Table 2. The observed type I error rate when testing for differential enrichment using counts from each peak calling strategy. Error rates for a range of specified error thresholds are shown. All values represent the mean of 10 simulation iterations with the standard error shown in brackets. RA: reference analysis using 10 000 randomly chosen true peaks.

ID	Error rate
	0.01	0.05	0.1
RA	0.010 (0.000)	0.051 (0.001)	0.100 (0.002)
1	0.002 (0.000)	0.019 (0.001)	0.053 (0.001)
2	0.003 (0.000)	0.030 (0.000)	0.073 (0.001)
3	0.006 (0.000)	0.042 (0.001)	0.092 (0.001)
4	0.033 (0.001)	0.145 (0.001)	0.261 (0.002)
5	0.000 (0.000)	0.001 (0.000)	0.005 (0.000)
6	0.088 (0.006)	0.528 (0.013)	0.893 (0.006)
7	0.010 (0.000)	0.049 (0.001)	0.098 (0.001)