Table 1. Simulation results averaged across 1000 replicates of eight-parent MAGIC populations.

M	N	%MISS	%F0	%F	%FC	%FK	%K	%B	%M
101	200	30	46.9	100	100	86.6	79.8	93.7	96.3
101	200	40	24.5	100	100	85.4	78.8	93.0	95.5
101	200	50	9.8	100	99.6	83.9	77.5	92.0	94.8
101	200	60	3.5	99.9	98.3	81.6	75.7	88.7	93.2
101	400	30	47.3	100	100	88.4	80.3	94.3	96.3
101	400	40	24.9	100	100	87.4	79.4	93.8	95.5
101	400	50	10.1	100	100	86.2	78.2	92.6	94.8
101	400	60	3.6	100	99.7	84.3	76.7	90.7	93.5
201	200	30	47.1	100	100	90.7	83.5	96.7	98.3
201	200	40	24.8	100	100	89.5	82.3	96.3	98.0
201	200	50	10.0	100	100	87.8	80.8	95.4	97.6
201	200	60	2.9	100	99.7	85.2	78.8	91.2	96.8
201	400	30	47.1	100	100	92.1	84.1	97.0	98.3
201	400	40	24.9	100	100	91.3	83.1	96.5	98.0
201	400	50	10.0	100	100	90.1	81.8	96.0	97.6
201	400	60	2.8	100	100	88.2	80.0	94.3	96.8

For each scenario we record the percent of markers with complete founder genotypes originally (%F0), the percentage complete after imputation (%F), the percentage of missing founder genotypes correctly imputed (%FC), the percentage correctly imputed based on the five nearest neighbor markers (%FK), the percentage of missing progeny genotypes correctly imputed based on the five nearest neighbor markers (%K), the percentage correctly imputed with BEAGLE (%B), and the percentage correctly imputed with R/mpMap (%M).