Fig. 2

Comparing sequence error types across different alignment filtering. The different types of sequencing errors, obtained from the MOTHUR error report file, were plotted in Graph Pad Prism 6. The x-axis shows the base pair position in the full-length bacterial 16S rRNA gene and the y-axis shows the sequence error rate on a log 2 scale. The abundance of substitution errors, insertion errors, and deletion errors using standard quality filtering a, with low stringency post alignment filtering b, and high stringency post alignment filtering c are shown. The standard quality filtering parameters were: maximum ambiguous sequences = 0, maximum number of homo-polymers 6, sequence quality average of 35 over a sequence quality window of 50 bp. The extra post alignment screening parameters were: post alignment screening using minimum sequence similarity and minimum alignment score of 80% b and post alignment screening using minimum sequence similarity and minimum alignment score of 90% c