Table 5 |
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|
SNP functional class membership |
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|
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. |
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|
Stothard et al. BMC Genomics 2011 12:559 doi:10.1186/1471-2164-12-559 |
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