Figure 2.

Patterns of nucleotide and codon representation across the three data sets. Reads were separated into those whose 5′ ends map to the first, second, or third reading frame within codons (frame 1, 2, or 3). The fold enrichment of each nucleotide was determined by dividing its number of counts at each position by the mean number of counts at positions within the same reading frame across the 27 nucleotides analyzed, thereby accounting for differences in expected nucleotide proportions among reading frames within codons. Enrichment is plotted in log₂ scale: red, adenine; blue, cytosine; green, guanine; and yellow, thymine. Each codon position overlapped by each read was also determined by identifying the nine consecutive codons beginning from the 5′ end, as indicated in Figure 1. The gray bars indicate the coefficient of variation (CV) as a measure of the degree to which each position deviates from the expected background frequency of the 61 sense codons; codon position 4 is indicated for reference.