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Table 3 Significant CNVR results comparing fat and lean samples using Mann Whitney (two tailed) testing

From: Genome wide analysis reveals single nucleotide polymorphisms associated with fatness and putative novel copy number variants in three pig breeds

Program

CNV ID

Chromosome

Start position

End position

Copy number

Fat

Lean

p(2)

U

cnvPartition

14.S1

14

49996213

53700421

0

29

18

0.05

1416

1

0

0

2

19

30

3

0

0

4+

0

0

cnvPartition

6.D1

6

68258924

78889296

0

27

16

0.05

1416

1

0

0

2

21

32

3

0

0

4+

0

0

cnvPartition

14.D1

14

50332490

53700421

0

29

40

0.05

888

1

0

0

2

19

8

3

0

0

4+

0

0

QuantiSNP

4.D3

4

79881

2580313

0

0

0

0.01

768

1

28

44

2

20

4

3

0

0

4+

0

0

QuantiSNP

4.D5

4

74926691

77748130

0

0

0

0.05

888

1

28

39

2

20

9

3

0

0

4+

0

0

QuantiSNP

5.D2

5

33971

9428425

0

0

0

0.003

744

1

23

40

2

25

8

3

0

0

4+

0

0

QuantiSNP

14.D1

14

47658364

58439670

0

0

0

0.01

768

1

12

28

2

36

20

3

0

0

4+

0

0

QuantiSNP

15.D2

15

90602719

95659643

0

0

0

0.05

888

1

29

40

2

19

8

3

0

0

4+

0

0

cnvPartition

14.T2

14

74855162

77603365

0

19

36

0.003

744

1

0

0

2

29

12

3

0

0

4+

0

0

cnvPartition

15.T1

15

19895180

21543806

0

4

18

0.01

816

1

0

0

2

44

30

3

0

0

4+

0

0

QuantiSNP

1.T2

1

18418830

18641391

0

0

0

<0.0001

456

1

17

46

2

31

2

3

0

0

4+

0

0

QuantiSNP

4.T5

4

43206823

45758968

0

0

0

0.05

1416

1

0

0

2

43

32

3

5

16

     

4+

0

0

  
  1. Table shows significant CNVs (determined by Mann Whitney U (two tailed) tests, present in more than 5 animals for both QuantiSNP and cnvPartition. The chromosome and start and end of each of the CNVRs, is given. The estimated copy number of the sequence and the number of animals in which each was observed is also provided. Each CNV was assigned a ‘CNV ID.’ For example ‘1.S2’ denotes that the CNV is on chromosome 1, it is from SLLW breed and it has been assigned the number ‘2’. Duroc and Titan CNVs were assigned the letter D and T respectively.
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BMC Genomics

ISSN: 1471-2164

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