Misidentification of runs of homozygosity islands in cattle caused by interference with copy number variation or large intermarker distances

Table 4 Results of the permutation test that checks whether the intersections between CNVR with copy loss (copy loss or both copy loss and copy gain) and ROH islands are due to chance alone

Breed	Software	ROHD^a	Estimate (ROHR^b)	Confidence interval		P value
Breed	Software	ROHD^a	Estimate (ROHR^b)	Lower	Upper	P value
Brown Swiss	PennCNV	0.630	0.072	0.069	0.074	0
	SVS	0.176	0.023	0.021	0.025	0
	Consensus	0.000	0.008	0.007	0.009	7.00E−38
Tyrol Grey	PennCNV	2.931	0.460	0.451	0.470	0
	SVS	2.453	0.150	0.143	0.157	0
	Consensus	2.135	0.084	0.079	0.088	0
Pinzgauer	PennCNV	4.824	0.420	0.410	0.430	0
	SVS	3.774	0.059	0.056	0.063	0
	Consensus	2.729	0.033	0.030	0.036	0

The number of iterations used for randomizing the locations of the ROH islands was 10,000
^aIntersections between CNVRs and ROH islands from the data
^bIntersections between CNVRs and randomized ROH islands

ISSN: 1297-9686