text: user7444: 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.
  
  user3389: The positions you see in the x-axis of this plot are positions on your reads, not on the reference genome. Since each read comes from a random position on the genome, the frequency of A/T/C/G on each base position should reflect the base composition of the entire genome. Therefore, the percentage of each base should be approximately constant across the read.
  Hope that helps!
  
original_text: 7444: <p>I have a question regarding "Per Base Sequence Content" plot for "fastqc":</p>
  
  <p>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."</p>
  
  <p>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.</p>
  
  <p>I would appreciate it if someone could help me, please.</p>
   3389: <p>The positions you see in the x-axis of this plot are positions on your <em>reads</em>, not on the reference genome. Since each read comes from a random position on the genome, the frequency of A/T/C/G on each base position should reflect the base composition of the entire genome. Therefore, the percentage of each base should be approximately constant across the read.</p>
  
  <p>Hope that helps!</p>
  