Additional file 7.

Figure S4 - per-locus distributions of degeneracy. Cumulative distributions of per-locus degeneracy are shown for each of the six reference genomic DNA templates used in this study. Degeneracy is defined as the ratio of d, the number of alignments for a read that overlap loci other than the locus of interest, to the read depth at a locus of interest. (Alternatively, Alignments/Reads - 1.) For example, a ratio of 1 indicates that every read overlapping the locus of interest has two valid alignments in the reference genome. Loci are binned into 12 groups and the cumulative frequency of all loci is reported at each degeneracy group. Estimates are shown using the ALL read map with k = 1, 2, and 3 mismatches.

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Simola and Kim Genome Biology 2011 12:R55   doi:10.1186/gb-2011-12-6-r55