CCDS levels of cross-alignment. Cross-aligning CCDS IDs detected using RNA-Seq. (a) Percentage of human CCDS IDs that are detected in each sample when aligning to the human reference. (b) Percentage of mouse CCDS IDs that are detected in each sample when aligning to the mouse reference. (c) CCDS IDs that cross-align are identified by subtracting the CCDS IDs detected in a homogeneous tissue sample (the “A” set) from the union of the mixed tissue samples (B,C, &D).