I was trying to use PhiX spike-in to estimate bisulfite conversion rate. When I processed my reads with Bismark aligning to the mouse genome (this is a mouse sample), the results seem reasonable:
C methylated in CpG context: 52.6% C methylated in CHG context: 4.5% C methylated in CHH context: 4.5%
Then I align the same sample against the PhiX genome. The alignment rate is less than 1% as expected, but the methylation rates are odd:
C methylated in CpG context: 98.0% C methylated in CHG context: 97.9% C methylated in CHH context: 97.8%
Why is it the opposite of what it should be? PhiX should be unmethylated. The output is generated by Bismark, so it's not possible that I used a wrong formula and the bisulfite conversion worked at least partially as demonstrated by the sample of interest. What am I missing here?