This is a question which plagues many people and today I was wondering it myself while writing a grant. Indeed, I've seen many people use the terms interchangeably, but they are all very different from each other.

So What is the difference between SNPs, Mutations and Structural Variations?

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    $\begingroup$ it is always good idea to start with googling and present some results in the question. then move to asking for clarifications,m instead of asking for definitions. $\endgroup$ Commented Jun 16, 2015 at 16:34

1 Answer 1


Lets state what a Mutation is first.

Mutation: A mutation is any change in an organism's genetic sequence which varies from that of the wild-type reference sequence (hg19/GrCH37 from 2009 or hg38/GrCH38 from 2013, which are the most current genome assembly).

Single Nucleotide Polymorphisms (SNPs): These are any single nucleotide base mutations which have been validated to be present in more than 1% of the population with the help of Genome-wide Association Studies.

Structural Variations: These are any mutations which cause a change in the organism's chromosome structure, such as Insertions, deletions, copy number variations, duplications, inversions and translocation.

For more please read Wiki Link here.

Thanks to WYSIWYG for his interesting question regarding SNPs.

This piqued my interest a bit, and to my surprise I found that the same actually applies to all other species for example chickens; This paper from way back in 2002 describes how EST mining was sometimes used to generate potential SNPs but also notes the possible false positives due to the possibility of RNA-Editing.

This paper describes the usage of SNPs to allocate bovine individuals to their source population. As does this paper which highlights the economic importance that SNPs may hold for identifying pure breeds and crossbreeds.

Apparently there are also SNP chips available for other animals as highlighted by this particular paper

  • $\begingroup$ Is this definition applicable to all species (esp regarding SNP. Can you add some info with references on that) ? $\endgroup$
    Commented Jun 16, 2015 at 15:03
  • $\begingroup$ I hope the new edits answer your question $\endgroup$ Commented Jun 16, 2015 at 15:32
  • $\begingroup$ Yes, these terms are well established terms for describing mutations in genetic data. SNV is the more general term for SNP (without restriction of > 1% in popn). You will also hear the terms indel (insertion + deletion) and mnp (multi nucleotide polymorphisms). It should be noted that SNP is often used synonymously with SNV. All these things (SV, SNP, SNV, indel, MNP) are types of genetic mutations. $\endgroup$
    – yingw
    Commented Jun 16, 2015 at 18:28
  • $\begingroup$ Nice. Just a minor comment, you don't need to do an association study to establish that an allele frequency is > 1%. Just genotyping. $\endgroup$
    – Roland
    Commented Jun 16, 2015 at 19:36

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