Tag-position bias analysis using Classic and Signature data from Arabidopsis. Plots A and B show the relationship between tag-position and the percentage of low-count genes. The gene density shows the distribution of genes with a given tag-position. The curves on the top of each plot show the relationship between tag-position and the percentage of low-count genes. Plots C and D show the dependence of measured abundance on tag-position for genes with significant associated tag-count. The scatter-plot shows all data points from five different libraries. The red curve represents a LOWESS smooth of all these data and the green curve represents the bootstrap credibility intervals (5–95%). (Inset) Each line except the bold black one represents a LOWESS smooth of an individual library, while the bold black one is the same as the red one in the main plot. Plots A and C are from Classic MPSS data while Plots B and D are from Signature MPSS data.