The topic of read mapping is a sufficiently distinct subset of the more general class of sequence alignment topics to warrant a dedicated tag. However, we should collapse
read-mapping as synonyms.
If the tag can’t work as the only tag on a question, it’s probably a meta-tag. Every tag you use should be able to work, more or less, as the only tag on a question. Meta-tags, like [beginner], [subjective], and [best-practices], are useless by themselves — they tell you nothing at all about the content of the question.
As user172818 pointed out in the comments, the term "mapping" has different meanings in different subfields. Therefore, "mapping" by itself doesn't tell us anything useful about the question; it needs to be combined with another tag (ngs, reads or whatever) in order to be informative. Therefore, it is not a useful tag and should just be removed.
The simplest way to remove tags is to just edit the questions that have them. If no questions are tagged with a given tag, the tag will be deleted from the system automatically. If, in future, we see the tag returning, we can ask for it to be blacklisted.
is about mapping between different types of affymetrix arrays. Here, I removed mapping and created a new tag affymetrix-arrays. I don't think it would be worth creating something as specific as affymetrix-array-mapping or similar.