<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>

CC BY-SA 4.0
2020-03-23T14:04:19.337Z
2020-03-23T14:04:19.337Z
PedroSebe
<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>

CC BY-SA 4.0
2020-03-23T14:53:48.130Z
Heads up: This question [has been cross-posted on biostars](https://www.biostars.org/p/428421/)
Ram RS
<ngs><genome><fastqc>
Per Base Sequence Content in fastqc
# 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/)  

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## 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!


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