Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array

BMC Genomics

Table 1 CNVs or CNVRs on Btau_4.0 and UMD3.1

Subspecies/groups	Sample	Count	Unique	Gain	Loss	Total Length
Btau_4.0
*Taurine*	447	20,302 (45.4)	1,044 (2.3)	7,916 (17.7)	12,386 (27.7)	814,447,018 (40,117)
*Indicine*	113	7,352 (65.1)	309 (2.7)	2,595 (23.0)	4,757 (42.1)	266,853,291 (36,297)
*Taurine × Indicine*	67	3,569 (53.3)	198 (3.0)	1,508 (22.5)	2,061 (30.8)	159,735,770 (44,756)
*African Breeds*	47	3,088 (65.7)	240 (5.1)	1,248 (26.6)	1,840 (39.1)	129,777,675 (42,026)
Total	674	34,311 (50.9)	1,791 (2.7)	13,267 (19.7)	21,044 (31.2)	1,370,813,754 (39,953)
CNVR	674	3,346 ^a	1,316 ^b	986 ^c	2,051 ^c	142,718,107 (42,653)
UMD3.1
*Taurine*	434	32,445 (74.8)	1,052 (2.4)	12,419 (28.6)	20,026 (46.1)	1,551,624,380 (47,823)
*Indicine*	97	8,715 (89.8)	327 (3.4)	3,102 (32.0)	5,613 (57.9)	394,966,292 (45,320)
*Taurine × Indicine*	63	5,332 (84.6)	237 (3.8)	2,268 (36.0)	3,064 (48.6)	256,749,182 (48,153)
*African Breeds*	36	3,212 (89.2)	230 (6.4)	1,197 (33.3)	2,015 (56.0)	151,559,764 (47,185)
Total	630	49,704 (78.9)	1,846 (2.9)	18,986 (30.1)	30,718 (48.8)	2,354,899,618 (47,378)
CNVR	630	3,438 ^a	1,360 ^d	1,054 ^e	2,042 ^e	146,905,950 (42,730)

Numbers in parentheses are values normalized by sample counts, except in the case of the parentheses values in the "total length" column, which are average lengths normalized by CNV counts. ^a These numbers represent nonredundent CNVR counts. In Btau_4.0, ^b 1,316 out of 3,346 CNVRs were unique to one sample, 2,030 CNVRs were shared by at least 2 individuals and 179 of 2,030 multiple events had a frequency > =5%. ^c Besides the 986 gain and 2,051 loss CNVRs, there were 309 CNVRs containing both loss and gain events. In UMD3.1, ^d 1,360 out of 3,438 CNVRs were unique to one sample, 2,078 CNVRs were shared by at least 2 individuals and 230 of 2,078 multiple events had a frequency > =5%. ^e Besides the 1,054 gain and 2,042 loss CNVRs, there were 342 CNVRs containing both loss and gain events.

ISSN: 1471-2164