Two peaks on FastQC plot "Per sequence GC content"

[simonandrews]

The “Per base sequence content” and “Per base GC content” graphs should not show contamination of the adapters?

They might show some effects. If you have adapter dimers then you'll see the adapter sequence superimposed on the sequence content graphs. If your adapters have markedly different GC content than your library in general then you might also see an overall effect on the GC level.

In the latest fastqc release there is a graph specifically to measure adapter content which will show exactly what proportion of the library is composed of read-through adapter which will illustrate this much better than trying to use sequence content plots.

[MichalGordon]

The “Per base sequence content” and “Per base GC content” graphs should not show contamination of the adapters?

[simonandrews]

If the secondary peak is very sharp it's probably a specific contaminant - often something which is found by the overrepresented sequences module.

If the peak is fairly sharp and not too far from your main distribution it could be long read through into adapters as suggested above.

If the secondary peak is quite broad then it might be that you have contamination with a different species. You could use something like fastq_screen to check for other species you work with regularly, but this won't pick up other odd sources of contamination.

[Wallysb01]

Its probably the adapters. Do some trimming and it will go away.

[mastal]

It suggests that maybe you have some kind of contamination.

What %GC content are you expecting for the species you are sequencing?

I would do adapter trimming/quality trimming and rerun FastQC afterwards to see whether that gets rid of the problem or not.

[Tommyliu]

Hi,
I just got illumina DNA genome re-sequencing data. All the items in FastQC reports passed but "Per sequence GC content". There are two peaks on the plot of "Per sequence GC content". The major peak centers around 40% GC content, while the minor peak centers around 70% GC content.

I would appreciate it if you can explain to me how this happened and what I should do to correct it or discard the minor peak.

Thanks in advance!