Table 1.

Summary of the Drosophila RNA-seq results.

Mapping summary	bam testis	wt testis	bam ovary	wt ovary
Total reads	41730579	30013546	32806238	29736261
Low-quality and no matched reads	14736702	8645118	14287662	8220597
Reads with multiple matches (>1 hits)	6952842	2667877	1862272	1094363
Uniquely mapped reads (genomic+junction)	20041035	18700551	16656304	20421301
Uniquely mapped non-redundant reads (genomic+junction)	13028364	10853191	11765719	11206968
Uniquely mapped non-redundant reads ( genomic+junction) subsample	10163916	10163916	10163916	10163916
Uniquely mapped non-redundant reads (genomic)	9780037	9827900	9763089	9774561
Uniquely mapped non-redundant reads (junction)	383879	336016	400827	389355
Unique and non-redundant reads mapping to annotated exons	9311716	9416811	9216015	9444989
Unique and non-redundant reads mapping to annotated introns	208725	174567	274958	152291
Unique and non-redundant reads mapping to intergenic region	259596	236522	272116	177281
ENSEMBL genes with at least 1RPKM	9383	10735	9486	8434
ENSEMBL genes with at least 5RPKM	7777	8233	7828	7147
Alternatively spliced genes	989	805	988	879
Total CFTRs	2123	2455	2487	1500
CFTRs in intron*	719	922	959	501
CFTRs in intergenic regions	1404	1533	1528	999
CFTRs supported by mRNA or EST	1402	1149	1727	1241
CFTRs predicted by N-SCAN or CONTRAST	332	370	408	304
CFTRs hit to NCBI non-redundant protein sequence	227	378	223	150
Average length of CFTRs (bp)	419	348	417	415

^*The RPKM of intronic CFTRs are ≥ 10% of neighboring gene’s (or genes’) RPKM.