Table 3.
Indel consequence counts of WES versus WGS as determined by variant effect predictor.
| Impact | Consequence | WES (%) | WGS (%) | ||||
|---|---|---|---|---|---|---|---|
| Common | Exclusive | Total | Common | Exclusive | Total | ||
| High | Frameshift | 1440 (93) | 109 (7) | 1549 | 1451 (84.8) | 260 (15.2) | 1711 |
| High | Splice acceptor | 69 (83.1) | 14 (16.9) | 83 | 71 (69.6) | 31 (30.4) | 102 |
| High | Splice donor | 107 (88.4) | 14 (11.6) | 121 | 107 (81.1) | 25 (18.9) | 132 |
| High | Start lost | 11 (100) | 0 (0) | 11 | 11 (84.6) | 2 (15.4) | 13 |
| High | Stop gained | 16 (76.2) | 5 (23.8) | 21 | 17 (56.7) | 13 (43.3) | 30 |
| High | Stop lost | 12 (92.3) | 1 (7.7) | 13 | 12 (85.7) | 2 (14.3) | 14 |
| High | All | 1602 (92.1) | 137 (7.9) | 1739 | 1615 (83.6) | 316 (16.4) | 1931 |
| Moderate | Inframe deletion | 709 (90.5) | 74 (9.5) | 783 | 710 (91.1) | 69 (8.9) | 779 |
| Moderate | Inframe insertion | 557 (92.4) | 46 (7.6) | 603 | 557 (90) | 62 (10) | 619 |
| Moderate | Protein altering | 13 (81.3) | 3 (18.8) | 16 | 13 (54.2) | 11 (45.8) | 24 |
| Moderate | All | 1267 (91.2) | 122 (8.8) | 1389 | 1268 (90.1) | 139 (9.9) | 1407 |
| Low | 3′ UTR | 173 (91.5) | 16 (8.5) | 189 | 176 (81.5) | 40 (18.5) | 216 |
| Low | 5′ UTR | 194 (96.5) | 7 (3.5) | 201 | 195 (91.5) | 18 (8.5) | 213 |
| Low | Splice region | 641 (94.8) | 35 (5.2) | 676 | 644 (92.9) | 49 (7.1) | 693 |
| Low | Start retained | 7 (100) | 0 (0) | 7 | 7 (100) | 0 (0) | 7 |
| Low | Stop retained | 10 (100) | 0 (0) | 10 | 10 (83.3) | 2 (16.7) | 12 |
| Low | All | 299 (94.3) | 18 (5.7) | 317 | 302 (92.9) | 23 (7.1) | 325 |
| All | 4333 (92.5) | 351 (7.5) | 4684 | 4364 (87.8) | 609 (12.2) | 4973 | |