<p>There is a pretty good description <a href="https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/2%20Per%20Base%20Sequence%20Quality.html" rel="nofollow noreferrer">here</a>. The position in the reads means literally the position in the reads, so position 2 means the quality of all bases on position 2 in the fastq file (all reads). In the description link, you can find how the boxplots and blue and red lines are calculated (and what they mean). They are all based on the total quality values of all bases on a certain position, all bases means all bases of all the reads on a particular position. </p>

CC BY-SA 4.0
2018-09-18T11:57:18.197Z
2018-09-18T12:25:08.353Z
2018-09-18T12:25:08.353Z
benn
<p>I am trying to figure out how to interpret the "Per Base Sequence Quality"? What does Position in reads (bp) mean? Also in order to draw this box-plot graphics, more than one quality scores are needed so we can sort them and calculate the mean, median and quartiles. In this diagram, how these values were calculated for each position? </p>

CC BY-SA 4.0
2018-09-19T08:29:32.133Z
"in order to draw this box-plot graphics, ": what box plot graphics? "In this diagram": what diagram? Please [edit] your question and include an example of the data you are looking at. Ideally, also show us the command you used to generate it so we can reproduce it on our systems.
terdon
CC BY-SA 4.0
2023-06-25T11:45:43.873Z
In this Page [you](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/2%20Per%20Base%20Sequence%20Quality.html) can find good answer.
yahya jand
<ngs><sequence-analysis><fastq>
Fastqc- Per Base Sequence Quality
# Fastqc- Per Base Sequence Quality

(Asked by: username_0 on 2018-09-18)

I am trying to figure out how to interpret the "Per Base Sequence Quality"? What does Position in reads (bp) mean? Also in order to draw this box-plot graphics, more than one quality scores are needed so we can sort them and calculate the mean, median and quartiles. In this diagram, how these values were calculated for each position?

**Tags:** ngs, sequence-analysis, fastq
> **Comments:**
> **username_1**: "in order to draw this box-plot graphics, ": what box plot graphics? "In this diagram": what diagram? Please [edit] your question and include an example of the data you are looking at. Ideally, also show us the command you used to generate it so we can reproduce it on our systems.  
> **username_2**: In this Page [you](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/2%20Per%20Base%20Sequence%20Quality.html) can find good answer.  

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## 1 answers

### Answer by username_3 on 2018-09-18. Score: 2

There is a pretty good description [here](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/2%20Per%20Base%20Sequence%20Quality.html). The position in the reads means literally the position in the reads, so position 2 means the quality of all bases on position 2 in the fastq file (all reads). In the description link, you can find how the boxplots and blue and red lines are calculated (and what they mean). They are all based on the total quality values of all bases on a certain position, all bases means all bases of all the reads on a particular position.


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