# Perplexing by the way of estimating the shared or different genes between humans and chimps

We share 98.5% genes with chimps (it means we have 98.5% same DNA sequeces ),so there is about one percent difference .It means we can approximately differ from them by one base pair every hundred base pairs on average.

The following is my question.

A human receive 3 billion base pairs from each of parents ,and has six billions in total .Do the math by using one hundred to divide six billions and then it equals sixty millions.

Due to that, The person have ,on average ,sixty-million-nucleotide differences with a chimp.

However,the professor of the online courses I attended said it's thirty-million-letter differences.

Dose that mean it's counted on haploid?Why?

Also ,I'm not sure that about one percent difference is calculated on one base pair or one nucleotide every thousand base pairs or nucleotides .Because he mentioned the both.

This is the course ,my questions occur at 1:58

In another course , similar questions occur at 3:11

• I do not really understand your question. What do you mean by 98.5% gene sharing? Do 98.5% of human genes have a homologous gene in chimpanzees? Or is there 98.5% sequence identity in human and chimpanzee genes (and if so, is the difference due to fixed differences?)? Is the one bp per 100 bp difference only related to gene regions? And I can by no means guess what you mean with your last sentence. Jun 15 '16 at 9:00
• Each of us ,on average ,varies from a chimp by about one nucleotide at particular loci every hundred basis. Jun 15 '16 at 9:39
• I'm the first-learner in this realm ,so I can't clearly explain that so much,but as what I learned,the conception could be a bit similar with SNP(Single Nucleotide Polymorphisms),but SNP only apply on a paticular species. Jun 15 '16 at 9:43
• I tried to explain the concepts in my answer. Note that there in fact are SNP between species, so called shared alleles or trans-species polymorphisms. Jun 15 '16 at 9:49
• You might want to read through the answers here: Do apes and humans share 99% of DNA or 99% of genes? What is the difference? Jun 15 '16 at 12:38

Even though I am not sure I understand your question completely, I want to try to explain to you the genetic difference between humans and chimpanzees. I will work through your questions:

We share 98.5% genes with chimps ,so there is about one percent difference .It means we can approximately differ from them by one base pair every hundred base pairs on average.

It is correct that humans and chimpanzees differ approximately every 100 nucleotides in their DNA sequence. This is does not mean that 98.5% of the genes are shared. It means that humans have about 98.5% (more precisely about 98.8%, The Chimpanzee Sequencing and Analysis Consortium, 2005) sequence identity with chimpanzees, disregarding indels. The main part of this difference (about 85% of the 30 - 35 Mio. different nucleotides) comes from fixed differences: a fixed difference is a position in the haploid genome in which every human has, say, a G and every chimpanzee has a T. Accordingly, the site is different between the two species for every individual of the respective species. The smaller part (about 15%) comes from sites that are either variable (SNP) in humans or variable in chimpanzees, or in both (there is even a small number of very old variants, i.e. shared alleles between humans and chimpanzees, e.g. see Azevedo et al., 2015). Note that the estimates get better the more individuals of the respective species are sequenced and compared.

A human receive 3 billion base pairs from each of parents ,and has six billions in total .Do the math by using one hundred to divide six billions and then it equals sixty millions.

Due to that, The person have ,on average ,sixty-million-nucleotide differences with a chimp.

However,the professor of the online courses I attended said it's thirty-million-letter differences.

Dose that mean it's counted on haploid?Why?

Yes, it is counted on the haploid genome. I would not make any sense to count it on the diploid genome. When looking at my last paragraph you might see why: Remember, we are looking at (i) fixed differences (both copies of a diploid human genome differ from both copies of a diploid chimpanzee genome) or (ii) at variable sites. Assume you find one site in one haploid genome that fulfills either (i) or (ii). If you then look at the same site in the other copy of the genome you already know that the position is either (i) or (ii). This means that it has already been counted as a difference. If you counted it again, in the worst case, over the complete genome, you would count everything twice. In general, you would strongly overestimate the absolute difference.

Also ,I'm not sure that about one percent difference is calculated on one base pair or one nucleotide every thousand base pairs or nucleotides .Because he mentioned the both.

I do not understand this. I had a brief look at the video and heard him talking of one nucleotide per thousand. He compares the sequence difference between human-chimpanzee (98.8% overlap, approx. 1 per 100, about 1.2% fixed differences and SNPS) and human-human (99.9% overlap, approx. 1 per 1000, 0.1% SNP), pairs. Note that in the last case we cannot look at fixed differences as there are no fixed differences between human populations. The 0.1% difference are the percentage of SNP in the human genome.

• I'm sincerely appreciated for your detailed answers,after reading the first and second parts ,the third question has been solved . But I am not sure that I really make sense of the difference between sequence identity and genes,can you explain that for me? Jun 15 '16 at 11:37
• According to your second answer ,I have question about "the same site".Does that mean the certain alleles at homologous chromosomes which control a certain gene have the completely same DNA sequences? – Jun 15 '16 at 12:26
• What you seem to be mixing is having (i) homologous genes and (ii) identical sequence. (i) does not imply (ii). You can easily have the same gene but non-identical sequence, i.e. different variants of that gene. Within species we call that alleles, between species homology. Additionally, only a few percent or so of DNA codes for gene products (e.g. protein, miRNA, tRNA, rRNA, ...). So the vast majority of sequence differences between humans and chimpanzees lies outside of genes. Jun 15 '16 at 12:30
• sorry , I have thought for a while ,my third question still exist ,the sentence might look weird , what I want to ask is that "why do we sometimes say one base pair of every hundred base pairs instead of saying one nucleotide of every hundred nucleotides? Jun 15 '16 at 12:33
• To response the comment of AlexDeLarge ,if the sequence of"the same" site is not identical ",how can we consider the one side by the other ? Jun 15 '16 at 12:53