How come BLAST result of my sample sequence is showing top sequences with 97-100% similarity but the bootstrap value on the branch point of my sample is only 30/100 in the phylogenetic tree? It's only the branch point of my sample with such low bootstrap value, the rest of the branch points have high bootstrap value. How do I interpret the result?
Bootstrap values show support for a particular branch configuration. Generally speaking, branch support is not correlated with percent identity of the entries. For example, it is possible to have 3-4 entries with >95% identity to each other, all on the same branch and with poor bootstrap support. It is also possible to have 3-4 entries with <80% identity to each other, all on the same branch and with high bootstrap support. Until you provide more details and the tree itself, it is impossible to answer this question except in general terms.