To discuss the DNA sequence variation, the primary concept is genetic variation, which is the variation in set of alleles of any gene. The prime source of this genetic variation is mutation. Once the parent genetic information is mixed to produce offspring this give rise to a new set of combination in the genetic makeup and also in this segregation process there are chances to get the mutated traits from the parents to offspring. Generally the mutations are rare and often neutral but the chances of a mutation to pass through the offspring depend upon natural selection and genetic drift.

The easiest approach to identify genetic variation among individual of same species is the observation of phenotype. According to Mendel the genetic variation can be qualitative judged eg. the color of flower petal. Also the measurement of genetic variation can be accessed quantitatively say height of individual. The variation in phenotype as a consequence of DNA sequence variation results from the order of nucleotides in a DNA. Since in the translational process DNA codes for protein expression with the help of various cofactors, enzymes etc. the order of amino acids that will be coded by DNA sequence can vary because of variation in DNA sequence. Such difference in the protein sequence can result in variation of protein structure and function