Table 3.

Assignment of accession nos to sequencing libraries

	Protocol	r1	r2
Dmel	NEBNext Ultra (+)	ERR557048	ERR557049
	NEXTflex (−)	ERR557050, ERR557052, ERR557054	ERR557051, ERR557053, ERR557055
	NEBNext DNA (+)	ERR557056	ERR557057
	TruSeq (−)	ERR832532	ERR832533
Dsim	NEBNext Ultra (+)	ERR557058	ERR557059
	NEXTflex (−)	ERR557060, ERR557062, ERR557064	ERR557061, ERR557063, ERR557065
	NEBNext DNA (+)	ERR557066	ERR557067
	TruSeq (−)	ERR832534	ERR832535

Dmel, Drosophila melanogaster; Dsim, Drosophila simulans; r1, replicate 1; r2, replicate 2.