Chart the distribution of quality scores. This tool is used for determining the overall 'quality' for a library in a given run. To that effect, it outputs a chart and tables indicating the range of quality scores and the total numbers of bases corresponding to those scores. Options include plotting the distribution of all of the reads, only the aligned reads, or reads that have passed the Illumina Chastity filter thresholds as described here. Note on base quality score options If the quality score of read bases has been modified in a previous data processing step such as GATK Base Recalibration and an OQ tag is available, this tool can be set to plot the OQ value as well as the primary quality value for the evaluation. Note: Metrics labeled as percentages are actually expressed as fractions!
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