Table 1 Total number of variants annotated in different genomic classes in the beef and dairy data sets
Class | Number variants in dairy | Number variants in beef |
|---|---|---|
Total Genomic | 632003 | 729254 |
Intergenic | 428255 (0.68) | 490982 (0.67) |
Intragenic (genic regions) | 203534 (0.32) | 237914 (0.33) |
Upstream variants | 23799 (0.04) | 27861 (0.04) |
Downstream Variants | 26453 (0.04) | 30780 (0.04) |
Introns | 195012 (0.31) | 227938 (0.31) |
Exon | 8913 (0.01) | 10416 (0.01) |
Protein Coding Sequence (CDS) | 6364 (0.01) | 7490 (0.01) |
Synonymous | 3968 (0.01) | 4768 (0.01) |
Missense | 2392 (0.004) | 2718 (0.004) |
UTR (5' & 3') | 2386 (0.004) | 2748 (0.004) |
Non-Coding Conserved | 6331 (0.01) | 7399 (0.01) |
microRNA Predicted Target | 1932 (0.003) | 2213 (0.003) |
Transcription Factor Binding Sites | 229 (0.0004) | 271 (0.0004) |
Frameshift SNPs | 1 | 1 |
Mature microRNA SNPs | 1 | 2 |
All Splice Sites | 720 (0.001) | 855 (0.001) |
All Stop sites | 86 (0.0001) | 88 (0.0001) |