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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)