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Individual #1, sequenced by 23andMe and then inputed into Promethease for SNP data has the following SNP output:

1) rs1935949(C;T) 2) rs2802292(G;T) 3) rs13217795(C;T) 4) rs13220810(C;T) 5) rs2764264(C;T) 6) rs9400239(C;T) 7) rs2153960(C;T) 8) rs2802288(A;G)

Thus individual #1 has eight reported SNPs.

Individual 2 also is sequenced by 23andMe and then inputed into Promethease for SNP data has the following SNP output:

1) rs2802292(T;T) 2) rs2764264(T;T)

Therefore individual #1 has eight reported SNPs for the FOXO3A gene and individual #2 has only two reported SNPs.

Since SNPs represent single nucleotide polymorphisms in the sequence, why does individual #2 only have two SNPs recorded rather than all eight?

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  • $\begingroup$ Welcome to Biology.SE! We encourage you to do some research on your own and then, informed by what you have learned, ask any questions you still have (ideally with references to reliable sources). For "homework" questions, you are required to show your attempt to answer the question and to use the "homework" tag. ——— Please take the tour and then go through the help pages starting with How to Ask questions effectively on this site. Thanks! 😊 $\endgroup$
    – tyersome
    Dec 22 '19 at 17:29
  • $\begingroup$ Why are there more brown-eyed people than blue-eyed people in Britain? Consider. It is the gene that exhibits polymorphism in the population, not the genome of an individual. The statement that someone has so many SNPs is incorrect. He has so many occurrences of the less common variant of a site that exhibits single nucleotide polymorphism. So your question is really why do individuals differ. I imagine you can suggest reasons for that. $\endgroup$
    – David
    Dec 22 '19 at 18:25
  • $\begingroup$ Thank you for the welcome:I think my confusion is based on visualizing SNPs as single base pair substitution in the gene: I thought SNPs can vary by basepair but not in total number - here 8 vs 2. In the example rs2802292 is possessed by both individuals but with #1 carrying (G;T), and #2 carrying ( T;T) SNPs for rs2802292 which makes sense. But, some rs #’s are only in person #1, such as rs1935949 (C;T). So person #2 can have (C;C), (T;C), (C;T), or (T;T). However #2 has no listing at all for rs1935949. How can it be that no SNP of any type is present at location rs1935949? Thanks! $\endgroup$
    – John Dough
    Dec 22 '19 at 23:50
  • $\begingroup$ So, if I'm understanding correctly your question is why you aren't getting SNP information for all the variable positions? That seems like something to ask 23andMe about. IIRC they don't actually sequence DNA and so, due to the technology they use, I suspect that for some locations they may not obtain information. $\endgroup$
    – tyersome
    Dec 23 '19 at 1:24
  • $\begingroup$ Perhaps they don’t report an SNP if your base is the same as their reference genome. $\endgroup$
    – canadianer
    Dec 23 '19 at 2:22

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