Cleavage profiles of long and short molecules surrounding CpGs. (A,B) Cleavage profiles surrounding all autosomal CpGs for short (A) and long (B) cfDNA molecules. Each line represents one sample. A cleavage window of 11 bases is shown. Positions 0 and 1 indicate cytosine and guanine, respectively. (C) Box plot of CGN/NCG motif ratios for long and short molecules. (D) Box plot of cleavage ratios between aggregating positions −4, −2, 1, and 4 and position −1. (E) AUCs for distinguishing patients with HCC from non-HCC subjects using the cleavage ratios in D. P-values of differences among groups by Kruskal–Wallis tests. Post hoc pairwise P-values by Wilcoxon rank-sum tests with Benjamini–Hochberg adjustment shown above horizontal lines (C,D).