Table 5 Gene models proposed by BRAKER2, before and after filtering
Initial model setIntermediate filtered setHigh-confidence set
Total Genes1,460,54532,36041,632
Average CDS length (bp)613.901099.081146.4
Average number of exons2.784.224.48
Average intron length (bp)2,3622,2333,894
Max intron length (bp)385,133159,9791,399,110
Total monoexonics941,6595,165
Total multiexonics518,88632,36036,466
  • 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.