Hi everyone. I would like to ask some doubts about the representation of data of FastQC. I have two cleaned files 1.fq and 2.fq of Illumina. When I make a analysis with FastQC. I saw that first file does not have any contigs with Phred score lower of 20. In contrast the second file shows a lot of contigs with lower Phred score of 20. However, when I merged both files into one. This unique file does not show a Phred score low of 20. I attached the images. Somebody can me explain the why of this? is it trustful?
File All merged