The attached graphs are the result of WES (paired end reads) Quality assessment with FASTQC. Sequencing was performed by the Illumina hiseq 4000.
What is the reason for the difference in quality paired end reads؟
there is no "attached graphs "
please, comment or validate (green mark on the left) all your previous questions: question about mtDNA graph coverage ; interpretation if fastqc ; Meaning of Per sequence quality scores in FastQC
This is a normal observation. Q-scores show a relative drop on R2 (specially towards the end of reads).