Additional file 1: Figure S1. of Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species

a. Phylogenetic tree of HNI, Hd-rR, and HSOK, deriving respectively from northern Japanese, southern Japanese, and Korean medaka populations. b. Frequency distribution of distances between pairs of proximal representative TSSs in the Hd-rR and HNI genomes. c. Spearman’s rank correlation coefficient matrix for dinucleotide content (AA or TT denoted by AA_TT, CC or GG by CC_GG), single nucleotide content (A, C, G, T, A or T represented by A_T, C or G by C_G), and their asymmetry values (Sa) upstream and downstream of TSSs in the Hd-rR (Hd) and HNI (HN) strains. Many pairs of parameters are highly correlated positively (colored red) or negatively (green), implying considerable redundancy of parameters. We noticed that each parameter was highly correlated with one of the parameters in the yellow boxes (Hd/HN_A/C/G/T_Up/Dw, Hd/HN_Sa_A/C/G/T). To reduce the number of parameters, we selected to use the parameters in the yellow boxes for further analysis. d. Nucleosome coverage distribution of each tissue. The vertical axis displays the cumulative fraction of nucleotides covered by > x nucleosome cores where x is the coverage shown in the horizontal axis. (PDF 752 kb