Figure 6: Analysis of SNP calling discrepancies between processing Pipelines A and B. The graphic shows mPileUP output, which is described in the text. Discrepancies can be attributed to an algorithmic limitation (Pipeline A) and stringency criterion (Pipeline B). These data suggest use of the most conservative criteria for SNP calling should be used for comparisons of two bacterial samples for forensic applications. Pipeline B can be improved to further reduce any spurious SNP calls by requiring all base calls exceed a specific quality score.