Table 3 Use the gffcompare tool to analyze new transcripts and genes in the samples and predict the coding sequence (CDS).

I (fully contained within a reference intron)

6,215

J (multi-exon with at least one junction match)

250

K (containment of reference (reverse containment)

78

M (retained intron(s), all introns matched or retained)

72

N (other same strand overlap with reference exons)

22

O (other same strand overlap with reference exons)

3

U (none of the above (unknown, intergenic))

912

X (exonic overlap on the opposite strand (like o or e but on the opposite strand))

982

All (All newly predicted transcripts and genes)

8,534