Alignment Summary

Group Sample View
Statistic	Definition
Group Index	The group number.
Sample Group	The sample group name, as specified in the input form.
# Replicates	The number of samples assigned to this sample group.
Total Aligned Reads (R1/R2)	The total count of PF reads aligning for the group (Read 1/Read 2).
Percent Aligned Reads (R1/R2)	The percentage of PF reads aligning for the group (Read 1/Read 2).
Overall Percent Aligned Reads	The percentage of PF reads aligning for the group across both reads 1 and 2.

Individual Sample View
Statistic	Definition
Sample Index	The sample number.
Sample Id	The sample identifier.
Sample Group	The sample group name, as specified in the input form.
Total Aligned Reads (R1/R2)	The total count of PF reads aligning for the group (Read 1/Read 2).
Percent Aligned Reads (R1/R2)	The percentage of PF reads aligning for the group (Read 1/Read 2).
Overall Percent Aligned Reads	The percentage of PF reads aligning for the group across both reads 1 and 2.