Table 3.

Copy Number Variations (CNVs) in populations of H. melpomene and H. cydno

Species	Butterfly	Del/dup	Gene	Chromosome	Scaffold size	Begin gene	End gene	Begin CNV	End CNV	Length CNV	Norm. RD	P-value
H. c. chioneus	553	dup	IR75q2	Chr15	190001	51255	62232	41501	62300	20800	2.64	3.87E-08
H. m. amaryllis	11-160	del	IR75q1	Chr15	190001	67972	71764	66901	72200	5300	0.44	3.01E-11
H. m. amaryllis	11-160	del	IR64a	Chr14	16065	3076	6448	2301	5400	3100	0.5	3.50E-06
H. m. melpomene	9315	dup	IR7d4	Chr14	89318	65125	66960	55501	68600	13100	6.52	0
H. m. melpomene	13435	dup	IR7d4	Chr14	89318	65125	66960	55001	68600	13600	3.75	0
H. m. aglaope	09-122	del	IR60a2b	Chr20	72055	37488	39341	38201	39400	1200	0.23	0.0174
H. m. aglaope	11-569	del	IR60a2b	Chr20	72055	37488	39341	38201	39400	1200	0.16	0.0023
H. m. amaryllis	09-216	del	IR60a2b	Chr20	72055	37488	39341	37401	39400	2000	0.37	0.0472
H. m. amaryllis	11-160	del	IR60a2b	Chr20	72055	37488	39341	38101	39400	1300	0.2	0.0127
H. c. chioneus	553	dup	IR60a2a	Chr20	72055	47451	49370	41401	49500	8100	2.15	0

Output of CNVnator is reported here. Butterfly ID, deletion or insertion, IR gene name, chromosomal position, scaffold size, coordinates of the IR gene, coordinates and length of the CNV, normalization and P-value are shown. Only insertion and deletion variants with a read depth >2 (duplications) and <0.5 (deletions) are reported