Table 1.
Results of re-annotation of Illumina probe sequences
| Platform | Source | Total number of probes | Perfect | Good | Bad | No match | Intronic | Intergenic | Splice junctions | Repeat sequences |
|---|---|---|---|---|---|---|---|---|---|---|
| Human WG-6 v3 | RefSeq | 36 079 73.5% | 28 154 78.0% | 909 2.5% | 6737 18.7% | 279 0.8% | 749 2.1% | 1306 3.6% | 2791 7.7% | 4254 11.8% |
| UniGene | 12 997 26.5% | 6389 49.2% | 88 0.7% | 5801 44.6% | 719 5.5% | 37 0.3% | 160 1.2% | 58 0.4% | 3987 30.7% | |
| Total | 49 076 | 34 543 70.4% | 997 2.0% | 12 538 25.5% | 998 2.0% | 786 1.6% | 1466 3.0% | 2849 5.8% | 8241 16.8% | |
| Human WG-6 v2 | RefSeq | 30 808 63.3% | 23 755 77.1% | 747 2.4% | 6028 19.6% | 278 0.9% | 747 2.4% | 1320 4.3% | 2246 7.3% | 3580 11.6% |
| UniGene | 17 894 36.7% | 7698 43.0% | 117 0.7% | 8435 47.1% | 1644 9.2% | 284 1.6% | 1211 6.8% | 57 0.3% | 5598 31.3% | |
| Total | 48 702 | 31 453 64.6% | 864 1.8% | 14 463 29.7% | 1922 3.9% | 1031 2.1% | 2531 5.2% | 2303 4.7% | 9178 18.8% | |
| Human WG-6 v1 | RefSeq | 26 098 55.2% | 20 769 79.6% | 783 3.0% | 4421 16.9% | 125 0.5% | 238 0.9% | 871 3.3% | 1681 6.4% | 2921 11.2% |
| UniGene | 21 198 44.8% | 4949 23.3% | 130 0.6% | 15 847 74.8% | 272 1.3% | 4113 19.4% | 9405 44.4% | 106 0.5% | 3463 16.3% | |
| Total | 47 296 | 25 718 54.4% | 913 1.9% | 20 268 42.9% | 397 0.8% | 4351 9.2% | 10 276 21.7% | 1787 3.8% | 6384 13.5% | |
| Human DASL | Total | 1506 | 1402 93.1% | 37 2.5% | 66 4.4% | 1 0.1% | 0 0.0% | 2 0.1% | 17 1.1% | 40 2.7% |
| Mouse WG-6 v2 | RefSeq | 23 031 50.9% | 19 115 83.0% | 556 2.4% | 3150 13.7% | 210 0.9% | 383 1.7% | 926 4.0% | 1080 4.7% | 1567 6.8% |
| MEEBO | 16 591 36.6% | 15 267 92.0% | 318 1.9% | 863 5.2% | 143 0.9% | 47 0.3% | 6 0.04% | 384 2.3% | 692 4.2% | |
| Riken | 5659 12.5% | 3574 63.2% | 292 5.2% | 1749 30.9% | 44 0.8% | 0 0.0% | 0 0.0% | 292 5.2% | 1636 28.9% | |
| Total | 45 281 | 37 956 83.8% | 1166 2.6% | 5762 12.7% | 397 0.9% | 430 0.9% | 932 2.1% | 1756 3.9% | 3895 8.6% | |
| Mouse WG-6 v1.1 | RefSeq | 32 342 69.3% | 28 560 88.3% | 394 1.2% | 3140 9.7% | 248 0.8% | 431 1.3% | 961 3.0% | 1026 3.2% | 1556 4.8% |
| MEEBO | 9512 20.4% | 7306 76.8% | 290 3.0% | 1322 13.9% | 594 6.2% | 191 2.0% | 19 0.2% | 113 1.2% | 953 10.0% | |
| Riken | 4784 10.3% | 2832 59.2% | 261 5.5% | 1644 34.4% | 47 1.0% | 0 0.0% | 0 0.0% | 171 3.6% | 1542 32.2% | |
| Total | 46 638 | 38 698 83.0% | 945 2.0% | 6106 13.1% | 889 1.9% | 622 1.3% | 980 2.1% | 1310 2.8% | 4051 8.7% | |
| Mouse WG-6 v1 | RefSeq + MEEBO | 34 159 85.5% | 29 196 85.4% | 530 1.6% | 4080 11.9% | 353 1.0% | 582 1.7% | 967 2.8% | 866 2.5% | 2211 6.5% |
| Riken | 5809 14.5% | 3665 63.1% | 294 5.1% | 1800 31.0% | 50 0.9% | 0 0.0% | 0 0.0% | 302 5.2% | 1694 29.1% | |
| Total | 39 968 | 32 861 82.2% | 824 2.1% | 5880 14.7% | 403 1.0% | 582 1.5% | 967 2.4% | 1168 2.9% | 3905 9.8% | |
| Rat RefSeq v1 | RefSeq | 22 523 | 15 534 69.0% | 322 1.4% | 6189 27.5% | 478 2.1% | 295 1.3% | 2533 11.2% | 933 4.1% | 1187 5.3% |
The number of probes in each annotation category is indicated; percentages (italics) indicate the corresponding proportion for the associated source.