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Some guy argued with me against evolution theory, and he claimed that human and mice share 98% just like human and chimpanzee.
I've tried to search online for a simple and accurate answer, but I couldn't yet.
In simple words, how much is the human genome (DNA) similar to the mouse genome?

Please use numbers as much as you can and provide references.

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This question cannot be answered as simply as you put it, but it's not too much to elaborate on.

The order of the base pairs will be drastically different, but the same proteins and amino acids will be coded for in genes, just at different points along the DNA. For example, you may find the same sequence to code for a protein in a mouse as in a human, but they will not be found in the same place along the DNA code (although they will still be read and eventually produce the same protein).

http://www.nature.com/nature/journal/v420/n6915/full/nature01262.html Additionally, this article shows that, if we take your question literally, "at the nucleotide level, approximately 40% of the human genome can be aligned to the mouse genome", that is, if human and mouse DNA was lined up side-by-side, and a percentage of identical match-ups was calculated.

However, taking a 'looser' approach, it is worth noting that about 5 percent of both of genomes consist of protein-coding genes (https://www.genome.gov/10001345), and the remaining 90%+ is non-coding. If we only count the protein-coding genes, the average similarity of genes between humans and mice in only protein-coding genes is 85%. The link above says that some are 99%, and some are 60% - there is a clear similarity here between humans and mice, albeit not 100% identical.

If you wish to know the explanation, simply it is because mice and humans both have a common ancestor (the last link also explains this) about 80 million years ago. Due to these similarities, and the striking similarities, scientists simulate genetic changes in mice that can occur to humans, and have used computers to analyse the similarities in mouse genome.

I hope this is understandable, if you need any clarification on terms, please ask :)

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    $\begingroup$ But what objective or rational reason does one have to only count the protein-coding genes? The other genes, as I understand it, are responsible for gene expression--in essence, the "program" running on top of the protein "building blocks". By that reasoning, Windows 3.11 is 90% the same as Windows 8, because they use almost the same underlying set of instructional building blocks in the processor, yes? Gene expression is an absolutely fundamental part of what makes up an organism, and it's absurd to just throw away some set of genes without a good reason to–I'm eager to hear such a reason! $\endgroup$
    – ErikE
    Mar 19, 2016 at 20:20
  • $\begingroup$ Fair point, it's just that OP's said that he wanted to know "in simple words". I did add about how 40%~ similarity can be aligned, but considering when you align only protein-coding parts of the genome, the percentage shoots up to an average of 85%.Considering these are found within all animals of nature, just like how Windows is all built upon the same, original code, then it can be seen as subjectively more important to focus on those ones, rather than including "junk DNA". I'm sorry for not fulfilling everything in my answer, but OP did want it to be 'simple'. I am only a student, after all $\endgroup$
    – Butallati
    Mar 19, 2016 at 20:31
  • $\begingroup$ The idea that "junk" DNA is actually junk is greatly disputed. Also, your answer lacks any references. Without that, it's just a random opinion. $\endgroup$
    – ErikE
    Mar 19, 2016 at 20:52
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    $\begingroup$ Well it was my first answer of this website, so I was limited to two links. I only use the term 'junk' DNA since it is widely used, and is only 'junk' from the perspective of "non-protein coding" and "protein-coding" DNA. I absolutely agree that 'junk' DNA is not 'junk' by definition, but in accordance to OP's question, I thought it was worth referring to it as such to further understanding of the difference in percentages being so drastic as a result of whether they code for proteins or not. I'm sorry if the answer was inadequate to you, but please add your own if you feel you can do better. $\endgroup$
    – Butallati
    Mar 19, 2016 at 20:55
  • $\begingroup$ I don't have time to post an answer, but I have already balanced comment. $\endgroup$
    – ErikE
    Mar 19, 2016 at 21:00

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