Table 3. SNPs belonging to different annotation categories.
| Annotation categories | Number (%) | Mean VAF (± SD) | No. homozygous (VAF ≥0.99) a |
|---|---|---|---|
| RNA | |||
| Intergenic | 162240 (57) | 0.99 (0.06) | 152732 (94%) |
| Up/downstream | 11793 (4) | 0.99 (0.07) | 10817 (92%) |
| Intronic | 58028 (20) | 0.99 (0.05) | 55744 (96%) |
| Exonic | 36702 (13) | 0.99 (0.08) | 33051 (90%) |
| Non-synonymous | 8599 (3) | 0.98 (0.11) | 7664 (89%) |
| Synonymous | 28094 (10) | 0.99 (0.07) | 25353 (90%) |
| Stop-gain/loss | 39 (<1) | 0.96 (0.16) | 34 (87%) |
| Splicing | 8 (<1) | 1 (0) | 8 (100%) |
| UTR3/UTR5 | 13421 (5) | 0.98 (0.09) | 11895 (88%) |
| ncRNA | 106 (<1) | 0.97 (0.13) | 100 (94%) |
| WGS | |||
| Intergenic | 2865498 (82) | 0.99 (0.07) | 2659382 (92%) |
| Up/downstream | 30741 (<1) | 0.99 (0.08) | 28558 (93%) |
| Intronic | 565323 (16) | 0.99 (0.07) | 522577 (92%) |
| Exonic | 34294 (1) | 0.98 (0.09) | 31875 (92%) |
| Non-synonymous | 8946 (<1) | 0.97 (0.11) | 8283 (86%) |
| Synonymous | 25274 (<1) | 0.99 (0.08) | 23526 (93%) |
| Stop-gain/loss | 74 (<1) | 0.98 (0.11) | 66 (69%) |
| Splicing | 17 (<1) | 0.97 (0.13) | 17 (100%) |
| UTR3/UTR5 | 12476 (<1) | 0.99 (0.07) | 11515 (92%) |
| ncRNA | 302 (<1) | 0.99 (0.07) | 277 (91%) |
| Overlap RNA and WGS b | |||
| Intergenic | 125218 (58) | 1 (0.04) | 112462 (89%) |
| Up/downstream | 9787 (4) | 0.99 (0.04) | 6908 (87%) |
| Intronic | 47894 (22) | 1 (0.04) | 43636 (91%) |
| Exonic | 22551 (10) | 0.99 (0.05) | 19533 (87%) |
| Non-synonymous | 5165 (2) | 0.99 (0.06) | 4486 (87%) |
| Synonymous | 17363 (8) | 0.99 (0.05) | 15030 (86%) |
| Stop-gain/loss | 23 (<1) | 1 (0.01) | 17 (39%) |
| Splicing | 5 (<1) | 1 (0) | 5 (100%) |
| UTR3/UTR5 | 9943 (5) | 0.99 (0.04) | 8475 (85%) |
| ncRNA | 73 (<1) | 0.99 (0.03) | 63 (86%) |
a The percentages are in relation to the number of SNPs within the annotation category.
b The percentages are in relation to the number of SNPs within the annotation category in RNA.