Table 5

SNP functional class membership

Functional class

Holstein

Black Angus

Intersection

Union


Intergenic

2,488,430(66.3)

2,131,566(65.7)

1,124,055(65.6)

3,495,941(66.1)


Intronic

1,003,805(26.7)

881,566(27.2)

469,082(27.4)

1,416,289(26.8)


Upstream

116,529(3.1)

103,589(3.2)

53,027(3.1)

167,091(3.2)


Downstream

104,762(2.8)

90,788(2.8)

48,128(2.8)

147,422(2.8)


Synonymous coding

16,161(0.4)

15,102(0.5)

8,051(0.5)

23,212(0.4)


Nonsynonymous coding

11,598(0.3)

10,723(0.3)

5,490(0.3)

16,831(0.3)


3' UTR

8,732(0.2)

7,753(0.2)

4,200(0.2)

12,285(0.2)


Splice sitea

2,921(0.1)

2,679(0.1)

1,421(0.1)

4,179(0.1)


5' UTR

1,591(0.0)

1,382(0.0)

680(0.0)

2,293(0.0)


Within non coding gene

791(0.0)

763(0.0)

344(0.0)

1210(0.0)


Essential splice siteb

197(0.0)

166(0.0)

94(0.0)

269(0.0)


Stop gained

126(0.0)

124(0.0)

46(0.0)

204(0.0)


Stop lost

13(0.0)

8(0.0)

5(0.0)

16(0.0)


Within mature miRNA

7(0.0)

2(0.0)

1(0.0)

8(0.0)


Total

3,755,663(100)

3,246,211(100)

1,714,624(100)

5,287,250(100)


aSNP is located 1-3 bases into an exon or 3-8 bases into an intron.

bSNP is located in the first two or the last two bases of an intron.

The predicted functional consequences of SNPs identified by sequencing of the Holstein and Black Angus genomes. Values in parentheses are the percentage of SNPs that are in the functional class, out of the total SNPs in the column.

Stothard et al. BMC Genomics 2011 12:559   doi:10.1186/1471-2164-12-559

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