Table 2.

Number of Sequences Remaining after Each Bioinformatic Steps

		Quality Filtering Q30		TopHat2 Mapping	PCR Duplicate Removal
Crosses	Sex	Input	Discarded	Input	Mapped	Output
♀ GH2 × ♂ BRE	M	203,732,076	43,590,513	160,141,563	144,201,576	64,795,806
					(90%)
♀ GH2 × ♂ BRE	M	278,553,568	62,102,488	216,451,080	197,048,330	84,039,096
					(91.0%)
♀ BRE × ♂ GH2	M	249,198,708	54,496,632	194,702,076	179,194,594	81,242,489
					(92.0%)
♀ BRE × ♂ GH2	M	237,406,392	52,577,939	184,828,453	169,678,849	79,231,052
					(91.8%)
♀ GH2 × ♂ BRE	F	197,048,594	34,868,591	162,180,003	147,618,963	76,799,603
					(91.0%)
♀ GH2 × ♂ BRE	F	226,038,046	42,007,698	184,030,348	167,729,763	86,451,322
					(91.1%)
♀ BRE × ♂ GH2	F	231,467,876	57,694,047	173,773,829	159,153,208	80,775,575
					(91.6%)
♀ BRE × ♂ GH2	F	320,963,252	81,771,733	239,191,519	220,417,355	103,756,971
					(92.2%)