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. 1999 Sep;9(9):868–877. doi: 10.1101/gr.9.9.868

Figure 5.

Figure 5

An example for calculation of scores of a match, a mismatch, a deletion, and an insertion. The quality values of bases are shown next to the bases. In each case, the average quality value of the column and the score are presented, where positive integer m is the match score factor, negative integer n is the mismatch score factor, and positive integer g is the gap extension penalty factor.