Answers.Body: <p>The answer is no if the question is read at face value,</p>
  <ol>
  <li>I don't know the metric used (is this just SNPs?), nor which part of the genome is included in the calculation, just the exome?</li>
  <li>Moreover, if the genetic identity between parents is unknown, then the similarity of their offspring to either parent cannot be calculated.</li>
  <li>Your calculation excludes <em>de novo</em> mutations, particular at neutral sites and copy number variation, e.g. microsatellites, however its not clear whether the data is simply the exome.</li>
  <li>Homologous recombination is excluded, i.e. particularly occurring in the parental germ-line, there must be stochastic effects even in the first generation.</li>
  <li>Finally, mtDNA is maternally inherited.</li>
  </ol>
  
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Answers.Text: 1) 0.1% is the common rate of base substitution across the whole genome. 2) the number roughly varies between 0.07% and 1.2% across populations. 0.1% is considered a decent ballpark. 3) the de novo mutation rate is $10^5$ smaller and can be ignored, though CNVs etc may contribute a lot. 4) Recombinations don't matter. Exactly 50% of your autosome is inherited from one of your parent. 5) is correct, but sex chromosomes make bigger differences.
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Answers.Text: Thanks, you're saying the figure is singly SNPs at the chromosome level. *"Exactly 50% of your autosome is inherited from one of your parent"*: we're talking homologous recombination in the parental germ-line, gamete formation. Homologous recombination is a major player in eukaryotic genetic diversity, unless the diversity of the markers used (SNPs) is so low it's difficult to track via linkage disequilibrium, i.e. breaks in physical linkage in a single generation. It will still be occurring. I dunno about homologous recombination in early mitotic events in embryogenesis.
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Answers.Text: Recombinations just switch the haplotypes to transmit. This doesn't change the calculation when you compare diploid genotypes.
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Answers.Text: It's a (over?) simplification. LD across a physical chromosome is a core calculation in eukaryotes. Humans too?
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Answers.Text: You are overthinking. I suggest you write down the calculation on a paper. It is simple. Recombination or LD is irrelevant to this question.
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Answers.Text: comment to (1),  according to https://www.nature.com/scitable/popular-students-page/132/ , coding region and non-coding region are included in the calculation of the 1% DNA sequence difference.
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Answers.Text: comment to (3),  in humans, a mutation rate of about 10 to the power -8 mutations/bp/generation was inferred from projects where both parents and their children were sequenced at high coverage.  (  http://book.bionumbers.org/what-is-the-mutation-rate-during-genome-replication/ )
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Answers.Body: <p>The common wording is that the difference between two human <em>haplotypes</em> is 0.1%. This number only counts base substitutions, not insertions/deletions (indels) or structural variations (SVs). SVs together affects more bases than base substitutions. Also, the number is smaller is non-Africans (~0.07%) and higher in Africans (~0.12%). Anyway, let's denote this number by <span class="math-container">$\theta$</span>, also known as the scaled mutation rate.</p>
  <p>Because human is diploid, you need to count genotype differences when you compare two human individuals. Under the Wright-Fisher model, the rate of genotype difference on autosomes is</p>
  <p><span class="math-container">$$\theta\cdot\left(1+\frac{1}{2}\cdot\frac{1}{2}+\frac{1}{3}\right)=1.58\theta$$</span></p>
  <p>The rate between a child and his/her parent is, I think:</p>
  <p><span class="math-container">$$\theta\cdot\left[1\cdot\frac{1}{2}+\frac{1}{2}\cdot\left(\frac{1}{3}+\frac{2}{3}\cdot\frac{1}{2}\right)+\frac{1}{3}\cdot\frac{1}{2}\right]=\theta$$</span></p>
  <p>Note that I am sure the rate can be theoretically calculated but I am not confident in my calculation. Also, the rate of genotype difference on sex chromosomes or mitochondrial DNA is different.</p>
  
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Body: <p>As far as I know, we as humans share 99.9 similarity in our genomes. Further, we inherit 50% of the genome from our parents. So, it is correct to say that parent children have a 99.95% similarity in their genome?</p>
  
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Comments.Text: Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer.
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Comments.Text: Where is your source on the 99.9% number, and how do you know it's not 99.9134% or 99.8976% or 99.9999%? Also, what are you comparing - 99.9% shared with whom? A total genetic stranger?
Comments.UserDisplayName: Ram RS
Tags: <genome>
Title: Human genome similarities
ThreadText: # Human genome similarities
  
  (Asked by: username_0 on 2023-06-22)
  
  As far as I know, we as humans share 99.9 similarity in our genomes. Further, we inherit 50% of the genome from our parents. So, it is correct to say that parent children have a 99.95% similarity in their genome?
  
