Per base sequence Quality in Fast QC report

Question

[Fizzah]

Hello

I am working with RNA seq data and generated FastQC quality report. In the report while checking section "per base sequence quality" I noticed that box plat for bases (showing upper and lower quartile) present towards the end of the chart but not from the start. Mean square line and median value is present through out the chart but lower and upper quartile is not consistent.

Kindly suggest what could be the possible reason.

Fast QC per sequence base quality report

Answer 1

[Papyrus]

Congratulations, your data seem to be of very good quality. It is normal for quality to drop towards the 3' end of the reads due to various phenomena that start to appear as the cycles of sequencing go on (signal decay, phasing... you can read about them here). In your case the quality of your reads is good even though they are fairly long (150 bp).