Strong <i>cis</i> effects on translation.

<p>For consistency with the figures, the fold changes are log2-transformed so that zero indicates no difference and one indicates a two-fold difference. Positive values indicate higher abundance in BY compared to RM. FP: footprints. NS: neither mRNA nor footprint difference was significant. (1) “Dubious” ORF, footprint data shows translated region only partially overlaps with annotation. The TE difference is due to a nonsense SNP in BY that results in early termination compared to RM. (2) YIL165C is a “dubious” ORF immediately downstream of YIL164C (<i>NIT1</i>); in RM, these two ORFs form a single, consistently translated ORF (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004692#pgen-1004692-g007" target="_blank">Figure 7C</a>). (3) Putative protein with frameshift in RM that leads to premature termination. Note that “dubious” ORFs were not included in our analyses of nonsense SNPs so that YDR133C and YJR015W were not included in those analyses.</p><p>Strong <i>cis</i> effects on translation.</p>