# Per Base GC Content

## Summary

Per Base GC Content plots out the GC content of each base position in a file.

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 line in this plot should run horizontally across the graph. The overall GC content should reflect the GC content of the underlying genome.

If you see a GC bias which changes in different bases then this could indicate an overrepresented sequence which is contaminating your library. A bias which is consistent across all bases either indicates that the original library was sequence biased, or that there was a systematic problem during the sequencing of the library.

## Warning

This module issues a warning it the GC content of any base strays more than 5% from the mean GC content.

## Failure

This module will fail if the GC content of any base strays more than 10% from the mean GC content.