A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds

BMC Genomics

Table 1 Overall assembly statistics

		Amel_4.5	10 × ^a	PacBio	Amel_HAv1^c	Amel_HAv2^d	Amel_HAv3^e
Size	Total (Mbp)	229.12	217.80	223.24	225.21	225.23	223.86
Contigs (all)	N	16,501	20,240	429	330	331	228
	Longest (Mbp)	0.333	0.288	9.726	13.399	13.399	13.400
	Mean (Mbp)	0.014	0.011	0.520	0.682	0.684	0.974
	N50 (Mbp)	0.046	0.031	3.086	5.167	5.167	5.381
	L50 (n)	1390	1968	23	14	14	13
Scaffolds (all)^b	N	5644	9734	–	–	280	177
	Longest (Mbp)	4.736	3.297	–	–	27.79	27.77
	Mean (Mbp)	0.041	0.024	–	–	0.816	3.340
	N50 (Mbp)	0.997	0.589	–	–	11.33	13.62
	L50 (n)	65	116	–	–	8	7
Scaffolds (anchored to nuclear chr.)	N	340	–	–	–	36	16
	Longest (Mbp)	4.736	–	–	–	27.79	27.77
	Mean (Mbp)	0.598	–	–	–	6.21	13.79
	N50 (Mbp)	1.209	–	–	–	11.60	13.62
	L50 (n)	52	–	–	–	7	7

^aLinked-read sequences taken as scaffolds. Contigs derived from splitting scaffolds on Ns
^bIndividual unplaced fragments counted as scaffolds
^cPacBio+10x
^dPacBio+10x + BioNano
^ePacBio+10x + BioNano+Hi-C

ISSN: 1471-2164