I am confused about bisulfite converted library GC content.

Fastqc per base sequence content looks like this:

<img alt="< image not found >" src="http://s28.postimg.org/x9rutbksd/Selection_001.png" style="height:400px; width:600px" />

(%G has decreased and %A has increased, compared to reference genome).

1. **Shouldn't %C have decreased instead of %G**?

 Bismark reports that >90% C's in CHG and CHH were methylated, however people from the wet lab say that in this organism only CpG methylation is possible.

2. **Seeing such result (methylation in CHH and CHG) can we speculate that something went bad with bisulfite conversion**?

3. **Bismark/BS Seeker2 maps only those reads that have non-converted Cs (this is way we get high CH methylation percentage). What can be the reason that reads with converted Cs don't map**?
<p>That&#39;s really really strange. In all of my datasets the C percentage falls toward 0, causing T to jump to near 50%. Is this some sort of targeted BS-seq dataset? Did you run other samples at the same time and did they produce similar results?</p>

<p>In general, the C and T percentages should be pushed away from 25% by the bisulfite conversion and G and A percentages should still be around 25%. Not seeing that (and also seeing &gt;90% CHH methylation when that&#39;s not expected) suggests pretty strongly to me that something either went very wrong during bisulfite conversion or the reads were treated in a very strange way prior to running fastQC. If you can confirm that no one monkeyed with the reads then I would suggest being very hesitant in trusting this dataset.</p>
