a, Schematic summarizing the SPLASH method. b, The most prevalent intersegment RNA interactions identified using SPLASH for the WSN (H1N1) IAV strain. The eight viral RNA segments are shown on the perimeter of the circle and the links indicate the regions involved in intersegment base pairing. The links are shaded by interaction frequencies based on the chimeric read contact matrix (see Methods). The dotted arrows point to SHAPE-MaP-guided RNA structure predictions of three representative interactions. c, Distribution of the ΔG energies associated with the interactions identified by SPLASH versus a permutated interaction dataset; ****P ≤ 1 × 10−16, two-sided Wilcoxon rank-sum test, n = 611 interactions in common between two biologically independent experiments.