I am having trouble interpreting some of my multiqc plots for my quality assessment of my fastq files (E. coli samples). I have the following chart which shows good results for the per sequence quality scores plot (all samples pass). See figure below.
However, when I look at the sequence quality histograms showing the mean quality scores for each bp, I have the majority of my samples "failing". See figure below.
Can anyone help explain what is going on here?