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How is FASTQC determining encoding in basic summary? Their documentation doesn't seem to cover anything in regard?
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Well, you probably should write to the authors if you want to know. As a guess I suspect that it is looking at all of the quality values and then determining the lowest and highest value it sees. From there it would be quite easy to figure out the encoding used.
In other words, given only one sequence it is hard to tell what the encoding is. Given 1,000,000 sequences it would be trivial.
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