Table 1.

R ² +/- standard deviation across replicates between inferred and true results, and percentage of assigned results using simulated data (dataset B)

	Half-sib family size
	4	6	8	10	20	40
1250 SNPs
PS	0.55 ± 0.37	0.65 ± 0.29	0.68 ± 0.27	0.77 ± 0.17	0.84 ± 0.07	0.84 ± 0.04
PS%	0.94 ± 0.13	0.96 ± 0.04	0.97 ± 0.02	0.97 ± 0.03	0.97 ± 0.03	0.98 ± 0.02
PSe	0.52 ± 0.36	0.64 ± 0.29	0.66 ± 0.27	0.75 ± 0.17	0.83 ± 0.07	0.83 ± 0.04
PSe%	0.96 ± 0.06	0.96 ± 0.04	0.97 ± 0.02	0.97 ± 0.03	0.98 ± 0.03	0.98 ± 0.02
SI	0.74 ± 0.25	0.81 ± 0.18	0.84 ± 0.17	0.90 ± 0.11	0.97 ± 0.03	0.99 ± 0.00
SI%	0.51 ± 0.09	0.71 ± 0.06	0.82 ± 0.05	0.88 ± 0.03	0.98 ± 0.02	1.00 ± 0.00
SIe	0.72 ± 0.23	0.80 ± 0.18	0.82 ± 0.18	0.89 ± 0.11	0.97 ± 0.03	0.99 ± 0.01
SIe%	0.53 ± 0.06	0.71 ± 0.06	0.82 ± 0.05	0.89 ± 0.03	0.98 ± 0.02	1.00 ± 0.00
5000 SNPs
PS	0.55 ± 0.36	0.74 ± 0.32	0.86 ± 0.19	0.91 ± 0.07	0.93 ± 0.03	0.94 ± 0.02
PS%	0.95 ± 0.10	0.97 ± 0.03	0.98 ± 0.03	0.98 ± 0.02	0.98 ± 0.02	0.98 ± 0.02
PSe	0.56 ± 0.36	0.74 ± 0.33	0.87 ± 0.22	0.92 ± 0.12	0.95 ± 0.04	0.95 ± 0.02
PSe%	0.98 ± 0.03	0.98 ± 0.02	0.99 ± 0.02	0.99 ± 0.02	0.99 ± 0.02	0.99 ± 0.01
SI	0.74 ± 0.23	0.86 ± 0.20	0.93 ± 0.12	0.97 ± 0.04	0.99 ± 0.01	1.00 ± 0.00
SI%	0.50 ± 0.07	0.70 ± 0.07	0.81 ± 0.05	0.88 ± 0.04	0.98 ± 0.01	1.00 ± 0.00
SIe	0.71 ± 0.22	0.83 ± 0.20	0.91 ± 0.13	0.95 ± 0.05	0.99 ± 0.01	1.00 ± 0.00
SIe%	0.51 ± 0.04	0.70 ± 0.07	0.81 ± 0.05	0.88 ± 0.04	0.98 ± 0.01	1.00 ± 0.00
10 000 SNPs
PS	0.58 ± 0.38	0.77 ± 0.32	0.90 ± 0.19	0.93 ± 0.10	0.96 ± 0.03	0.96 ± 0.02
PS%	0.95 ± 0.13	0.98 ± 0.02	0.99 ± 0.02	0.99 ± 0.02	0.99 ± 0.02	0.99 ± 0.01
PSe	0.48 ± 0.36	0.71 ± 0.33	0.84 ± 0.21	0.90 ± 0.09	0.92 ± 0.04	0.92 ± 0.04
PSe%	0.97 ± 0.04	0.98 ± 0.03	0.98 ± 0.03	0.98 ± 0.02	0.98 ± 0.02	0.98 ± 0.02
SI	0.75 ± 0.25	0.87 ± 0.20	0.95 ± 0.11	0.97 ± 0.06	1.00 ± 0.01	1.00 ± 0.00
SI%	0.50 ± 0.09	0.69 ± 0.06	0.80 ± 0.06	0.88 ± 0.06	0.99 ± 0.01	1.00 ± 0.00
SIe	0.75 ± 0.22	0.85 ± 0.20	0.93 ± 0.12	0.96 ± 0.06	0.99 ± 0.01	1.00 ± 0.00
SIe%	0.52 ± 0.06	0.69 ± 0.06	0.80 ± 0.05	0.88 ± 0.05	0.99 ± 0.01	1.00 ± 0.00

120 half-sib families with varying numbers of offspring per family (between 4 and 40) and different SNP marker densities were used; PS: paternal strand detection; PS%: percentage of markers assigned to paternal strands; PSe: paternal strand detection with 1% genotyping error; PSe%: percentage of markers assigned to paternal strands with 1% genotyping error; SI: sire genotype imputation, SI%: percentage of sire markers imputed; SIe: sire genotype imputation with 1% genotyping error, SIe%: percentage of sire markers imputed with 1% genotyping error.