Fig. 2: Summary of DNM rates.
From: Human de novo mutation rates from a four-generation pedigree reference
a, The number of de novo germline mutations, PZMs and indels (<50 bp) for the parents (G2) and eight children in CEPH 1463. TR DNMs (<50 bp) are shown for G3 only because they have greater parental sequencing depth and we can assess transmission (Methods). The hatched bars show the number of SNVs confirmed as transmitting to the next generation. b, Germline SNVs (n = 626) have a mean allele balance of near 0.50 across the sequencing platforms, while the mean postzygotic SNV (n = 119) allele balance is less than 0.25. The box plots show the median (centre line), the interquartile range (IQR) (box limits) and the whiskers extend to 25% − 1.5 × IQR and 75% + 1.5 × IQR; outliers are shown as dots. c, A strong paternal age effect is observed for germline de novo SNVs (+1.55 DNMs per year; two-sided t-test, P = 0.013) but not for PZMs (P = 0.72). We observe no significant maternal age effect for DNMs (+0.20 DNMs per year, P = 0.54) or PZMs (P = 0.74). The solid lines are regression lines that were fitted using a linear model function; the surrounding shaded areas represent their 95% confidence intervals. d, The estimated SNV DNM rate by region of the genome shows a significant excess of DNM for large repeat regions, including centromeres and SDs. Assembly-based DNM calls on the centromeres and Y chromosome (chr.) show an excess of DNM in the satellite DNA. A significant difference from the autosomal DNM or PZM rate was determined using two-sided t-tests; *P < 0.05, **P < 0.001. P values for each comparison are as follows: 0.0066 (alignment-based DNMs in SDs), 0.049 (alignment-based PZMs in SDs), 0.017 (alignment-based DNMs in centromeres), 0.34 (alignment-based PZMs in centromeres), 0.13 (assembly-based DNMs in centromeric flanking regions), 0.14 (assembly-based DNMs in centromeric HORs), 0.59 (assembly-based DNMs in chromosome Y euchromatic regions) and 0.00025 (assembly-based DNMs in Yq12).
