Table 2.

Demographic scenario: Mean, median, and SD of the RMSE are listed for LDJump (with segment lengths of 1 kb, type I error of 0.05 and the 0.35 quantile) and LDpop using samples simulated under demography

$\rho$	Program	Mean	Median	SD
0.0010	LDJump	0.0080	0.0074	0.0014
	LDpop	0.0066	0.0067	0.0005
0.0013	LDJump	0.0108	0.0096	0.0032
	LDpop	0.0090	0.0091	0.0005
0.0022	LDJump	0.0170	0.0160	0.0027
	LDpop	0.0154	0.0154	0.0006
0.0027	LDJump	0.0194	0.0190	0.0014
	LDpop	0.0190	0.0190	0.0006
0.0039	LDJump	0.0273	0.0272	0.0004
	LDpop	0.0275	0.0277	0.0009
0.0045	LDJump	0.0316	0.0314	0.0005
	LDpop	0.0318	0.0320	0.0008
0.0054	LDJump	0.0383	0.0378	0.0013
	LDpop	0.0388	0.0390	0.0008
0.0062	LDJump	0.0439	0.0434	0.0012
	LDpop	0.0441	0.0441	0.0005
0.0071	LDJump	0.0495	0.0494	0.0007
	LDpop	0.0512	0.0512	0.0003
0.0080	LDJump	0.0561	0.0560	0.0007
	LDpop	0.0579	0.0583	0.0008
0.0085	LDJump	0.0604	0.0600	0.0017
	LDpop	0.0614	0.0614	0.0007
0.0091	LDJump	0.0645	0.0637	0.0023
	LDpop	0.0653	0.0654	0.0006
0.0100	LDJump	0.0699	0.0694	0.0012
	LDpop	0.0723	0.0720	0.0008

The results are obtained based on 10 replicates of different background rates. 16 sequences of length 30 kb containing two hotspots both of length 1 kb with intensities of 20 and 35 are simulated.