Table 2.

Number of reads obtained, retained after quality control, and mapped to the reference genome.

Treatment	Replicate	Total reads	Reads after quality control		Reads mapped to reference genome
		Number	Number	%	Number	%
Control	1_gaII	38,623,190	38,595,804	99.93	36,658,295	94.98
Control	2_TruSeq_4	32,414,845	32,413,140	99.99	31,382,402	96.82
Control	6_TruSeq_6	28,893,141	28,891,426	99.99	27,923,563	96.65
Control	9_TruSeq_7	31,672,204	31,672,204	100.00	30,671,362	96.84
Hyd1	3_gaII	39,050,068	39,031,083	99.95	36,931,211	94.62
Hyd1	3_TruSeq_2	28,074,997	28,074,997	100.00	27,151,330	96.71
Hyd1	10_TruSeq_12	31,084,062	31,084,062	100.00	30,070,722	96.74
MSRO	2_gaII	36,838,900	36,824,546	99.96	34,640,850	94.07
MSRO	1_TruSeq_2	31,841,684	31,832,465	99.97	30,867,941	96.97
MSRO	5_TruSeq_5	30,537,077	30,535,822	100.00	29,442,640	96.42
MSRO	8_TruSeq_6	30,124,318	30,124,318	100.00	29,172,390	96.84
wMel	4_TruSeq_4	32,691,282	32,691,282	100.00	31,449,013	96.20
wMel	7_TruSeq_5	27,032,887	27,032,887	100.00	26,073,220	96.45
wMel	11_TruSeq_7	28,550,836	28,548,722	99.99	27,595,195	96.66