The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, often because they are poorly imaged (on the edge of the field of view etc), however these should represent only a small percentage of the total sequences.
If a significant proportion of the sequences in a run have overall low quality then this could indicate some kind of systematic problem - possibly with just part of the run (for example one end of a flowcell).
Results from this module will not be displayed if your input is a BAM/SAM file in which quality scores have not been recorded.
A warning is raised if the most frequently observed mean quality is below 27 - this equates to a 0.2% error rate.
An error is raised if the most frequently observed mean quality is below 20 - this equates to a 1% error rate.
This module is generally fairly robust and errors here usually indicate a general loss of quality within a run. For long runs this may be alleviated through quality trimming. If a bi-modal, or complex distribution is seen then the results should be evaluated in concert with the per-tile qualities (if available) since this might indicate the reason for the loss in quality of a subset of sequences.