PhiX Statistics: How are they generated, and where are they located?

A: The insert reads generated in each G4 run automatically align to the PhiX reference genome starting at cycle 40. A number of metrics, including accuracy and alignment, are generated in the 'phix_stats' customer output folder. Because PhiX alignment starts at cycle 40, only insert reads greater than or equal to 40 base pairs or longer will generate PhiX statistics. Metrics generated by MultiQC for PhiX include: % error, % reads aligned to PhiX, and mean base quality by cycle.

The phix_stats output folder for each lane should appear as shown below: