Alignment lengths

HBV is a circular genome and so the genomes found on NCBI have been linearised. The following plot shows the % of the genome which aligns to the reference (in black), where around 1000 genomes seem to only have 50% matching. If we rotate the genomes in order to all start at the same place then we can improve this (coloured dots).

Genomes with over 90% match: (rotated) vs (NCBI)

Genomes with over 80% match: vs