The region where recombination breakpoints had the highest probabilities was recognized as crossover region, which is a region that one parental genotype switches to another. Upstream sequence of crossover region will have specific mutation of one genotype but with no specific mutation of another, downstream just opposite. At the same time, these two genotypes should share same sequence at crossover region. We indicated the crossover region in direct alignment by black bars in Figure S3 initially and marked it in recombination map by colorful bars in Figure 3A and black bars in Figure 3B . The clonal sequences of 2006 showed 17 unique crossover regions in fragments A, B and C. We could not identify any common motif within these sequences that might suggest a common mechanism for crossovers in the HBV. The size of switch region share the same sequence are different in different strains, from 6-174 bp (6 bp for Y2M-2 clone in Figure S7 and 174 bp for Y2M-29 clone in Figure S8 ).