Detection of copy number variations in brown and white layers based on genotyping panels with different densities

Table 3 Summary of CNVR detected for each line and genotyping panel

Line	SNP panel^a	Number of CNVR	Number of deletions		Number of duplications		Number of complex CNVR^c	Number of CNVR with a frequency > 1%^d (maximum)
Line	SNP panel^a	Number of CNVR	Singletons	N ≥ 2^b	Singletons	N ≥ 2^b	Number of complex CNVR^c	Number of CNVR with a frequency > 1%^d (maximum)
W1	50K w	625	89	85	286	98	67	5 (5.7)
W1	600K	251	101	44	86	12	8	41 (52.8)
W2	50K w	562	60	43	265	139	55	2 (1.2)
	50K b	576	57	40	243	176	60	10 (2.2)
	600K	586	128	56	331	50	21	13 (46.4)
Hybrids	600K	1218	79	30	933	150	25	29 (35.1)
B1	50K b	1146	92	199	419	230	284	17 (2.8)
B1	600K	440	254	110	50	12	10	73 (33.6)
B2	42K	569	167	95	128	79	100	19 (13.9)

^aw white-egg lines, b brown-egg lines
^bN ≥ 2 = CNVR observed in at least two individuals
^cComplex CNVR = CNVR within which both deletions and duplications were observed
^dCNVR with a frequency higher than 1% within line and panel, calculated as the number of individuals with the CNVR divided by number of individuals genotyped that passed quality control (see Table 2 column 4)

ISSN: 1297-9686