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Table 5 Annotation of variants by functional class

From: Deep sequencing of Danish Holstein dairy cattle for variant detection and insight into potential loss-of-function variants in protein coding genes

Functional class SNP Indel
Intergenic 7,345,721 (68.0) 866,042 (66.9)
Intronic 2,656,868 (24.6) 334,542 (25.8)
Upstream 367,709 (3.4) 46,226 (3.6)
Downstream 317,069 (2.9) 41,330 (3.2)
3′ UTR 19,677 (0.2) 3150 (0.2)
5′ UTR 4364 (0.0) 453 (0.0)
Splice regiona 6393 (0.1) 896 (0.1)
Splice donorb 230 (0.0) 53 (0.0)
Splice acceptorc 218 (0.0) 82 (0.0)
Initiator codond 74 (0.0) 1 (0.0)
Stop gain 395 (0.0) -
Frameshift - 1302 (0.1)
Missense 34,183 (0.3) 44 (0.0)
Synonymous 40,055 (0.4) -
Coding sequencee 125 (0.0) 135 (0.0)
Inframe deletion - 261 (0.0)
Inframe insertion - 194 (0.0)
Stop lost 29 (0.0) -
Stop retained 25 (0.0) -
Within non coding exonf 3569 (0.0) 270 (0.0)
Within mature miRNA 70 (0.0) 29 (0.0)
Nc transcriptf 20 (0.0) 26 (0.0)
Total 10,796,794 (100.0) 1,295,036 (100.0)
  1. aVariant in which a change has occurred within the region of the splice site either within 1–3 bases of the exon or 3–8 bases of the intron
  2. bVariant is located in the first two bases of an intron
  3. cSNP is located in the last two bases of an intron
  4. dSNP changes at least one base of the first codon of a transcript
  5. eSNP is located in coding sequence with indeterminate effect
  6. fSNP is a transcript variant of a non-coding RNA. Values in parentheses are the percentage of variants in the functional class of the total variants in the column