Table 4.
SNV consequence counts of WES versus WGS as determined by variant effect predictor.
| Impact | Consequence | WES (%) | WGS (%) | ||||
|---|---|---|---|---|---|---|---|
| Common | Exclusive | Total | Common | Exclusive | Total | ||
| High | Splice acceptor | 97 (97) | 3 (3) | 100 | 98 (89.9) | 11 (10.1) | 109 |
| High | Splice donor | 137 (97.9) | 3 (2.1) | 140 | 139 (88) | 19 (12) | 158 |
| High | Start lost | 63 (96.9) | 2 (3.1) | 65 | 63 (100) | 0 (0) | 63 |
| High | Stop gained | 237 (97.9) | 5 (2.1) | 242 | 232 (92.8) | 18 (7.2) | 250 |
| High | Stop lost | 35 (100) | 0 (0) | 35 | 36 (97.3) | 1 (2.7) | 37 |
| High | All | 569 (97.8) | 13 (2.2) | 582 | 568 (92.1) | 49 (7.9) | 617 |
| Moderate | missense | 43,518 (99.3) | 309 (0.7) | 43,827 | 43,419 (98.1) | 821 (1.9) | 44,240 |
| Moderate | All | 43,516 (99.3) | 309 (0.7) | 43,825 | 43,417 (98.1) | 821 (1.9) | 44,238 |
| Low | 3′ UTR | 2022 (97.9) | 43 (2.1) | 2065 | 2031 (94.7) | 114 (5.3) | 2145 |
| Low | 5′ UTR | 2458 (99.5) | 13 (0.5) | 2471 | 2459 (98.6) | 35 (1.4) | 2494 |
| Low | Splice region | 3938 (99.5) | 21 (0.5) | 3959 | 3923 (98.7) | 50 (1.3) | 3973 |
| Low | Stop retained | 60 (100) | 0 (0) | 60 | 58 (96.7) | 2 (3.3) | 60 |
| Low | Synonymous | 87,341 (99.6) | 321 (0.4) | 87,662 | 87,182 (98.9) | 956 (1.1) | 88,138 |
| Low | All | 88,584 (99.6) | 336 (0.4) | 88,920 | 88,417 (98.9) | 975 (1.1) | 89,392 |
| All | All | 144,012 (99.4) | 834 (0.6) | 144,846 | 143,745 (98.5) | 2194 (1.5) | 145,939 |