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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?

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    $\begingroup$ Welcome to BiologySE! Thanks for your question...can you give a little more detail about your question, specifically the rationale behind it so other individuals can follow along and better understand what you're asking? You may want to check out the help center as well, for some great tips on how to ask a great question... biology.stackexchange.com/help $\endgroup$ Jul 6, 2016 at 19:34
  • $\begingroup$ Are you talking about when a single read in your deep-sequencing experiment has differences in base composition compared to other reads mapping to the same locus? Are you suspecting a duplication event where the original copy is CpGpA and the copy you are referring to is CpA? $\endgroup$
    – dblyons
    Jan 8, 2017 at 23:04

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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.

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