Table 1.

Summary of Data Acquisition.

Sample	Totala	Genomeb	Exon (I)c,d	Exon (U)c,e
F1 RNA-R1	40.95	32.30	25.92	26.41
F1 RNA-R2	44.81	34.41	26.44	26.60
F1 RNA-R3	42.58	32.78	28.28	29.00
F1 DNA-T1	50.47	25.07	10.51	10.74
F1 DNA-T2	47.25	23.84	10.20	10.45
F1 DNA-T3	44.22	22.59	9.90	10.10

^aThe total number of reads (in millions) output by the Illumina GAIIX (including alignments to the mitochondrial genome).

^bThe number of reads that aligned anywhere in the Drosophila melanogaster genome (R5.26) in millions.

^cThe number of reads that aligned unambiguously in exonic regions in millions.

^dTwo initial reference genomes were considered: the melanogaster R 5.26 and a Drosophila simulans reference (initial references, I).

^eInitial exonic reference sequences were updated based on RNA-seq data from the parental lines and an updated reference (U) was created for both parents.