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A SNP is when variability exists at a specific nucleotide location. A haplotype refers to the set of SNP alleles across a specific chromosomal region.

Single nucleotide polymorphisms (SNP) and haplotypes are used to relate DNA sequence differences to various phenotypes for mapping purposes, and to compare genetic relationships across families, and across species.

Below is the DNA sequence of a chromosomal segment of four individuals.

Individual DNA Sequence
1 ACTGACGAT……CGATAGCTA……GCGAGCTAG……CGATGTACTAG…..TTCAACGCGA
2 ACTGACGAT……CGATAACTA……GCGAGCTAG……CGATGTGCTAG…..TTCAACGTGA
3 ACTGATGAT……CGATAGCTA……GCGAGCTAG……CGATGTACTAG…..TTCAACGCGA
4 ACTGACGAT……CGATAGCTA……GCGAGCTAG……CGATGTGCTAG…..TTCAACGTGA
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