Supplementary Figure 1: An example of a de novo mutation at paralogous positions.

We examine a G>A de novo mutation in the largest patriline with 86 meioses (the same patriline shown in Fig. 1), where sequence reads with the mutation map to three paralogous positions that are flanked by identical sequence in the human reference genome (NCBI b36), each shown in a separate depiction of the patriline: (a) 23,235,573 (rAMP7), (b) 24,071,677 (PAL1 arm 1), (c) 26,710,008 (PAL1 arm 2) and (d) with all reads combined (adjusting for the reverse complement orientation of reads at position 24,071,677 relative to positions 23,235,573 and 26,710,008). The allele state of the human reference sequence is indicated after the text "ref." Each square represents a male in the patriline, with vertical position scaled by birth year and the lines between squares representing Y-chromosome transmission events. The filled squares represent males demarcating the branches to which mutations can be assigned. Males with WGS data are indicated underneath a subset of filled squares by counts of alleles mapped to forward and reverse strands at the shown position(s) and inside each such square is the genotype called on the basis of these alleles. When examined separately, the genotypes called for the WGS males at the three positions provide inconsistent results about the branch on which the mutation occurred and the number of mutations required to account for the distribution of genotypes in the patriline. However, when the genotypes at all three positions are combined (d), it becomes clear that a single G>A mutation occurred on the branch labeled with the mutation event. We note, however, that it is not possible to resolve at which of the three positions the mutation occurred. Thus, for the purposes of this mutation rate study, each of the three paralogous positions was assigned one-third of a mutation, i.e., a weight of 1/3.