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Annotated spliced pangenome (GFA fields)

S Segment line

Tag Type Description
EX Z Comma (,) separated values for each exons the node is part of. Annotated as [Transcript].[Exon_Number]
LN i Sequence length
NC i Count of read that cover the node
IL Z Comma (,) separated values for counting in-links position over the sequence. Annotated as [Index].[Count]
OL Z Comma (,) separated values for counting out-links position over the sequence. Annotated as [Index].[Count]
Example:
S	5	AAA	LN:i:3	EX:Z:Ttest.1
S       577768  ATTTAT  LN:i:6
S       549841  TTCATCTGGTAGTTCTTG      LN:i:18 EX:Z:ENST00000284878.4,ENST00000400166.4,ENST00000400165.4,ENST00000400169.4
S       579999  GTCAGGTCATGTGAAAGCTTAC	LN:i:22 IL:Z:0.256,20.2 OL:Z:22.272,20.3,3.1,19.4,17.1,11.1,4.1,8.1

L Link line

Tag Type Description
JN Z Comma (,) separated values for each junction between exons. Annotated as [Transcript].[Exon_From].[Exon_To]
RC i Count of read that cover the link
ID Z Tag N to identify a novel link
Example:
L	15	+	16	+	0M	JN:Z:Ttest.2.3
L       548094  +       548095  +       0M
L       580290  +       580291  +       0M      JN:Z:ENST00000284885.6.7,ENST00000422787.7.8,ENST00000474775.3.4
L       548097  +       548099  +       0M      RC:i:10	ID:Z:N