I have a question regarding "Per Base Sequence Content" plot for "fastqc":
In the fastqc documentation, it is written: "In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other."
But I don't understand why different bases in a read should follow the same pattern of allele frequency ("A/T/C/G"). I mean they are different positions in the genome and it is normal that each position has different allele.
I would appreciate it if someone could help me, please.