First off, you are right that you sequence an individual and not a whole species–however, species tend to be very close in genetic code, especially compared to other species further out in the tree of life, so an individual can be a very good representative of a species.
Second, to “sequence” something is to literally identify the full “sequence” of genetic code bases (A/C/T/G) making up all the genetic material of that individual’s original code. This might be split up among chromosomes and different locations and such, but most of it is all a linear series of these 4 bases in a specific order.
A “genome” is another word for this full sequence.
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