Additional file 6.

Figure S3 - relationship between posterior probability and read degeneracy. Box and whisker plots showing the distribution of posterior probabilities Q (stringency) for all SNPs identified in each of five replicates for two different simulations (ribosomal protein loci (RPL) and 2 × RPL + 10%), grouped by per-locus degeneracy. For example, the 0 ≤ < d < 0.1 group contains loci with at least a 1/10 ratio of alignments at another locus versus alignments overlapping the locus of interest. Box plots represent the entire distribution of Q values for each degeneracy bin, where the red line indicates median and the box indicates the 25th and 75th percentiles. SNPs were obtained using the 25-fold coverage simulations allowing k ≤ 1 mismatch.

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