Fig. 3: Sex chromosome assembly, transmission and X chromosome inactivation skewing.

a Stacked barplot showing X chromosome assembly continuity and mappability relative to the T2T-CHM13v2.0 reference across haplotypes. Each horizontal line represents one haplotype. The assembled contigs in each haplotype traverse the 1 Mbp window of the reference (no more than 3) and have at least ≥95% sequence overlap. Colored segments indicate SDs (yellow), centromeres (red), and gaps (black) on the reference cytogenetic band. b Continuity and mappability of Y chromosome assemblies relative to the T2T-CHM13v2.0 reference (Yq12 heterochromatic region was masked). c Transmitted X assemblies from father to two daughters in the 12832 family with sequence identity visualized using gradient colors. d Transmitted Y assemblies from father to sons in 14317 family. Pseudoautosomal regions (PARs), centromeres (Cen) and satellites (Sat), and X-transposed region (XTR) annotations were derived from Rhie et al. ⁷¹. e Haplotype-resolved methylation at CpG islands (CpGIs) on the X chromosome in nine female-female quads. Mean methylation levels were calculated for each haplotype across 889 CpGIs and their ±5 kbp flanking regions on the X chromosome for 18 female individuals. Red denotes the maternal haplotype, while blue represents the paternal haplotype. A subset of individuals shows evidence of skewing of X inactivation. Source data are provided as a Source Data file.