(A) Three representative genes used for measurement of transition points with the HMM. In green, the affected region after FP treatment as established by the HMM, the transition point being the endpoint of this region. In black, repeat regions where reads couldn’t be aligned uniquely. (B) Average of HMM derived transition points of the FP timecourse (red) or Trp timecourse (blue) plotted against the time of drug treatment. Error bars are standard deviation from the mean. The numbers of the genes with high confidence HMM measurements are next to each data point. (C) Elongation rates derived from the FP time course. Elongation rate is the distance traveled in the time spanning 5–12.5 min (top; n = 141), 12.5–25 min (middle; n = 938) and 25–50 min (bottom; n = 245). All elongation rates can be found in the Figure 3—source data 1. (D) RNA-seq intron gradient relative to the 3′ splicing site (3′SS). Introns longer than 10 kb (n = 17,828) in the refseq gene list are grouped by their sizes, and the average RNA-seq read count per 100 bp bins are plotted by the distance from the 3′SS for each group. Read density in the windows is normalized to the level of reads at the 3′ SS, to compensate for expression differences between genes. The average and the standard deviation of the slope are shown. (E) The RNA-seq gradients of the mid elongation rate genes (12.5–25 min) in the introns (1650 introns longer than 10 kb in 938 genes) grouped by the quartiles of the elongation rate (n = 413, 415, 411, 411 respectively for the slowest, slower, faster, and the fastest). Note that the slower genes have greater negative slope than the faster genes. (F) The RNA-seq intron gradients of the refseq introns upstream of 25 kb from TSS (n = 380) and introns downstream of 50 kb (n = 854) on the same gene for a smaller region.