Per Base Sequence Content FastQC

Question

[Ariadna]

Dear colleagues,

A questions popped up while examining the RNA-seq material.

When examining Per Base Sequence Content of FastQC the Babraham institute describes the following thresholds:

Warning This module issues a warning if the difference between A and T, or G and C is greater than 10% in any position. Failure This module will fail if the difference between A and T, or G and C is greater than 20% in any position.

https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/4%20Per%20Base%20Sequence%20Content.html

Could someone explain why the differences are calculated only between A and T as well as G and C?

Answer 1

[shelkmike]

The difference between (A or T) and (G or C) may reflect the GC composition of the genome. Thus, it is not indicative of some sequencing problem. For example, the GC content of the nuclear genome of Plasmodium falciparum is just 19%; thus, a large difference between the number of [AT] and [GC] is normal for it.