Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-03-23T14:04:19.337Z
Answers.LastActivityDate: 2020-03-23T14:04:19.337Z
Answers.UserDisplayName: PedroSebe
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-23T14:53:48.130Z
Comments.Text: Heads up: This question [has been cross-posted on biostars](https://www.biostars.org/p/428421/)
Comments.UserDisplayName: Ram RS
Tags: <ngs><genome><fastqc>
Title: Per Base Sequence Content in fastqc
ThreadText: # Per Base Sequence Content in fastqc
  
  (Asked by: username_0 on 2020-03-23)
  
  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.
  
  **Tags:** ngs, genome, fastqc
  
  > **Comments:**
  > **username_1**: Heads up: This question [has been cross-posted on biostars](https://www.biostars.org/p/428421/)  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2020-03-23. Score: 2 | Accepted answer
  
  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!
  
  
  ---
  
  