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