Estimating autozygosity from high-throughput information: effects of SNP density and genotyping errors

Table 4 Comparison of F _ROH values obtained by allowing different numbers of heterozygous SNPs

Breed	Source	Class	F _ROH>1	F _ROH>2	F _ROH>4	F _ROH>8	F _ROH>16
Brown Swiss	50 k panel	A	0.154^b	0.129^ab	0.103^a	0.073^ab	0.039^dfhi
	50 k panel	B	.	.	.	.	0.036^bceg
	HD panel	C	0.151^b	0.132^b	0.109^b	0.079^c	0.042ⁱ
		D	0.147^a	0.128^a	0.105^a	0.076^b	0.040^gh
		E	.	0.129^ab	0.105^a	0.075^b	0.038^ef
		F	.	.	0.105^a	0.071^a	0.035^cd
		G	.	.	.	0.068^a	0.033^b
		H	.	.	.	.	0.028^a
Pinzgauer	50 k panel	A	0.069^c	0.048^ab	0.037^a	0.026^bc	0.014^f
	50 k panel	B	.	.	.	.	0.013^ed
	HD panel	C	0.062^b	0.049^b	0.039^b	0.027^d	0.014^fe
		D	0.060^a	0.048^ab	0.038^ab	0.026^dc	0.013^fe
		E	.	0.048^a	0.037^a	0.026^bc	0.012^d
		F	.	.	0.036^a	0.025^ab	0.012^c
		G	.	.	.	0.024^a	0.011^b
		H	.	.	.	.	0.008^a
Tyrol Grey	50 k panel	A	0.080^c	0.054^a	0.042^a	0.029^abc	0.017^df
	50 k panel	B	.	.	.	.	0.015^ce
	HD panel	C	0.066^b	0.052^a	0.042^a	0.030^c	0.017^f
		D	0.063^a	0.051^a	0.041^a	0.029^b	0.016^d
		E	.	0.051^a	0.040^a	0.029^b	0.016^ed
		F	.	.	0.040^a	0.028^ab	0.015^c
		G	.	.	.	0.026^a	0.013^b
		H	.	.	.	.	0.010^a

Definition of Class is according to the number of heterozygous SNPs allowed within ROH length categories (see Table 2).
F_ROH values were obtained by allowing different numbers of heterozygous SNPs in each ROH length category; different letters indicate statistical significance within the same column and breed (P < 0.05, paired t-test); P values were corrected for multiple tests using the step-down Bonferroni method of Holm [18].

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