I am currently analysing Illumina sequences for a metabarcoding project. The primers used in the process have NOT been removed from the raw data. But after exploring the data, I found that ~5% of my raw data has no primers.

What could explain this 5% ? Should I discard these primerless sequences?

PS: The data was prepared according to the following protocole : 16 Metagenomic Sequencing Library Preparation Part #15044223 Rev. B (copy paste on internet to find it)

Thank