Fig. 6

Background PCR errors are found in distinct clusters throughout the sequenced RAD tags. ORP libraries sequenced to 10,000× OPE depth contained 109 false positive mutations when SNPs were called with Lofreq using default parameters without a minimum allele frequency cutoff above the level of background error. These mutations appeared in distinct clusters throughout the sequenced RAD tags. The SNPs are plotted across the 14 Kb of sequenced RAD tags. Each blue bar represents a cluster of 2–3 errors. Of the 140 RAD tags sequenced, only 45 contained PCR errors, and each of those contained an average of 2.6 PCR errors. The maximum allele frequency of the sequencing errors was 0.002 at this read depth