The frequencies of the mismatches observed between the HBV reference sequences (Supplementary Table 3) and the reads are shown as a function of distance from the 5′ end. C > T (5′) and G > A (3′) mutations are shown in red and blue, respectively. All other possible mismatches are shown in grey. Insertions are shown in purple, deletions in green and clippings in orange. The count of reads matching HBV for each sample is shown in parentheses. a, Damage patterns for RISE563, DA222, DA119, RISE254, DA195, DA27, DA51, RISE386, RISE387, DA29, DA45, RISE416 and RISE154. b, Damage patterns for DA222 without (left) and with (right) USER treatment. c, Damage patterns with 10, 20, 50, 100, 200, 500 and 1,000 reads sampled from RISE563, in which each opaque line corresponds to one replicate set of reads.