Table 2 Results of quantitative real-time PCR analyses of the 17 confirmed CNVRs

CNVR	Chromosome	Start^{^a}	End^{^a}	Type	Frequency	Primer	Positive Samples			Negative Samples
CNVR	Chromosome	Start^{^a}	End^{^a}	Type	Frequency	Primer	Sample No.	Sample Confirmed	Positive Predictive Rate	Sample No.	Samples Confirmed	Negative Predictive Rate
43	1	284433601	284517960	Loss	91.67	CGH1-1	11	11	1.0000	1	1	1.0000
						Gene2-2	11	11	1.0000	1	1	1.0000
47	1	296124751	296565810	Loss	75	E1-2	9	3	0.3333	2	0	0.0000
72	10	22215991	23388810	Loss	58.33	LD1-2	7	7	1.0000	5	3	0.6000
						LD1-3	7	7	1.0000	5	3	0.6000
105	11	62691810	62798160	Gain	100	F1-2	12	12	1.0000	0	0	—
						F1-3	12	12	1.0000	0	0	—
108	11	62977560	62993310	Loss	16.67	RD2B-4	2	2	1.0000	10	2	0.2000
114	11	70562251	71910060	Both	66.67	J1-3	8	8	1.0000	4	1	0.2500
152	13	34207351	34233930	Loss	91.67	CGH3-1	11	11	1.0000	1	1	1.0000
						Gene9-4	11	11	1.0000	1	1	1.0000
339	2	61350751	61455330	Loss	16.67	R1-3	2	2	1.0000	10	7	0.7000
418	3	95980501	95990220	Gain	100	CGH7-1	12	12	1.0000	0	0	—
						CGH7-3	12	12	1.0000	0	0	—
441	4	5501251	5544300	Loss	16.67	D1	2	2	1.0000	10	6	0.6000
						D5	2	1	0.5000	10	0	0.0000
464	4	99641791	99708810	Gain	58.33	F2	7	6	0.8571	5	2	0.4000
						F4	7	6	0.8571	5	1	0.2000
579	7	24621751	24759180	Gain	58.33	RD14A-2	7	7	1.0000	5	3	0.6000
						RD14B-2	7	4	0.5714	5	0	0.0000
588	7	50301961	50677050	Loss	16.67	D1-1	2	1	0.5000	11	0	0.0000
						D2-1	2	1	0.5000	11	0	0.0000
620	8	43301791	43891650	Gain	16.67	CGH2-1	2	2	1.0000	10	0	0.0000
						kit6	2	2	1.0000	10	0	0.0000
659	9	29231131	29275230	Gain	8.33	K5	1	1	1.0000	10	0	0.0000
734	X	91336681	91353210	Loss	66.67	CGH6A-2	8	8	1.0000	4	2	0.5000
						CGH5B-1	8	8	1.0000	4	2	0.5000
736	X	92583421	92609190	Loss	25	R2-2	3	3	1.0000	8	6	0.7500
Average									0.8971			0.4125

↵a The Sus scrofa assembly (10.2) (http://www.ensembl.org/Sus_scrofa/Info/Index) was used to indicate the position of the CNVRs.