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Table 1 The annotated classes along with the number of variants in each class from the 28 million sequence variants

From: Variance explained by whole genome sequence variants in coding and regulatory genome annotations for six dairy traits

Class Total Number of Variants Percentage of WGS
3prime UTR 60,880 0.211%
5prime UTR 13,455 0.047%
Antisense RNA 14,198 0.049%
Exon coding sequence (CDS) 185,089 0.640%
DNA methylated regions in bovine placenta 204,702 0.708%
Downstream 5 k 731,297 2.531%
Exon 269,805 0.934%
Frameshift 93 0.000%
Intergenic 21,243,235 73.508%
Intragenic 6,961,936 24.091%
Intron 6,555,900 22.686%
Long noncoding RNA 147,025 0.509%
microRNA predicted target 79,205 0.274%
Missense deleterious 27,297 0.094%
Missense tolerated 71,908 0.249%
Splice site region 7988 0.028%
Stop codons 676 0.002%
Synonymous 105,598 0.365%
TFBS 8570 0.030%
Upstream 5 k 857,823 2.968%
Total 28,899,038  
  1. The Percentage of WGS column represents the total proportion of annotated variants in each class as a percentage of the total WGS sequence variants. The majority of the annotations were obtained from Ensembl release 77 [44] except for the 3prime untranslated region (UTR), 5prime UTR, synonymous, missense deleterious and missense tolerated which came from the NGS-SNP pipeline [45]. MiRNA predicted target sites came from MicroCosm [46]. DNA methylated regions came from the study by Su J et al. [23]. Long noncoding RNA (lncRNA) and antisense RNA (asRNA) were obtained from the study by Koufariotis L et al. [49]. Transcription factor binding sites (TFBS) were from Bickhart D.M et al. [47]. Downstream 5 k and Upstream 5 k represent all variants that are found within 5 kilobases either upstream of a gene transcription start site (TSS) or downstream of a gene transcription termination site (TTS)