[throwaway07Ju19]

23andme will let you download a zip file of your sequence data. But if I recall the data had only about 4 million nucleotides. So I assumed that I need to get their "baseline" human full genome somewhere and my file is just the difference.

But the above assumption can't be correct given that it still costs $1000 for a full sequence according the the parent article. Can anyone clarify ?

[ben1040]

23andMe ran a microarray analysis, which probes your genome at a specific set of locations.

If you want to know how your genome differs versus what's called the "reference genome," then you'd need a whole-genome sequence. That process shards up your genome, sequences it, aligns the pieces back to the human reference, and then calculates a "consensus" that represents the software's best guess as to how your genome relates to the reference.

Then they could provide you with a diff of the consensus with respect to the reference, which would probably be distributed to you in a VCF file (variant call format).

This process is the one that costs more money versus 23andMe's $99.

[davecap1]

23andMe only tests for known relatively common mutations (single nucleotide polymorphisms, or SNPs) that have been identified by non-profit large scale sequencing projects done in the past (basically public data now, see dbSNP for instance). You will almost certainly have mutations that are not covered by their panel, so it is not a matter of comparing your 23andMe results to the "baseline" (or "reference genome"). Their panel costs in the hundreds of dollars to run since it is so focused (at least 10x less than a full "exome" test, which would look at the full sequence of all known genes).