Galba: genome annotation with miniprot and AUGUSTUS

BMC Bioinformatics

Table 4 Summary of protein-coding gene structures predicted in the previously unannotated whale and dolphin genomes of Zoonomia [38], and in Coix aquatica

Species	#Genes	#Transcripts	Mono:Mult	Max exons	#Incomplete	BUSCO C (%)	\(\Delta\)BUSCO C
Balaenoptera bonaerensis	78,621	85,752	1.18	117	19,085	53.0	1.1
Eubalaena japonica	65,123	75,137	1.02	124	10,478	74.1	0.8
Inia geoffrensis	53,435	63,147	0.86	117	8,405	66.0	1.7
Kogia breviceps	72,288	81,084	1.21	160	15,792	65.9	0.2
Phocoena phocoena	56,156	68,654	0.93	158	6,365	85.8	0.1
Platanista gangetica	72,926	80,263	1.13	67	16,080	57.2	1.9
Ziphius cavirostris	75,609	81,048	1.41	77	29,926	38.0	1.9
Coix aquatica	93,399	98,979	1.07	80	102	97.8	0

Number of genes (#Genes), number of transcripts (#Transcripts), number of incompletely predicted transcripts where start- and/or stop-codon are lacking (#Incomplete), Mono:Mult ratio (considering only the first of each possible alternative splicing isoforms of genes with multiple isoforms), the maximum number of exons in a single gene, BUSCO completeness according to vertebrata_odb10, the difference to BUSCO completeness on genome level (\(\Delta\)BUSCO C, defined as the difference of BUSCO C on genome level - BUSCO C in the predicted gene set)

ISSN: 1471-2105