Table 3.

Results from a simulation study on for a range of values of genetic similarity p_gs and expected numbers of fragments m₁ and m_2, 10,000 replicated pairs of AFLP profiles, 1,000 bootstrap resamples, fldF_S from A. thaliana with N = 450

Parameter settings			Part I Results for
			Mean and SE			95% BCa bootstrap ci
pgs	m1	m2	Mean	Mean after bias correction	Bootstrap SE	Non-coverage % (too low, too high)	Length
0.0	40	40	−0.0009	−0.0008	0.0651	5.55 (3.15, 2.40)	0.2605
	70	70	−0.0017	−0.0014	0.0698	5.17 (2.68, 2.49)	0.2725
	120	120	−0.0021	−0.0015	0.0754	5.55 (2.99, 2.56)	0.2944
0.1	40	40	0.0989	0.1000	0.0749	4.52 (2.28, 2.24)	0.2957
	70	70	0.0996	0.1005	0.0721	5.05 (2.50, 2.55)	0.2815
	120	120	0.0978	0.0986	0.0733	5.17 (2.93, 2..24)	0.2861
0.3	40	40	0.2978	0.3004	0.0824	4.78 (2.34, 2.44)	0.3213
	70	70	0.2987	0.3003	0.0718	5.11 (2.43, 2.68)	0.2798
	120	120	0.2984	0.2995	0.0672	5.14 (2.56, 2.58)	0.2622
0.5	40	40	0.4977	0.5008	0.0789	4.38 (2.17, 2.21)	0.3075
	70	70	0.4978	0.4996	0.0655	4.80 (2.36, 2.44)	0.2558
	120	120	0.4982	0.4994	0.0582	5.26 (2.83, 2.43)	0.2275
0.7	40	40	0.6974	0.7001	0.0658	4.67 (2.43, 2.24)	0.2587
	70	70	0.6988	0.7003	0.0531	4.69 (2.41, 2.28)	0.2085
	120	120	0.6987	0.6997	0.0455	5.29 (2.51, 2.78)	0.1786
0.9	40	40	0.8979	0.8991	0.0391	3.78 (2.32, 1.46)	0.1618
	70	70	0.8994	0.9001	0.0309	4.28 (2.43, 1.85)	0.1253
	120	120	0.8997	0.9001	0.0259	4.62 (2.44, 2.18)	0.1040
0.95	40	40	0.9495	0.9501	0.0267	5.26 (1.74, 3.52)	0.1188
	70	70	0.9497	0.9500	0.0215	4.02 (2.21, 1.81)	0.0914
	120	120	0.9498	0.9500	0.0181	4.43 (2.34, 2.09)	0.0749
0.5	100	50	0.4978	0.4994	0.0600	5.19 (2.60, 2.59)	0.2342
0.5	100	80	0.4982	0.4997	0.0610	5.09 (2.69, 2.40)	0.2381
0.7	70	40	0.6981	0.6999	0.0551	4.97 (2.37, 2.60)	0.2160
0.7	80	70	0.6985	0.6999	0.0517	4.94 (2.71, 2.23)	0.2030

			Part II Results for truncated
			Median and SE			95% BCa bootstrap ci
			Median	Median after bias correction	Bootstrap SE	Non-coverage % (too low, too high)	Length
0.0	40	40	0	0	0.0390	2.40 (2.40)	0.1524
	70	70	0	0	0.0395	2.49 (2.49)	0.1409
	120	120	0	0	0.0414	2.56 (2.56)	0.1419
0.1	40	40	0.0982	0.0992	0.0652	4.52 (2.28,2.24)	0.2510
	70	70	0.0997	0.1007	0.0621	5.05 (2.50,2.55)	0.2311
	120	120	0.1002	0.1011	0.0618	5.17 (2.93,2.24)	0.2249
0.3	40	40	0.2985	0.3013	0.0821	4.78 (2.34,2.44)	0.3204
	70	70	0.2999	0.3017	0.0716	5.11 (2.43,2.68)	0.2798
	120	120	0.2986	0.2997	0.0670	5.14 (2.56,2.58)	0.2618

Part I shows mean, mean after bias correction, mean of the bootstrap standard error, non-coverage percentage of 95% BC_a bootstrap confidence intervals (with left and right non-coverage percentages), and mean length of the interval. Part II shows, for p_gs ≤ 0.3, the same type of results as part I, but for truncated at zero. Instead of means, medians are given. At p_gs = 0.0, only non-coverage at the right of p_gs = 0.0 is considered