Isoquant Major Exon Elongation

Question

[aico]

Hi all, long time lurker first time poster. I've been running Isoquant to assign Nanopore reads to one transcript isoform, and even though they align, the vast majority of my reads are assigned "inconsistent_non_intronic". I look at the individual read assignments, and most of the reads have "mono_exon_match,terminal_position_match_precise:0,major_exon_elongation:599" under the "assignment_events" column.

From the Isoquant docs, this means "major_exon_elongation_5/3 - significant exon extension at 5'/3' end (exceeding 30bp);". My question is, does the 599 mean how long the reads are extended past either the 5' or 3' end? Has anyone else run into this sort of problem with inconsistently assigned reads?