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