(A) Spearman correlation, across LCLs, between mCDS translation and uaCDS translation (red histogram). Using random (mCDS, uaCDS) pairs, matched for length and pairwise distance, we computed an empirical null distribution of Spearman correlations (gray histogram). At 10% FDR, 917 inferred (uaCDS, mCDS) pairs have significant negative correlation (shaded red region). (B) 365 orfQTLs (genetic variants associated with ORF usage; i.e., whether the mCDS or uaCDS of a transcript is translated) were identified at 10% FDR (41 pairs of mCDS/uaCDS). (C) Illustrating an example of an orfQTL in the histocompatibility minor serpin domain-containing (HMSD) gene (introns removed for better visualization). The most significant variant (marked x) lies within an intron between the mCDS and uaCDS of the transcript.