Table 1.

Class codes used to describe how assembled transcripts compare to reference annotation.

Class code	Description
=	Predicted transcript has exactly the same introns as the reference transcript.
c	Predicted transcript is contained within the reference transcript.
j	Predicted transcript is a potential novel isoform that shares at least one splice junction with a reference transcript.
e	Single exon predicted transcript overlaps a reference exon plus at least 10 bp of a reference intron, indicating a possible pre-mRNA fragment.
i	Predicted transcript falls entirely within a reference intron.
o	Exon of predicted transcript overlaps a reference transcript.
p	Predicted transcript lies within 2 Kb of a reference transcript (possible polymerase run-on fragment).
r	Predicted transcript has more than 50% of its bases overlapping a soft-masked (repetitive) reference sequence.
u	Predicted transcript is intergenic in comparison to known reference transcripts.
x	Exon of predicted transcript overlaps reference but lies on the opposite strand.
s	Intron of predicted transcript overlaps a reference intron on the opposite strand.