When evaluating methylation status at various CpG sites after sequencing, how much consideration should one give to random single base pair insertions and deletions. Suppose there is a CA dinucleotide; can we assume that the CA is native to the sequence or results from a G deletion especially when the latter is suspect once comparing to other sequences. Is there really a set standard sequence to compare it?
I agree with Vance, we need a little more detail to better answer your question. From what I can tell, you are asking whether a single nucleotide polymorphism (SNP) that results in the addition of a cytosine base to your sequence is of concern when examining the methylation signature of that sequence.
I would first determine whether the polymorphism is common in the population using NCBI. The more common the polymorphism, the less likely it is to have a serious effect. However, that is not to say that it doesn't have any effect.
I would then examine how much the methylation of that one site varies compared to samples without the additional cytosine base.
Finally I would determine the importance of the location of the SNP. Is it located in a CpG island? Or is it located on the shores, shelves or 'open sea'? (see work by Sandoval et al.)
Without knowing all the above it is hard to make a call on how important/unimportant the SNP is in your methylation analysis.