Table 2.

Comparison of copy number calls at variant regions

CN	0	1	2	3	4	0	1	2	3	4	0	1	2	3	4
	Region 1					Region 2					Region 3
	Chr2:242,648,367					Chr3:53,010,599					Chr7:133,441,893
Partek	0b	4	24	0	0	0	1	24	0	0	0	1	5	0	0
GTC	0	4	24	0	0	1	3	21	0	0	0	1	4	1	0
Birdsuite	0	4	24	0	0	1	3	21	0	0	1	3	2	0	0
qPCR	0	4	24	0	0	1	3	21	0	0	1	3	2	0	0
	Region 4					Region 5					Region 6
	Chr8:144,776,429					Chr19:56,824,268					Chr19:56,838,253
Partek	0	0	8	0	0	0	0	13	13	0	0	0	7	6	0
GTC	1	0	7	0	0	0	0	17	3	6	0	0	6	3	4
Birdsuite	1	2	5	0	0	0	0	26	0	0	0	2	11	0	0
qPCR	1	2	5	0	0	1	6	19	0	0	0	2	11	0	0
	Region 7					Region 8					Region 9
	Chr20:1,522,539					Chr22:22,643,636					Chr22:22,713,888
Partek	0	4	13	7	0	0	0	23	5	0	0	0	14	12	0
GTC	0	4	13	0	7	1	0	24	3	0	1	1	16	6	2
Birdsuite	17	7	0	0	0	12	11	5	0	0	2	13	11	0	0
qPCR	18	6	0	0	0	0	0	28	0	0	2	14	10	0	0

^aGTC = Genotyping Console 2.0

^bValues are numbers of samples called each copy number at each region.