Table 1. RetroCNVs in Arabidopsis.

PG	AS	E-E	E-I	I-E	IS	N	Flank	PolyA	TSD	TTAAAA	Mechanism
AT3G06040.1	Can-0	7	17	14	Chr2(+): 7.9M	3		N	N	Y	Uncertain
AT3G08580.2	No-0	25	22	25	Chr2(−): 11.7M	14	LTR/LTR	N	N	N	LTR
AT5G58720.1	Oy-0	108	73	72	Chr4(+): 7.6M	3		Y	Y	Y	L1-like
AT5G51410.2	No-0	26	18	26	Chr1(+): 12.3M	1		N	N	N	Uncertain

“PG” means the parental gene from which the retroCNV is derived. Since parental gene could encode multiple isoforms, only one transcript model (“0.1” or “0.2”) with the highest sequence similarity to the retroCNV is listed. “AS” denotes the accession in which the retroCNV is assembled, while “N” denotes the number of accessions in which the retroCNV is present. In the columns entitled “E-E” (reads mapped to exon-exon junctions), “E-I” (reads mapped to exon-intron junctions) or “I-E” (reads mapped to intron-exon junctions), the numbers refer to the total count of reads mapped to the corresponding junctions. “IS” is the coordinate of the insertion site with “+/−” showing the orientation of the retroCNV relative to the sense strand of the inserted chromosome (Chr). “Flank” shows the retrotransposons in the 5′/3′ flanking region of the retroCNV. Only the retroCNV derived from AT3G08580.2 is flanked by LTR retrotransposon at both sides whereas no recognizable retrotransposon is associated with the other three cases. The next three columns “PolyA”, “TSD” and “TTAAAA” list whether there is polyA, TSD or TTAAAA-like sequences in the flanking region, respectively. Given these sequence features, the mechanism is inferred in the last column.