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I am new to reading raw DNA. When comparing two people's raw data, why does one person have a different SNP than the other, at the same location, on specific chromosome? But on a different chromosome there will be the same SNP, at the same location, for both people.

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  • $\begingroup$ Genetic variation, my friend. People are bound to share similarities and have differences in their DNA, as influenced by errors in transcription, the environment, inheritance, etc. SNPs can be functionally significant or insignificant. $\endgroup$
    – Anne
    Jan 30 '15 at 22:25
  • $\begingroup$ I think it is important to point out that "on a different chromosome [..] at the same location" is not the same location, and that there is not necessarily any relation between similar positions on different chromosomes. I presume you mean something like 'at basepair #74 501 on Chr1 and then also basepair #74 501 on Chr6'. These are totally unrelated positions in the genome, these chromosomes are independent. 2 genomes may vary at one position and not at the other, it's unsurprising. Is this what you mean? We should be clear about this. $\endgroup$
    – Teige
    Feb 3 '15 at 23:24
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Because that's how genetic variation works. SNPs are called single nucleotide polymorphisms for a reason: they are polymorphisms. This means that they are loci where different individuals will have a different nucleotide. This is precisely why they are studied and why we have databases of SNPs and the various genotypes they can manifest.

Remember that mutations can occur spontaneously in a single individual. In fact, they can appear spontaneously in a single cell. This means that if you sequence the genome of two different cells of the same individual it is actually possible that you will find small differences.

Finding small differences between different individuals is certain. Our genomes are not identical and while most differences will be in non-coding regions, you will also have SNPs within genes. How much of our phenotypic variation depends on such small differences is an active topic of research but it is safe to assume that small, single nucleotide changes cause at least some of the variation you see in the people around you.

In any case, what would be surprising is if two individuals were to share the exact same SNP forms for all SNPs in their genomes (I'm sure this happens, but I would expect it to be the case only for close relatives and probably not even then). This variation is the whole point of SNP and the only reason we analyze them.

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It sounds to me as though you have misunderstood something about the chromosomes that make up a human genome.

on a different chromosome [..] at the same location

is not the same location at all. There is no surprise in finding 2 genomes to differ in one place, and not at another unrelated place.

edit If this is a mis-reading of your question, and you meant that the 2 persons' SNP was "at the same location" as the other person, then the rest of the answer is irrelevant. 'A SNP' refers to a location, given a name/identifier for the purpose of measuring variation with SNP-chips; necessarily the same location in any person, which may vary, but needn't always differ between everyone (come on, there are only 4 possible values). You should re-phrase your question "why do they differ at SNP 1 and not at SNP2?".

Background

SNP means nothing more than 'a single basepair in the genome, that might vary in a population', so let's just talk of 'difference at a position'.

A single haploid set of the human genome consists of 23 chromosomes, 22 of these are quite 'ordinary', while 1 is involved in sex determination. Of course, most of our cells are diploid and so we have 2 of these sets, with pairs of Chr1, Chr2, ...Chr22 and X/Y.

What I think your problem isn't, that you perhaps thought it was

I haven't analysed large bits of genomic data but I believe heterozygous positions (positions at which one individual's paired chromosomes differ) are represented in that individual's sequence data. For this reason, I do not think your question is asking 'how can 2 persons have a difference at basepair x on one copy of Chr1, and no difference on the other copy of Chr1' - because both copies of Chr1 are merged as one person's dataset.

In fact it's impossible to assign (meaning to group in to haplotypes) heterozygous sequence to either one copy or the other without more information, i.e. sequences from parents & grandparents, to see which variants are inherited together (are linked).

What I think your problem really is

I think you are asking 'how can 2 persons have a difference at basepair x on Chr1, and no difference at basepair x on Chr6 (say)?' This is easily answered. Basepair 100 of Chr1 is a completely different and unrelated position in the genome to basepair 100 of Chr6. There is no reason to expect that these positions should be related.

A helpful thought experiment

We can concatenate the chromosomes rather than re-setting our count at the beginning of each, then bp 100 of Chr6 will instead be denoted (approximately) bp 1,080,000,100 of the genome - this makes the difference in these positions crystal clear.

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