Genomic characteristics of cattle copy number variations

BMC Genomics

Table 1 CNV events by species and breeds.

Btau_4.0	Sample	Count	Unique	Gain	Loss	Gene	Total Length
Taurine^a	366	2,256(6.23)	239(0.66)	1,454(4.02)	802(2.22)	4,744(13.10)	373,001,599(165,337)
Composite	46	330(7.17)	23(0.50)	224(4.87)	106(2.30)	651(14.15)	113,483,966(142,032)
Indicine	70	799(11.41)	62(0.89)	401(5.73)	398(5.69)	1,464(20.91)	57,402,891(173,948)
African Breeds	39	281(7.21)	38(0.97)	213(5.46)	68(1.74)	775(19.87)	54,728,022(194,761)
CNV^a	521	3,666(7.09)	362(0.70)	2,292(4.43)	1,374(2.66)	7,634(14.77)	598,616,478(163,288)
CNVR^b	521	682	278^c	216^d	370^d	1,263	139,786,166(204,965)
Outgroup^e
CNV	18	1,003(55.72)	284(15.78)	48(2.67)	955(53.06)	2,603(144.61)	442,235,607(440,912)
CNVR	18	483	187	21	458	1,593	276,846,573(573,181)

The numbers in parentheses are normalized by sample counts except that the lengths in parentheses are average lengths normalized by CNV counts. ^aAt sample level, each sample has 7.09 (3666/517) CNVRs averagely and 6.23 (2256/362) for Taurine, since there are 4 taurine individuals without identified CNVs; ^b These numbers are nonredundent CNVR counts. ^c 278 CNVRs are unique to one sample while 404 CNVRs are shared by at least 2 individuals or breeds and 18 of 404 multiple events have frequency >5%; ^d Besides 370 loss and 216 gain CNVRs, there are 96 CNVRs containing both loss and gain events; ^e Outgroup animals are not included in the total counts for CNV and CNVR.

ISSN: 1471-2164