Fig. 3: Characteristics of SVs detected in the Japanese population.

a Distribution of minor allele frequency (MAF). SVs were categorized as follows: singleton (minor allele count [MAC] = 1), rare (MAC > 1 and MAF < 1%), low (MAF ≥ 1% but <5%), and common (MAF ≥ 5%). b Distribution of the SV size in each MAF category. *P = 0.00098 and **P < 2 × 10⁻¹⁶, Holm adjusted Wilcoxon rank-sum test. The numbers of SVs belonging to each category are shown in Fig. 3a. Each boxplot has a box that represents the interquartile range (IQR) and whiskers that extend 1.5 × IQR from the box edges. The median is shown in a horizontal line in the box. c Overlap between our dataset and a previous report³⁵. The numbers of SVs identified in this work (TMM), and previous work (deCODE) are shown in red and blue, respectively. The number of SVs identified in both studies is shown in green. d Bar plot showing the proportion of MAF categories in DELs (left) and INSs (right) identified in the TMM dataset only (unique) and in both the TMM and deCODE datasets (overlapped). e Scatterplot showing the allele frequencies estimated in the deCODE study (x axis) and this study (y axis). The Pearson correlation coefficient (cor) and P values are shown. n = 8568 and 9762 for DEL and INS, respectively. f Scatterplot showing the allele frequencies estimated in the East Asian subset of the gnomAD study (x axis) and this study (y axis). The Pearson correlation coefficient (cor) and P values are shown. n = 3491 and 3515 for DEL and INS, respectively.