...

A Phred score is a measure of base call accuracy with a higher score indicating greater accuracy. By convention, a score above 20 is considered adequate. As we can see, the standard error bars in the graph show that some reads have quality scores below 20 for some of their base pair calls near the 3' end.

Based on the results of Pre-alignment QA/QC, while most of the reads are high quality, we will need to perform read trimming and filtering. 

...