Single base changes between homologous DNA fragments

plus

Small insertions and deletions (indels)

 One method to detect SNPs is to "resequence" the same DNA fragment from a number of individuals. One method of doing this is to compare the DNA sequence of the same region of the genome of a set of diverse individuals or genotypes. We analyze and compare such sequence data using software that determines the quality of  DNA sequence data followed by alignment of the sequences using additional software available through the  Univ. of Washington SNPs are then detected using  PolyBayes SNP discovery software from Washington Univ. in St. Louis, MO. Typical output from PolyBayes is shown below. SNPs are detected at bases 154 (C vs. T vs. A) and 178 (G versus A).