Table 3.

Regions containing putative lethal recessive haplotypes with an effect on total number born using the S × MGS model

Region	Step 1A	Step 1C	Step 2, S × MGS model
	$P(O[H]=0|E[H])$	$P(O[H]=0|S,MGSCarriers)$	P value of MS	$R$	Number of SE from the expectation of a lethal recessive effect	Number of SE from no effect
1.1	2.15 × 10 −3	3.37 × 10 −1	6.99 × 10 −5	0.092	1.39	3.95
1.2	1.17 × 10−3	2.89 × 10−1	7.11 × 10−3	0.070	2.13‡	2.68
1.1 and 1.2 †			2.07 × 10 −4	0.122	0.09	3.68
6.1	7.84 × 10−4	4.61 × 10−1	3.25 × 10−3	0.103	0.62	2.93
10.1	5.30 × 10−3	4.74 × 10−6	7.69 × 10−3	0.083	1.37	2.65
14.1	1.77 × 10 −3	8.67 × 10 −3	6.28 × 10 −10	0.101	1.45	6.04
14.2	1.50 × 10 −2	1.93 × 10 −2	1.01 × 10 −5	0.084	2.11 ‡	4.36
14.1 and 14.2 †			2.97 × 10 −6	0.097	1.33	4.59

Regions containing a putative lethal recessive haplotype are named based on the chromosome and their order along that chromosome, i.e. 6.1 refers to the first region containing a putative lethal recessive haplotype located along chromosome 6. P values are given for the probability of observing no homozygotes within the population given the number expected based on the frequency of the haplotype ($P(O[H]=0|E[H])$), the probability of observing no homozygous offspring given the expected number from matings between a carrier sire and a carrier maternal grand sire ($P\left(O[H]=0|S,MGSCarriers\right)$) and the significance of mating status (MS) using the S × MGS model. $R$ is the relative reduction in total number born as a result of matings between two carriers compared to matings between a carrier and a non-carrier. The number of standard errors that $R$ was from the expectation of a lethal recessive effect and from no effect are given. ^‡ indicates a departure from the expectation of a lethal effect. P values are nominal, with the haplotypes that achieve Bonferroni corrected significance (P < 3.25 × 10⁻⁴) for MS highlighted in italics. Results arising from the concurrent assessment of two putative lethal recessive haplotypes are denoted by ^†