Table 2. Percentage of data sets where linkage phase configuration was correctly estimated for parents P and Q in simulation 2.

Preferential pairing		0.00			0.25			0.50
Quadrivalent formation		0.00	0.25	0.50	0.00	0.25	0.50	0.00	0.25	0.50
Autotetraploid
$\eta =3$	P	100.0	99.0	91.5	98.5	98.5	90.0	80.5	93.0	87.5
		100.0	99.5	99.5	98.5	99.5	97.5	57.5	88.5	97.0
		99.5	97.5	98.5	100.0	98.5	94.0	55.0	85.5	94.5
		100.0	100.0	99.5	99.0	98.0	98.0	60.5	86.5	93.0
		99.5	99.5	97.0	98.5	97.0	95.5	67.5	84.5	97.5
	Q	100.0	98.5	90.0	100.0	97.0	90.0	60.0	91.5	86.0
		100.0	100.0	98.0	99.5	100.0	99.0	65.0	89.0	93.5
		100.0	98.5	98.0	97.0	98.5	94.5	41.0	82.0	93.5
		100.0	100.0	99.0	99.5	98.0	98.0	56.5	84.5	90.0
		99.5	99.5	98.0	99.0	98.5	94.5	58.0	82.0	94.0
$\eta =5$	P	100.0	99.5	93.0	100.0	99.5	95.0	98.0	99.0	95.0
		100.0	100.0	100.0	100.0	100.0	100.0	90.0	99.5	99.0
		100.0	99.5	100.0	100.0	100.0	99.5	86.0	98.5	100.0
		100.0	100.0	100.0	99.5	100.0	99.5	86.5	98.5	100.0
		100.0	100.0	100.0	100.0	100.0	100.0	90.5	96.0	100.0
	Q	100.0	99.5	93.0	100.0	99.0	94.0	88.0	98.5	95.5
		100.0	100.0	100.0	100.0	100.0	100.0	91.5	99.5	99.5
		100.0	99.5	100.0	99.5	100.0	99.0	85.0	98.0	100.0
		100.0	100.0	100.0	99.5	100.0	99.5	86.0	97.5	98.5
		100.0	100.0	99.5	100.0	100.0	100.0	92.0	96.0	99.0
Autohexaploid
$\eta =3$	P	84.0	78.5	70.5	69.0	63.5	61.0	2.5	10.5	19.0
		99.0	94.0	91.0	93.0	84.5	80.0	6.5	16.0	22.0
		89.0	94.0	88.0	80.0	84.0	80.5	10.5	16.0	32.5
		93.0	90.5	86.0	88.5	84.0	80.0	9.0	16.5	28.5
		96.0	92.5	91.5	89.5	94.0	87.5	19.0	30.5	44.5
	Q	85.0	81.0	71.0	68.0	52.5	57.5	1.5	3.5	8.5
		99.0	95.0	91.0	86.5	90.0	88.5	9.0	28.0	37.5
		90.0	90.0	86.0	79.0	82.0	77.0	9.5	18.0	28.0
		96.5	92.5	89.5	90.0	89.0	89.0	25.5	35.5	41.0
		95.0	92.0	92.5	89.5	91.0	88.0	16.0	23.0	39.0
$\eta =5$	P	86.0	84.5	75.5	77.5	69.5	72.5	27.0	36.5	52.5
		100.0	97.5	96.5	98.5	98.0	91.0	55.5	70.5	74.5
		91.5	95.5	93.0	90.5	94.5	89.5	68.0	68.5	77.5
		96.5	94.0	91.0	99.5	99.0	96.5	65.0	78.5	85.0
		98.0	98.5	100.0	97.5	99.0	99.0	73.0	87.5	91.0
	Q	86.5	83.5	75.0	69.5	68.5	72.0	17.5	20.0	39.5
		100.0	99.5	99.0	100.0	99.5	100.0	74.0	81.0	92.5
		91.5	95.5	93.0	91.0	95.0	89.5	67.5	71.5	77.0
		99.0	97.5	93.5	100.0	100.0	99.5	80.0	89.0	92.0
		98.0	98.5	100.0	97.5	99.0	99.0	83.0	83.0	90.5