Table 5.

Number of intra-molecular chimeric transcripts

	Chimeric reads in all librariesa	Number of clustersb	Singletonsc	D. melanogaster		D. pseudoobscura
				Male	Female	Male	Female
				Counts (%)d	Counts (%)d	Counts (%)d	Counts (%)d
atp6/atp8	85	37	19	64 (1.51)	9 (1.65)	11 (2.03)	1 (0.24)
cytb	60	25	16	45 (1.26)	10 (3.00)	5 (2.91)	0 (0)
cox1	87	27	15	69 (0.91)	14 (2.09)	0 (0)	4 (1.42)
cox2	48	25	11	37 (0.87)	5 (1.26)	3 (1.12)	3 (1.58)
cox3	37	21	14	27 (0.69)	7 (2.28)	2 (0.55)	1 (0.48)
nd1	4	4	4	4 (0.38)	0 (0)	0 (0)	0 (0)
nd2	11	3	1	11 (3.78)	0 (0)	0 (0)	0 (0)
nd3	7	5	4	4 (0.46)	0 (0)	0 (0)	3 (8.57)
nd4/nd4L	12	12	12	12 (0.76)	0 (0)	0 (0)	0 (0)
nd5	17	9	7	15 (1.56)	0 (0)	1 (1.47)	1 (1.39)
nd6	2	2	2	1 (0.39)	0 (0)	1 (4.76)	0 (0)
rrnL	426	64	40	356 (0.79)	19 (0.39)	29 (0.51)	22 (0.45)
rrnS	1	1	1	0 (0)	1 (0.25)	0 (0)	0 (0)
Total	797	235	146	645 (0.85)	65 (0.83)	52 (0.65)	35 (0.54)

^aTotal number of chimeric reads in the four libraries.

^bEach cluster represents a different type of chimeric transcript.

^cNumber of clusters with only one read (number of molecules sequenced only once).

^dPercentage of the total counts for each gene.