Table 5. Gene models proposed by BRAKER2, before and after filtering.

	Initial model set	Intermediate filtered set	High-confidence set
Total Genes	1,460,545	32,360	41,632
Average CDS length (bp)	613.90	1099.08	1146.4
Average number of exons	2.78	4.22	4.48
Average intron length (bp)	2,362	2,233	3,894
Max intron length (bp)	385,133	159,979	1,399,110
Total monoexonics	941,659	—	5,165
Total multiexonics	518,886	32,360	36,466

Intermediate set was filtered by removing monoexonic models, models with greater than 50% of their length in a masked region, models annotated as retrodomains, and models lacking functional annotation with EnTAP. The high-confidence set includes the intermediate set, plus monoxonic and multiexonic models derived from transcript evidence, removing any fully nested gene models.