Fig. 2From: Lost genome segments associate with trait diversity during rice domesticationSV discovery. a Histograms illustrating frequencies of different sizes of SVs. b SVs from each sample were merged using a nonredundant strategy starting with J-SN265 and iteratively adding unique calls from additional samples. The growth rate of the nonredundant SVs declines as the number of samples increases. SVs shared among all samples are shown as red portions of each bar. c Stacked bar graphs showing the proportion of repeat types for all annotated insertions and deletions. Count, the proportion of individual repeat annotations; bp, the proportion of cumulative repeat sequence length; Other, other repeat types. d Structural variation density from repeat/non-repeat genomic regions in continuous 200-kb windows. Significance was tested by Fisher’s exact test; ***, p < 0.001. e Frequency for each variant type (insertion and deletion). Compared to deletions, a greater proportion of insertions were shared among all rice accessions. f, g Comparisons of the TE number (f), GC content (f), single-nucleotide mutation rate (f), and gene expression level (g) between SV and non-SV regions. Data are presented as means ± 95% CIBack to article page