Table 2.

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

Region	Step 1A	Step 1B	Step 2, S × D model
	$P(O[H]=0|E[H])$	$P(O[H]=0|S,DCarriers)$	P value of MS	$R$	Number of SE from the expectation of a lethal recessive effect	Number of SE from no effect
6.1	7.84 × 10−4	1.00 × 10−2	5.62 × 10−2	0.157	1.13	1.91
10.1	5.30 × 10−3	1.78 × 10−3	4.79 × 10−2	0.157	1.18	1.97
14.1	1.77 × 10 −3	1.34 × 10 −5	2.03 × 10 −5	0.190	1.34	4.24
14.2	1.50 × 10−2	5.64 × 10−3	9.71 × 10−4	0.196	0.91	3.31
14.1 and 14.2 †			1.02 × 10 −4	0.240	0.16	3.93

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 dam ($P\left(O[H]=0|S,DCarriers\right)$) and the significance of mating status (MS) using the S × D 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. P values are nominal, with the haplotypes that achieved 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 ^†