Beyond genomic variation - comparison and functional annotation of three Brassica rapagenomes: a turnip, a rapid cycling and a Chinese cabbage

Table 1 Comparisons of Chiifu gene models made by MAKER and obtained from BRAD

		BRAD_only	MAKER_only	Overlap_reciprocal	Overlap_split	Overlap_join	Overlap_total
100%	Gene	8,500	26,118	11,271	156	2,880	32,519
	Exons	30,121	42,416	164,479	26	895	176,454
75%	Gene	6,437	11,715	25,848	187	2,815	34,582
	Exons	21,838	34,590	179,737	47	964	184,743
50%	Gene	5,229	8,601	29,857	203	2,762	35,790
	Exons	19,385	31,639	184,909	78	1,007	187,198
25%	Gene	4,239	6,544	33,617	719	2,719	36,780
	Exons	18,270	30,178	187,577	347	1,039	188,313

Four different minimum overlap requirements (expressed as a fraction of the Chiifu reference gene model) used to compare two gene models at both gene level and exon level. The BRAD_only and MAKER_only columns represent features found only in the reference gene model and MAKER generated gene model respectively. Intersections between two gene models mainly include the fraction overlap reciprocal for both (overlap_reciprocal), overlaps that split one reference feature to many MAKER features (overlap_split) or join many reference features to one MAKER feature (overlap_join).

ISSN: 1471-2164