Examples of patterns of translation at putative premature stop codons.

Grey arrows indicate the position and strand of ORFs. Footprints (red) and mRNA (blue, inverted scale) for BY and RM are plotted beneath. The positions of putative premature stop codons in BY or RM are shown as light blue, longer horizontal bars, while all sequence differences between BY and RM are shown as light blue tickmarks above the ORF. The mRNA and footprint densities are shown as log transformed numbers of read starts in 30 bp wide smoothed windows. They are only shown for the strand of the displayed ORFs. A. An example of a premature translation termination in CUE2 in RM compared to BY. B. Two putative nonsense SNPs in TRM2 are in fact upstream of the translated and transcribed ORF. C. The gene NIT1 in BY is the result of a premature termination of a full length ORF that in RM includes the downstream ORF YIL165C.