Table 1.
Number of variants annotated in different functional classes in Korean Hanwoo cattle using sequence level single nucleotide polymorphism (SNP) data1.
| Functional class | Number of variants | Proportion (%) |
|---|---|---|
| Intergenic region | 7,928,883 | 70.303 |
| Intron variant | 3,246,727 | 28.788 |
| Exon variant | 99,204 | 0.880 |
| Synonymous variant | 50,040 | 0.444 |
| Missense variant | 21,064 | 0.187 |
| Downstream gene variant | 469,605 | 4.164 |
| Upstream gene variant | 460,915 | 4.087 |
| 5′ UTR variant | 5,119 | 0.045 |
| 3′ UTR variant | 24,773 | 0.220 |
| Splice region variant | 8,903 | 0.079 |
| All stop variants | 226 | 0.002 |
| Splice acceptor variant | 184 | 0.002 |
| Splice donor variant | 177 | 0.002 |
| Start lost variant | 26 | 0.000 |
1Functional annotation of SNP variants was performed based on the cattle genome reference sequence (UMD 3.1) using SnpEff ver. 4.3p and SnpSift software (Cingolani et al., 2012a,b). The cumulative value is higher than 100% as some variants are located in several transcripts and therefore, could be allocated to multiple regions.