Here's the deal: You have said that the genetic differences between these species look like mutations because they are the result of mutations. You then have to explain how humans and chimps have only acquired enough mutations to differ by 1%, as did baboons and macaques, while humans and baboons acquired enough mutations to differ by 5%. And you have to do it with one explanation. You not allowed to flip-flop between explanations, depending on which comparison you happen to be looking at.
You then have to explain why every child born has around 60 new mutations compared with their parents and yet this accumulated mutation has only made humans less than your claimed 99% for humans and chimps???
Are chimps born with these same numbers of mutations? We must assume so I guess since we are only as you claim 1% different, so the random mutations must be randomly identical across generations.......
Or (supposing evolution is true - and I am going against truth here) most of the mutations are neutral and so have no overall affect, while the mutations in baboons had more effect.... Just because a mutation is neutral in one animal, does not mean a mutation will be neutral in another.
And isn't the 1% a little optimistic???
"The first comprehensive comparison of the genetic blueprints of humans and chimpanzees shows our closest living relatives share perfect identity with 96 percent of our DNA sequence, an international research consortium reported today."
And as stated, that is after you delete the non-coding regions. The coding regions share only 29% similarity..... "At the protein level, 29 percent of genes code for the same amino sequences in chimps and humans." So in the region which actually codes for proteins, what makes each animal distinct, we in reality are only 29% similar.
And Y chromosome? Let's see, how did the authors put it?
Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content
"Indeed, at 6 million years of separation, the difference in MSY gene content in chimpanzee and human is more comparable to the difference in autosomal gene content in chicken and human, at 310 million years of separation."
And what about differences between human men and women? "If we look at base pairs, the difference between men and women would be 59 million divided by 3.2 billion or about 1.8%. This translates to men and women being 98.2% the same. Men and women are actually a bit more similar as the Y chromosome has about 5% of its DNA sequences in common with the X chromosome. This would change the number to 98.4% the same. If the 98.7% number for chimp-human similarity is right, then by this measure, men and women are less alike than are female chimps and women."
Now, all of you are certainly allowed to believe that humans and chimps differ less than male and female humans if you like...... Or you can simply accept the truth and that they cut and snip, pick and choose what to include when they compare human and chimp genomes......
Believe your mother is further related from you than a chimp is if you like. Just don't expect me to fall for that number playing game.......