SNP vs. genotype definition

Recently, a friend asked for the difference between a SNP and genotype. After some babbling on my part, here is a summary.

SNP Positions of the genome that have a mutation
Genotype Alleles of at a given SNP

Typically we only call a mutation if is seen above a certain frequency (typically > 0.1%) across the population. Otherwise, these are known as private mutations.

Confused? Here is a simple analogy. A metabolic disease called diabetes exists but not everyone has diabetes. A medical diagnosis is required to determine the diabetic status of an individual.

Similarly, genotyping is the process of determining the SNP alleles. Here is example for three individuals:

Position Individual 1 Individual 2 Individual 3
1 A/A A/A

A/A

2

C/C

C/C

C/C

3

G/G

G/G

G/G

4

C/T

T/T

C/C

Nucleotides in positions 1 – 3 are identical across all individuals and therefore not considered a SNP in this sample. The nucleotide in position 4 is a SNP. The genotype for individual 001 at position 4 is C/T.

More generally, in the human genome, there are approximately 40 million SNPs which represent about 1.25% of the genome. In other words, the genomes of two unrelated individuals are identical at around 99% of the nucleotides.


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