Fig. 1: Detection of complex tandem repeats outside segmental duplications in individual genomes.

a Examples of complex tandem repeats in an intron of RFC1. The first column shows the two groups of TRs classified by the surrounding nearest-neighbor SNVs shown in the 3rd column (group I is identical to the reference). The 2nd column shows five examples of tandem repeat patterns, and the 3rd and 4th tandem repeats are complex. The 3rd column illustrates each pattern by colored waves associated with the nearest-neighbor SNVs. The last shows the count of each pattern in our study. Each pattern is confirmed by multiple HiFi reads. b HiFi reads with TRs from each individual are anchored to the human genome reference (hg38). Loci with TRs are called TR loci. Reads are clustered into one or two alleles with TRs (denoted as TR alleles) at each TR locus according to sequence similarity. The SNVs closest to the TRs are searched in the peripheral region (indicated by black squares). c TR alleles collected from all individuals are clustered into TR representatives in terms of sequence similarity. The TR representatives are then classified into TR groups with the same nearest-neighbor SNVs enclosed in parentheses. d The frequency distribution (blue) of TR groups with the same nearest SNVs when the minimum difference in length between the longest and shortest TR representatives is set to various thresholds in the x-axis. The frequency distribution of TR loci is also shown (orange).