Fig. 7

Assemblies and variants of the Chinese Quartet at the extended major histocompatibility complex region. a Alignment of paternal and maternal haplotypes to GRCh38 at the extended major histocompatibility complex (xMHC) region (chr6: 25,701,783–33,480,577). Both haplotypes covered the xMHC region with only one contigs. Gray links between haplotypes and GRCh38 are the protein coding genes resolved. b Genetic characteristics of two haplotypes. c Violin plot shows the variants difference between two haplotypes in 10 k bp windows. The variant difference in the xMHC region is significantly higher than that in other, randomly selected, regions (Wilcoxon rank-sum two-sided test; P < 0.0001). d Violin plot shows the heterozygous and homozygous variants count in 10 k bp windows. The number of heterozygous SNVs and indels in xMHC regions are significantly more than those in other random regions, while homozygous variants have no significant difference. P-value was calculated with Wilcoxon rank-sum two-sided test. ns, not significant; *P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.0001