Copy number variation analysis. (A) Log (ln) ratio of read coverage between the FLM and the FB genomes. (B) Scatter plot of copy number variation versus methylation differences between FB and FLM; the log ratio of methylation levels (FLM/FB) and the log (ln) ratio of coverage are on the x-axis and y-axis, respectively. (C) Fold-enrichment of genes and TEs and associated expression features in CNV versus non-CNV regions. (D) Distribution of methylation levels in CNV and non-CNV regions.