Table 3:

Metrics for evaluation against GENCODE annotation

Metric	FSM	ISM	NIC	NNC	Others
Count	✓	✓	✓	✓	✓
Reference Match (RM)*	✓
_3´ poly(A) supported	✓	✓	✓	✓
_5´ CAGE supported	✓	✓	✓	✓
_3´ reference supported	✓	✓	✓	✓
_5´ reference supported	✓	✓	✓	✓
Supported Reference Transcript Model (SRTM)	✓	✓
Supported Novel Transcript Model (SNTM)			✓	✓
Distance (nts) to TSS/TTS of matched transcript	✓	✓
Redundancy	✓	✓
% Long Read Coverage (%LRC)	✓
Longest Junction Chain		✓	✓	✓
Intron retention level		✓	✓
Illumina Splice Junction Support	✓	✓	✓	✓	✓
Full Illumina Splice Junction Support	✓	✓	✓	✓	✓
% Novel Junctions			✓	✓
% Non-canonical junctions	✓	✓	✓	✓	✓
% Transcripts with non-canonical junctions	✓	✓	✓	✓	✓
Intra-priming	✓	✓	✓	✓	✓
RT-switching	✓	✓	✓	✓	✓
Number of exons	✓	✓	✓	✓	✓

^*See Table 2 for description of LRGASP metrics

^**X indicates the LRGASP metric in the row is applied to the structural category in the column