How much confidence do we have that the literal base pair encoding of DNA encodes the entirety (or even the majority) of the information needed to construct an

How much confidence do we have that the literal base pair encoding of DNA encodes the entirety (or even the majority) of the information needed to construct an individual, anyway? As the author mentions, you have things like histone dynamics as well as other potentially relevant variations in the many organelles that make up the cell. Eggs in particular are chock full of proteins that are directly passed down from the parent that could have important implications for gene expression frequency. These effects would either have to be self-propagating in some way via further protein synthesis or their effect would be primarily early-developmental, but they could still have large effects on grown individual. As evidence for this we know there are all sorts of heritable epigenetic effects. It would also partially explain the partial failure of GWAS to pinpoint all an individual's features as was previously hoped before the human genome project completed. It seems like there's a process called Somatic Cell Nuclear Transfer that might make possible to evaluate aspects of this, but it doesn't appear to have been performed sufficiently many times with different individuals to draw major conclusions.