Fig. 6

In each of the above panels A–C, the human chromosomes 1–3 (demarked by alternating dark and light grey horizontal bars) are plotted for different oHMMed analyses: In A, the average GC proportion in every 100 kb window is coloured by the oHMMed-inferred GC state. The three lower states are in blue and the two higher ones in green, with the shades lightening with higher GC proportion. In B, the number of protein coding genes for every 100 kb window are shown in colours corresponding to the oHMMed-inferred gene density states: yellow, orange, and red mark increasing gene density states. Note that in both A and B, the black lines trace the posterior (inferred) means returned by oHMMed with normal and gamma-poisson emissions respectively. These position-specific posterior means are the sum of estimated means times the respective probabilities of each state, thus combining both estimated mean values and the algorithm’s certainty of the assigned state. In C, Spearman’s correlation for the two posterior means is shown in rolling windows of 40 collated \(100\,{\text {kb}}\) windows