Table 5.

Comparison of bootstrap confidence intervals for p_gs 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			Results for : 95% bootstrap confidence intervals for pgs
			Percentile bootstrap c.i.		Bias corrected bootstrap c.i.		BCa c.i.
pgs	m1,	m2	Non-coverage% (too low, too high)	Length (trunc)	Non-coverage% (too low, too high)	Length (trunc)	Non-coverage% (too low, too high)	Length (trunc)
0.0	40	40	6.98 (5.57, 1.41)	0.2495 (0.1324)	6.50 (4.73, 1.77)	0.2517 (0.1386)	5.34 (3.04, 2.30)	0.2584 (0.1522)
	70	70	5.68 (3.63, 2.05)	0.2670 (0.1332)	5.60 (3.40, 2.20)	0.2672 (0.1354)	5.45 (2.88, 2.57)	0.2680 (0.1396)
	120	120	5.40 (3.08, 2.32)	0.2862 (0.1382)	5.48 (3.23, 2.25)	0.2862 (0.1381)	5.38 (3.11, 2.27)	0.2862 (0.1387)
0.1	40	40	5.70 (4.16, 1.54)	0.2893 (0.2369)	5.21 (3.47, 1.74)	0.2904 (0.2416)	4.53 (2.28, 2.25)	0.2942 (0.2511)
	70	70	5.25 (3.18, 2.07)	0.2777 (0.2255)	5.28 (3.01, 2.27)	0.2778 (0.2778)	4.93 (2.53, 2.40)	0.2781 (0.2297)
	120	120	5.05 (2.95, 2.10)	0.2796 (0.2220)	4.98 (2.86, 2.12)	0.2797 (0.2220)	4.92 (2.80, 2.12)	0.2797 (0.2223)
0.3	40	40	5.49 (3.30, 2.19)	0.3201 (0.3187)	5.34 (2.90, 2.44)	0.3200 (0.3189)	4.73 (2.16, 2.57)	0.3205 (0.3197)
	70	70	5.54 (2.89, 2.65)	0.2781 (0.2776)	5.51 (2.80, 2.71)	0.2780 (0.2776)	5.29 (2.55, 2.74)	0.2780 (0.2776)
	120	120	5.19 (2.57, 2.62)	0.2580 (0.2578)	5.25 (2.60, 2.65)	0.2581 (0.2579)	5.08 (2.58, 2.50)	0.2582 (0.2579)
0.5	40	40	4.97 (2.66, 2.31)	0.3074	4.75 (2.44, 2.31)	0.3072	4.30 (2.17, 2.13)	0.3070
	70	70	5.09 (2.42, 2.67)	0.2548	5.04 (2.41, 2.63)	0.2547	4.72 (2.30, 2.42)	0.2548
	120	120	5.23 (2.66, 2.57)	0.2246	5.24 (2.62, 2.62)	0.2246	4.99 (2.68, 2.31)	0.2250
0.7	40	40	5.73 (2.41, 3.32)	0.2568	5.48 (2.49, 2.99)	0.2573	4.76 (2.47, 2.29)	0.2586
	70	70	5.22 (2.28, 2.94)	0.2065	5.14 (2.32, 2.82)	0.2068	4.76 (2.41, 2.35)	0.2078
	120	120	5.63 (2.32, 3.31)	0.1760	5.53 (2.41, 3.12)	0.1762	5.38 (2.73, 2.65)	0.1770
0.9	40	40	6.30 (1.62, 4.68)	0.1517	5.53 (1.76, 3.77)	0.1542	3.83 (2.18, 1.65)	0.1613
	70	70	5.89 (1.58, 4.31)	0.1202	5.33 (1.83, 3.50)	0.1213	4.29 (2.36, 1.93)	0.1250
	120	120	5.64 (1.63, 4.01)	0.1004	5.49 (1.91, 3.58)	0.1011	4.65 (2.36, 2.29)	0.1032
0.95	40	40	9.15 (0.85, 8.30)	0.1020	7.07 (1.04, 6.03)	0.1060	5.16 (1.59, 3.57)	0.1173
	70	70	7.63 (1.18, 6.45)	0.0829	6.48 (1.49, 4.99)	0.0850	4.63 (2.22, 2.41)	0.0907
	120	120	6.82 (1.31, 5.51)	0.0682	5.99 (1.48, 4.51)	0.0708	4.37 (2.30, 2.07)	0.0742
0.5	100	50	5.30 (2.79, 2.51)	0.2337	5.37 (2.72, 2.65)	0.2336	5.03 (2.56, 2.47)	0.2336
0.5	100	80	5.23 (2.68, 2.55)	0.2364	5.17 (2.65, 2.52)	0.2365	5.03 (2.65, 2.38)	0.2367
0.7	70	40	5.62 (2.33, 3.29)	0.2150	5.35 (2.20, 3.15)	0.2149	4.81 (2.17, 2.64)	0.2157
0.7	80	70	5.48 (2.54, 2.94)	0.2009	5.51 (2.63, 2.88)	0.2012	5.21 (2.83, 2.38)	0.2021

Shown are non-coverage percentages (with left and right non-coverage percentages) and mean length of (1) 95% percentile bootstrap c.i., (2) 95% bias-corrected bootstrap c.i., and (3) 95% accelerated bias-corrected (BC_a) bootstrap c.i