Fig. 3

Methylation abnormalities in a KHDC3L^c.1A>G embryo. a Scatterplot comparing methylation determined by PBAT in a single whole KHDC3L^c.1A>G preimplantation embryo with PBAT of a bulk population of control blastocysts (Okae et al. [30]). Each point is a 20-kb window. b Screenshot of methylation in the KCNQ1OT1 imprinted domain in control blastocysts (Okae et al. [30]) and the KHDC3L^c.1A>G embryo. Each vertical bar is a 20-kb window, height and colour-coded for % methylation. c Box and whisker plots comparing ratio of methylation maintenance in control blastocysts and the KHDC3L^c.1A>G embryo at maternal gDMRs retaining ≥ 20% DNA methylation in the oocyte (n = 38), maternal-methylated domains (n = 285), paternal-methylated domains (n = 2471), maternal-methylated CGIs (n = 735) and paternal-methylated CGIs (n = 299). d Box and whisker plots comparing methylation maintenance ratio in control blastocysts and the KHDC3L^c.1A>G mole at maternal and placenta-specific gDMRs (n = 40) retaining ≥ 20% DNA methylation in KHDC3L^c.1A>G oocytes. In c and d, boxes represent the interquartile range; lines, the medians; whiskers, the 1.5× the interquartile range; and dots beyond the whiskers, outliers. Comparisons in c and d are all statistically significant (p = 0.0125 for maternal gDMRs in c and p < 0.0001 for all others). Detailed statistical measures are given in Additional file 4: Table S3