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Since all organisms are different from each other - that is, we all have different alleles, some SNP, microsatellites, etc. -, what does it exactly mean, for the genome of a species, to be sequenced? I understand what it means for an organism's genome to be sequenced, but I don't really get what it means for a species.

I'm quite confused about this. Thanks in advance for the help!

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Sequencing a "species" builds a reference genome that is considered to be a good "representative" of the species. Of course there will be genetic variation between the reference and healthy specimens in practice (usually SNPs), however it should be minimal.

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