Simultaneous testing of rule- and model-based approaches for runs of homozygosity detection opens up a window into genomic footprints of selection in pigs

Table 2 Number of ROH regions for each investigated potential selection event. For each phenotype, tool and parameter set, the number of ROHRs, the number of SNPs of all ROHRs and number of overlapping genes from the genome annotation are indicated. In addition, the total length of all ROHRs (in bp) and the coverage of the autosomal genome (in %) are provided

Phenotype	Tool + Parameter set	Number of ROHRs	Number of SNPs	Intersecting genes	ROHR length [bp]	Genome coverage [%]
Heritage breed	PLINK_A	22,396	974,847	3,583	47,244,400	2.09
Heritage breed	PLINK_B	15	1,235	10	71,087	0.00
Heritage breed	RZooRoH	15,924	1,760,741	4,341	129,231,106	5.70
Lop ears	PLINK_A	31,913	2,759,191	4,831	136,669,724	6.03
Lop ears	PLINK_B	2,007	299,821	582	15,562,455	0.69
Lop ears	RZooRoH	14,824	2,482,022	4,299	165,751,847	7.32
Prick ears	PLINK_A	9,839	328,033	1,684	15,768,865	0.70
Prick ears	PLINK_B	0	0	0	0	0.00
Prick ears	RZooRoH	5,812	604,787	1,630	41,990,018	1.85
Disease resistance	PLINK_A	13,427	621,064	2,417	31,092,255	1.37
Disease resistance	PLINK_B	279	43,728	78	2,261,875	0.10
Disease resistance	RZooRoH	11,774	883,853	2,969	58,704,190	2.59

ISSN: 1471-2164