Table 3.

Summary across four Hymenopteran insect genomes and de novo annotation pipelines

Species	Method	#Genes	#Transcripts	#Good Predictions	#Bad Predictions	Score Quartiles	BUSCO C (%)	$\mathrm{\Delta }$BUSCO C
Vespula vulgaris	GALBA	14,087	16,766	5,393	11,373	0, 67, 90	95.8	-0.9
	BRAKER2	12,338	13,808	4,974	8,834	45, 67, 90	95.8	-0.9
	Funannotate	12,200	12,200	2,970	9,230	0, 45, 67	82.7	12.2
Vespula pensylvanica	GALBA	14,071	16,897	5,767	11,130	0, 67, 90	98.0	-1.8
	BRAKER2	12,891	14,327	5,134	9,193	45, 67, 90	97.4	-1.2
	Funannotate	12,580	12,580	3,146	9,434	0, 45, 90	85.6	10.6
Vespula germanica	GALBA	14,413	17,070	5,354	11,716	0, 64, 90	94.8	-1.2
	BRAKER2	12,956	14,409	4,919	9,490	45, 67, 90	94.6	-1
	Funannotate	10,267	10,267	3,177	7,090	45, 67, 90	84.7	8.9
Polistes dominula	GALBA	15,590	18,505	5,645	12,860	0, 64, 90	96.4	-0.7
	BRAKER2	15,322	17,075	5,145	11,930	22, 64, 90	96.2	-0.5
	Funannotate	9,637	9,637	2,061	7,576	0, 45, 67	65.6	30.1

Number of good and bad predictions, as well as score quartiles, as summarized by GeneValidator. BUSCO completeness according to the hymenopteran lineage hymenoptera_odb10. ($\mathrm{\Delta }$BUSCO C, defined as the difference of BUSCO C on genome level - BUSCO C in the predicted gene set)