Pre-alignment QC After Adapter Trimming

The QC results table below indicates adapter trimming resulted in some samples losing reads. This is because not all reads passed the QC criteria. Also, the average read length has been reduced as the adapters are removed from the reads. However, as indicated in the base quality and quality distribution plots, adapter trimming did not affect read quality.

As reads will have differing amounts of adapter contamination (ie. the number of adapter bases that appear), the trimming procedure will produce reads of varying lengths as indicated in the sample level read length distribution plot.