Comparison of introns between the Gencode reference and the 24 tracks, ordered by decreasing sensitivity, over the 31 test regions. Gencode validates 3,618 unique introns and a total of 9,693 introns in its alternative transcripts. (a) Projected measure: each intron is counted only once per method. Introns with the same coordinates as Gencode introns are shown in green and novel introns in red. The Gencode introns missed in each track (false negative) correspond to the distance between the 'true positive' bar and the Gencode reference, but are not explicitly represented. (b) Quantitative measure: all alternative variants are counted separately. Introns identical to Gencode introns, but over-used relative to Gencode are counted (in yellow) separately from novel introns that are not known to Gencode.