# Per Base Sequence Content

## Summary

Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

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 lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

If you see strong biases which change in different bases then this usually indicates 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 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.