Fig. 2
From: Mapping intron retention events contributing to complex traits using splice quantitative trait locus
Quantification of intron retention (IR) in an upland cotton population. a Percent spliced in (PSI) scores were calculated by taking the ratios of junctions observed over annotated splice junctions. The two examples show one intron region in two different accessions. n2 is the count of junction reads for the single intron, and n1 is the count for surrounding exons. b Pie plot showing the distribution of IR-coupled genes of TM-1 expressed genes. c IGV visualization of intron retention in two genes with different PSI scores. The red dotted box indicates the intron of interest; PSI was calculated in two accessions. d The distribution of PSI difference (PSI (max) − PSI [4]) among the population. e Principal component analysis (PCA) based on PSI scores, which shows a distinct separation of wild and cultivar groups. f Number of IR events identified for each gene. The x-axis and y-axis represent the number of IR events identified per gene and the number of genes in each group, respectively. g Box plot of Pearson’s correlation coefficient (PCC) for the PSI scores of different samples. “Same” and “diff” indicate whether the two samples are biological replicates. Boxes span the first to third quartiles and center lines indicate the second quartile (median)