I am following the standard RNA-seq analysis workflow to make sense of some experimental data, using the DESeq2 package. Here is the MA-plot I have:

I am not concerned about the low log-fold change, but this looks a bit weird, since I would have expected the major part of the genes to be found in the low counts range.

I followed the standard pipeline for this analysis. Is there any obvious reason why I am having this kind of result?

Thank you.

Sorry, what is not expected here? DESeq2 moderates the LFC from genes with little to no information for accurately estimating the LFC. Please see the DESeq2 paper or the vignette section on LFC shrinkage.