Table 2.
Functional classification of variants detected in the cattle haplotype reference panel.
| Reference b | SNP Array c | |||
|---|---|---|---|---|
| Classification a | Variants | Genes | Variants | Genes |
| Protein-changing | 332,714 | 21,066 | 29,519 | 10,673 |
| High impact | 14,773 | 9084 | 545 | 509 |
| Non-synonymous SNP | 318,269 | 20,978 | 29,011 | 10,576 |
| Potentially regulatory | 327,357 | 18,110 | 13,072 | 8076 |
| Untranslated region (UTR) | 318,495 | 15,288 | 12,447 | 7557 |
| Non-coding RNA | 8940 | 2822 | 627 | 519 |
| Intergenic | 38,694,029 | 396,306 | ||
| Intronic | 19,533,912 | 272,510 | ||
| Total | 59,198,026 | 21,334 | 715,402 | 10,683 |
a Variants classified with snpEff v4.3 using ensembl ARS-UCD1.2.96 annotation. b Variants detected in the cattle haplotype reference panel and imputed from the low-pass sequence. c Autosomal and pseudo-autosomal variants detected in the reference panel and with usable SNP array genotypes in Germplasm Evaluation Project cattle.