Fig. 5: Joint conditional probability analysis reveals a shift in the timing of major conformational changes in the MiMIC insertion.

A-A” Plot of PDFs for MiMIC insertion pairwise E1-PPE (A), E2-PPE (A), or E1-E2 (A”) distances (μm), generated from Gaussian kernel density estimation of measured distances. Each distance data point is modeled as a probability distribution centered at the observed value, resulting in the solid line traces. The shaded region surrounding each of the solid line traces represents the confidence interval from 2.5% to 97.5%. Adjacent heatmaps show two-sided Kolmogorov–Smirnov (K-S) test p-values (Benjamini–Hochberg corrected for multiple comparisons) using a color scale: yellow/pink is significant (p < 0.05 indicated by bracket and *), whereas purple/black is not; self-comparisons (black, p = 1.0) run diagonally through each heat map square. Arrows indicate the occurrence of significant change. For MiMIC insertion, the major changes are from nc13 “2” to nc14 early “3” for E1-PPE and from pre-nc13 “1” to nc13 “2” for E2-PPE. B–E 2D projection of 3D contour data for MiMIC insertion over time. Color scale from white, purple, to orange displaying regions of low, medium or high probability of PPE location relative to the other CRMs. Grayscale along x shows E2 positional likelihood. F–H Subtraction contours in which the second sample (blue: the earlier time point) is subtracted from the first sample (red: the later time point). Red indicates a higher probability for the first genotype, blue for the second. The most probable position (MPP) of the first genotype is filled circles while the second genotype is shown as hollowed squares with their respective colors of blue (E1), green (PPE) and red (E2). All E1-E2 possible distances are shown below with the top grayscale being the first genotype. Distance modes for each triangular configuration are indicated by solid (contour 1) or dashed (contour 2) lines. Global two-sided Simes P-values and their interpretations are shown for each subtraction contour. See also Fig. S3 and Tables S2, S3 for number of embryos imaged, number of doublets counted for each condition, and individual p-value as well as other relevant statistics.