Analysis Output | Summary Analysis Report | Amplicon Summary

Amplicon Summary

Table 9 Read Level Statistics Table
Statistic	Definition
Total Aligned Reads (R1/R2)	The total number of reads passing filter present in the data set that aligned to the reference genome. Numbers are calculated per read.
Percent Aligned Reads (R1/R2)	The percentage of reads passing filter that aligned to the reference genome.
Overall Aligned Reads	The percentage of reads passing filter that aligned to the reference genome across both reads (R1 and R2). The value is the average of the individual Percent Aligned Reads values.

Table 10 Base Level Statistics Table
Statistic	Definition
Total Aligned Bases (R1/R2)	The total number of bases present in the data set that aligned to the reference genome. Numbers are calculated per read.
Overall Total Aligned Bases	The total number of bases present in the data set that aligned to the reference genome across both reads (R1 and R2). The value is the average of the individual Total Aligned Bases values.
Percent Aligned Bases (R1/R2)	The percentage of bases that aligned to the reference genome. Numbers are calculated per read.
Overall Percent Aligned Bases	The percentage of bases that aligned to the reference genome across both reads (R1 and R2). The value is the average of the individual Percent Aligned Bases values.
Percent Q30 (R1/R2)	The percentage of bases with a quality score of 30 or higher.
Mismatch Rate (R1/R2)	The average percentage of mismatches to the reference genome across both reads 1 and 2 over all cycles.