Table 1.
Summary of differences between ORFs found by ORFanage and the originally annotated ORFs for all transcripts in RefSeq and GENCODE protein-coding genes. Comparisons to the MANE annotation refer to the ORFs from the MANE gene set, which is fully contained within both RefSeq and GENCODE.
| Reference annotation | RefSeq | GENCODE |
|---|---|---|
| ORFanage finds the same ORF as reference | 117,212 | 63,966 |
| ORFanage finds a different ORF that matches MANE perfectly | 2,212 | 786 |
| No ORF annotated on reference transcript, ORFanage finds an ORF that matches MANE | 1,194 | 147 |
| No ORF annotated on reference transcript, ORFanage finds an ORF that is different from MANE | 9,240 | 35,393 |
| Other combinations | 5,836 | 27,994 |
| Total number of protein-coding transcripts | 135,694 | 128,286 |