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

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

   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
  1. 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).