Experimental Design and Sequence Read Mapping (A) Illumina reads were sequenced and mapped from libraries generated from Drosophila female, male, and tra pseudomale head tissues. For each genotype, there are three independent biological samples, which were sequenced with two technical replicates. The sex hierarchy gene activity and sex chromosome composition for each genotype is shown. Grey indicates that no functional protein is made. The dosage compensation complex (DCC) is not active in females and tra pseudomales that have two × chromosomes. The number of sequence reads and genes that the reads map to are shown. The number of biological (BR) and technical replicates (TR) are indicated. (B) FPKM distribution of all genes covered by sequence reads (green in C). Arrow at lower tail of distribution indicates approximately where FPKM values are for dsx and fru. (C) Illumina reads mapped to 9,473 genes (green) with FPKM values of at least 1in all six replicates within at least one genotype. There were 4,354 genes (yellow) that had reads mapped to the gene, but not with FPKM greater than 1 in all six replicates within at least one genotype. There were 1,031 genes (beige) that had no reads mapped to the gene. (D) Illumina reads were mapped to exons (60%, purple), introns (37%, grey), and intergenic regions (3%; white).