(A, B) Boxplots showing the distribution of DNA-Seq read densities (in non-overlapping 1 kb windows) mapped to chromosome arms in S2 cells (A) and the distribution of RNA-Seq expression values at the gene-level (B). Pie charts (A, B) show the distributions of copy numbers on each chromosome arm (for expressed genes only). See Figure 1 for copy number color key. The X chromosome is in red. (C, D) Boxplots showing the distribution of RNA-Seq expression values by copy number (C) and expression per copy (D). Equivalent expression medians for two copies on the X and four copies on the autosomes are indicated (dashed line). For all boxplots, the 25th to 75th percentiles (boxes), medians (lines in boxes), and ranges (whiskers, 1.5 times the interquartile range extended from both ends of the box) are shown. Asterisks indicate significant differences from all other chromosome arms (A, B) or from the 2X or 4A baseline (C).