0.05 0.15(0.03) 0.14(0.03) 997(114) 1039(156) 0.74(0.09) 0.74(0.10)

Table 5: Comparison of the average value of the simulation parameters for true positives(T+) and false negatives(F−), where ρ denotes the cutoff value for region FDR; λ denotes the mean rate for generating the distance from read to read; L denotes the length of peak region; p denotes the probability to generate dominate reads. The number in the parentheses is the standard error. Since the number of T+ and F- are not equal, the interpretation of the standard error should be cautious.