Sequencing of 6.7 Mb of the melon genome using a BAC pooling strategy

BMC Plant Biology

Table 3 Metrics for BAC assemblies and final results after manual correction.*

	35 BACs	23 BACs	Global assembly 57 BACs (two pools together)	Manual correction
No. of contigs ^a	514	247	797	-
No. of bases in contigs	3,936,343	2,325,066	6,127,262	-
Average contig size (bp)	7,658	9,413	7,687	-
N50 contig size (bp)	32,583	32,458	30,630	-
Largest contig size (bp)	117,242	112,451	123,360	-
Q40 plus bases	99.5%	99.5%	99.5%	-
No. of scaffolds	58	32	87	73
No. of scaffolds larger than 20 kb	41	25	62	57
No. of bases in scaffolds	4,040,161	2,307,575	6,206,490	6,340,685
Average scaffold size	69,657	72,111	71,338	86,882
N50 scaffold size	107,196	113,599	107,604	113,787
Largest scaffold size	222,620	200,453	212,424	303,725^b
No. of unscaffolded contigs ^c	479	234	798	744
No. of bases in unscaff. contigs	224,871	121,734	417,982	382,726
Average unscaff. contig size	469	520	524	514
Coverage	x46	x25	x39	x39

*Reads from all 57 BACs were processed together in one assembly run. Additional assemblies of each BAC pool were independently done and served for comparison purposes and to manually correct some scaffolds in the global assembly
^aOnly contigs larger than 500 bp
^bTwo previously published BACs were included in this scaffold (see Methods section and Additional file 1 Figure S1)
^cContigs larger than 100 bp

ISSN: 1471-2229