Hi Josie - by default the units will be substitutions per site (see here for an introduction), however for our ncov datasets we multiply this by the genome size to give overall mutations. This won’t always be the same as simply counting the mutations relative to the root (Wuhan/Hu-1 or similar), as the underlying phylogenetic model will consider reversions and multiple mutations at the same site. There is some uncertainty in the phylogeny, so as that changes the divergence may change. If the alignment changed, you should see a different set of mutations to the root when clicking on a tip.