A word about AG3. I'm sure you and others have noticed that it is called AG3_damage. Normally, when non-UDG treated aDNA is processed, we identify the number of bases from the 3' and 5' ends where we see evidence of post-mortem deamination in the form of C-->T and G-->A substitutions, and we trim a certain number of bases from the ends of reads to discard deaminated bases.

With AG3, and with a couple of genomes I processed, the OPPOSITE was done, in other words discard the non-damaged bases, and retain the damaged bases.. It may sound crazy, but this is really the only option we have when we see that modern human DNA contamination is substantial, and here is why.

Since we can't differentiate modern human DNA from aDNA, pretty much the only option we have left is to retain the damaged bases because we know those are ancient, and discard the non-damaged bases. This comes at a very high price though, because we can end up discarding 90% of the sequences. Not only that but we introduce some biases because we are only retaining T and A bases. This is what was done to AG3, hence the word damage. This is also what I have done with EHG_I0061_PMDS. In other words my definition of PMDS is equivalent to Fu et al's damage.