Fig. 2

Local eQTL characterization. a Genes with local eQTLs occur more frequently at adjacent positions than expected by chance. The x-axis indicates the number of intervening genes between two genes in the ZS11 genome. The light red triangles indicate the number of gene pairs observed with local eQTL mapping. The blue histograms indicate the distribution of gene pairs from 1000 random permutations. The green histogram in the inset indicates the distribution of adjacent gene pairs based on 1000 random permutations. b CDF plots show that all adjacent gene pairs with any local eQTLs exhibit the highest expression correlation. Class I indicates the correlation coefficient distribution of adjacent genes with any local eQTLs. Class II indicates the correlation coefficient distribution of adjacent genes with local eQTLs detected on either gene. Class III indicates the correlation coefficient distribution of adjacent genes that do not map local eQTLs on both genes. Class IV indicates the correlation coefficient distribution of non-adjacent genes with local eQTLs mapped on both genes. c The violin plot depicts the highest correlation of expression of adjacent genes when local eQTLs regulating two class I adjacent genes which are in the same chromatin open state. In the horizontal axis, “Both open” indicates that the local eQTLs for both class I genes are located in the ATAC chromatin open region; “One open” indicates that the local eQTLs for only one class I gene are located in the ATAC chromatin open region. “Both closed” indicates that the local eQTLs of both class I genes are not located in the open region of ATAC chromatin. ***P < 0.001 compared with “One open” in Student’s t test