Table 2:

Validation of A. funestus genome assemblies using BUSCO gene set completeness, agreement of the assemblies with RNA-Seq transcriptome data, and structural accuracy inferred using PacBio long-read data

Assembly	BUSCO statistics				Transciptome data statistics (%)			Structural variants called with long reads
	C/S	C/D	F	M	Alignment rate	Multi-mapped reads	Transcripts in a single contig	Deletions	Duplications	Inversions	Insertions
AfunF1	2,756	16	27	16	81.79	23.92	84.96	9,036	455	152	3,798
AfunF3 contigs	2,765	1,068	18	17	84.34	36.97	91.16	NA	NA	NA	NA
AfunF3 primary	2,685	54	30	81	84.86	27.03	89.40	571	6	10	702

AfunF1 represents the prior reference assembly, AfunF3 contigs denotes the complete long-read assembly with all contigs included, and AfunF3 primary denotes the assembly after deduplication and scaffolding. For BUSCO categories C denotes “complete genes,” S denotes “single copy genes,” D denotes “duplicated genes,” F denotes “fragmented genes,” and M denotes “missing genes.”