Hi everyone. I would like to ask some doubts about the representation of data of FastQC. I have two cleaned files 1.fq and 2.fq of Illumina. When I make a analysis with FastQC. I saw that first file does not have any contigs with Phred score lower of 20. In contrast the second file shows a lot of contigs with lower Phred score of 20. However, when I merged both files into one. This unique file does not show a Phred score low of 20. I attached the images. Somebody can me explain the why of this? is it trustful?

Regards.

**File 1**

<img alt="file 1 image" src="http://www.freeuploadimages.org/images/bfo0u37lvdl4877hib.jpg" style="height:291px; width:400px" />

**File 2**

<img alt="file 2 image" src="http://www.freeuploadimages.org/images/wtl2esrkihw4go8seg.jpg" style="height:291px; width:400px" />

**File All merged**

[<img alt="file all merged image" src="http://www.freeuploadimages.org/images/zzk2gchqlmqc463mfgza.jpg" style="height:291px; width:400px" />][1]

 [1]: http://www.freeuploadimages.org/images/zzk2gchqlmqc463mfgza.jpg
<p>simply, in these boxplots the lower whisker represents the <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/2%20Per%20Base%20Sequence%20Quality.html">10th percentile</a>, which means that 10% of the points are lower than that and are not displayed. when you merge two datasets the 10% will be higher, exactly as you see in your data. there are still quite a considerable number of sequences which have bases with a lower quality than 20 at the end.</p>