  **Tags:** genome
  
  > **Comments:**
  > **username_1**: Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer.  
  > **username_2**: Where is your source on the 99.9% number, and how do you know it's not 99.9134% or 99.8976% or 99.9999%? Also, what are you comparing - 99.9% shared with whom? A total genetic stranger?  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_3 on 2023-06-22. Score: 2
  
  The answer is no if the question is read at face value,
  
  1. I don't know the metric used (is this just SNPs?), nor which part of the genome is included in the calculation, just the exome?
  2. Moreover, if the genetic identity between parents is unknown, then the similarity of their offspring to either parent cannot be calculated.
  3. Your calculation excludes *de novo* mutations, particular at neutral sites and copy number variation, e.g. microsatellites, however its not clear whether the data is simply the exome.
  4. Homologous recombination is excluded, i.e. particularly occurring in the parental germ-line, there must be stochastic effects even in the first generation.
  5. Finally, mtDNA is maternally inherited.
  
  > **Comments:**
  > **username_4**: 1) 0.1% is the common rate of base substitution across the whole genome. 2) the number roughly varies between 0.07% and 1.2% across populations. 0.1% is considered a decent ballpark. 3) the de novo mutation rate is $10^5$ smaller and can be ignored, though CNVs etc may contribute a lot. 4) Recombinations don't matter. Exactly 50% of your autosome is inherited from one of your parent. 5) is correct, but sex chromosomes make bigger differences.  
  > **username_3**: Thanks, you're saying the figure is singly SNPs at the chromosome level. *"Exactly 50% of your autosome is inherited from one of your parent"*: we're talking homologous recombination in the parental germ-line, gamete formation. Homologous recombination is a major player in eukaryotic genetic diversity, unless the diversity of the markers used (SNPs) is so low it's difficult to track via linkage disequilibrium, i.e. breaks in physical linkage in a single generation. It will still be occurring. I dunno about homologous recombination in early mitotic events in embryogenesis.  
  > **username_4**: Recombinations just switch the haplotypes to transmit. This doesn't change the calculation when you compare diploid genotypes.  
  > **username_3**: It's a (over?) simplification. LD across a physical chromosome is a core calculation in eukaryotes. Humans too?  
  > **username_4**: You are overthinking. I suggest you write down the calculation on a paper. It is simple. Recombination or LD is irrelevant to this question.  
  > **username_5**: comment to (1),  according to https://www.nature.com/scitable/popular-students-page/132/ , coding region and non-coding region are included in the calculation of the 1% DNA sequence difference.  
  > **username_5**: comment to (3),  in humans, a mutation rate of about 10 to the power -8 mutations/bp/generation was inferred from projects where both parents and their children were sequenced at high coverage.  (  http://book.bionumbers.org/what-is-the-mutation-rate-during-genome-replication/ )  
  
  ---
  
  ### Answer by username_4 on 2023-06-23. Score: 2
  
  The common wording is that the difference between two human *haplotypes* is 0.1%. This number only counts base substitutions, not insertions/deletions (indels) or structural variations (SVs). SVs together affects more bases than base substitutions. Also, the number is smaller is non-Africans (~0.07%) and higher in Africans (~0.12%). Anyway, let's denote this number by $\theta$, also known as the scaled mutation rate.
  
  Because human is diploid, you need to count genotype differences when you compare two human individuals. Under the Wright-Fisher model, the rate of genotype difference on autosomes is
  
  $$\theta\cdot\left(1+\frac{1}{2}\cdot\frac{1}{2}+\frac{1}{3}\right)=1.58\theta$$
  
  The rate between a child and his/her parent is, I think:
  
  $$\theta\cdot\left[1\cdot\frac{1}{2}+\frac{1}{2}\cdot\left(\frac{1}{3}+\frac{2}{3}\cdot\frac{1}{2}\right)+\frac{1}{3}\cdot\frac{1}{2}\right]=\theta$$
  
  Note that I am sure the rate can be theoretically calculated but I am not confident in my calculation. Also, the rate of genotype difference on sex chromosomes or mitochondrial DNA is different.
  
  
  ---
  
  