Figure 1

Acceptable and unacceptable substitutions in a pairwise alignment and a candidate SNP from a real data set. (A) The line shows an alignment of query and anchor sequences with thick parts indicating highly similar regions. The large rectangular box gives a detailed view of the small box. On the left is an unacceptable substitution that is flanked by a block of low-quality bases, and on the right is an acceptable substitution that is flanked by a perfect block on each side. The quality value of each query base in the large box is shown next to the base. (B) Shown is a candidate SNP with allele frequencies from PolyFreq on a real data set (Hs. 119589) in Table 1.