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

Table 2 CNVR numbers, lengths and coverage for each CNV detection method used

Software	Copy state	N^a	CNVR length (bp)				Total (Mb)	Coverage (%)^b
Software	Copy state	N^a	Mean	Median	Min	Max	Total (Mb)	Coverage (%)^b
Brown Swiss
PennCNV	Loss	210	51,633.0	24,514.5	1358	483,799	10.843	0.43
	Gain	66	84,062.2	24,387.5	2809	1,879,682	5.548	0.22
	Both	30	241,581.7	104,390.5	7538	1,347,298	7.247	0.29
	Overall	306					23.638	0.94
SVS	Loss	141	41,221.0	6858.0	1086	1,217,387	5.812	0.23
	Both	46	37,702.4	10,232.5	1774	353,135	1.734	0.07
	Overall	187					7.546	0.30
Consensus	Loss	9	42,871.3	47,761.0	4693	90,545	0.386	0.02
	Both	21	197,095.7	53,252.0	1404	945,913	4.139	0.16
	Overall	30					4.525	0.18
Tyrol Grey
PennCNV	Loss	502	95,870.1	49,568.0	1358	2,611,715	48.127	1.65
	Gain	90	47,216.2	24,954.0	2455	279,361	4.249	0.15
	Both	14	518,196.6	256,469.0	5035	1,646,040	7.255	0.25
	Overall	606					59.631	2.04
SVS	Loss	115	167,013.8	11,531.0	1369	4,210,187	19.207	0.66
	Both	38	44,509.8	11,567.0	1774	652,218	1.691	0.06
	Overall	153					20.898	0.72
Consensus	Loss	49	142,561.0	75,065.0	3620	1,432,454	6.985	0.24
	Both	22	205,619.5	58,194.5	2270	790,623	4.524	0.16
	Overall	71					11.509	0.39
Pinzgauer
PennCNV	Loss	390	63,906.2	26,759.5	1300	951,876	24.923	0.99
	Gain	100	35,733.7	20,985.5	1950	279,361	3.573	0.14
	Both	38	373,093.4	164,810.5	4038	2,050,695	14.17755	0.56
	Overall	528					42.67433	1.70
SVS	Loss	119	66,791.9	8018.0	1169	1,311,740	7.94824	0.32
	Gain	1	307,583.0	307,583.0	307,583	307,583	0.307583	0.01
	Both	58	31,875.8	10,004.5	1369	320,050	1.848796	0.07
	Overall	178					10.10462	0.40
Consensus	Loss	17	66,484.7	31,556.0	4895	459,485	1.13024	0.05
	Both	33	179,520.3	34,711.0	1774	947,366	5.924169	0.24
	Overall	50					7.054409	0.28

^aN = Number of CNVRs
^bThe coverage percentage is based on the bovine autosomal genome size of 2511 Mb covered by the BovineHD SNP chip

ISSN: 1297-9686