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Table 5 SNP functional class membership

From: Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery

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)
  1. aSNP is located 1-3 bases into an exon or 3-8 bases into an intron.
  2. bSNP is located in the first two or the last two bases of an intron.
  3. 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.