Identification of Mendelian inconsistencies between SNP and pedigree information of sibs

Table 5 Counts of numbers of deleted and non-dele ted animals

Test		Permuted pedigree¹	Deleted	Type I	Type II
PAR-OFF + SIB	PAR-OFF	19.7	13.8	3.9	5.8
		206.8	142.7	38.3	64.1
		509.9	336.0	80.9	173.9
	SIBCOUNT	19.7	4.5	0.3	1.3
		206.8	57.0	10.1	7.3
		509.9	149.9	41.0	24.0
	SIBREL	19.7	4.0	0.4	1.8
		206.8	50.2	9.7	13.9
		509.9	136.2	36.5	37.7
	PAR-OFF +	19.7	18.3²	4.2³	1.3⁴
	SIBCOUNT	206.8	199.7	48.5	7.3
		509.9	485.9	121.9	24.0
	PAR-OFF +	19.7	17.9	4.2	1.8
	SIBREL	206.8	192.9	48.0	13.9
		509.9	472.2	117.5	37.7
SIB ONLY	SIBCOUNT	19.7	18.1	0.7	1.6
		206.8	195.7	46.0	11.1
		509.9	474.4	140.0	35.6
	SIBREL	19.7	17.0	1.0	2.8
		206.8	183.2	39.9	23.6
		509.9	446.0	119.0	64.0

Counts of correctly deleted animals (Deleted), and incorrectly deleted (Type I) and incorrectly non-deleted (Type II) animals
¹Numbers of animals with permuted data, when pedigree data was permuted against genotype data for either 1%, 10%, or 25% of the animals. For SIBCOUNT and SIBREL after performing PAR-OFF, these numbers decrease to 5.9, 64.1, and 173.9, respectively (i.e. by subtracting the number of animals correctly deleted by PAR-OFF);
²sum of the number of animals deleted by PAR-OFF and SIBCOUNT (or SIBREL);
³sum of the type I errors of PAR-OFF and SIBCOUNT (or SIBREL);
⁴this figure is equal to the type II errors of SIBCOUNT (or SIBREL)

ISSN: 1297-9686