Per base sequence quality in FastQC

Question

[khatami.s.83]

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؟

[Pierre Lindenbaum]

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

Answer 1

[GenoMax]

This is a normal observation. Q-scores show a relative drop on R2 (specially towards the end of reads).

Possible reasons:

• Reagents sit at 6-7C for duration of run and may show some degradation
• Clusters start getting fatter over time and software starts having difficulty telling clusters apart