Fig. 4

Features of H-specific variations. (A) Density plot of sequencing coverage on mutation sites. (B) Fractions of Indels and SNPs in H-specific and nonspecific sites. P-value was calculated by Chi-square test. (C) Fractions of missense and synonymous SNPs in H-specific and nonspecific sites. P-value was calculated by Chi-square test. (D) For the H-specific or nonspecific sites, their unique genes were studied separately. dN (missense substitution rate) values were displayed by boxplot. P-value was calculated by KS test. (E) Comparison of dN values of genes on chromosomes 7 and 17 versus other chromosomes. P-value was calculated by KS test. (F) Spearman’s correlation (p-value <2E-16) between the dN values of genes and the ratio of missense to synonymous SNPs. Only the H-specific SNPs were used to calculate the missense to synonymous ratio on each gene