text: user146: My understanding is that indels are from 1bp to 10Kb, and a healthy genome has ~400K-500K Indels. Surely most of these are small. 
  What is the distribution of insertion sizes in a healthy human genome? What is the distribution of deletion sizes? What is an average ratio of insertions:deletions? 
  I have not found a definitive reference.
  
  user37: Genome-In-A-Bottle (GIAB; version 3.3.2) contains 3.21M SNPs on auto+X chromosomes and 0.51M INDELs in 2.58Gb confident regions. The ins:del ratio is 0.92. On the CHM1-CHM13 pacbio assembly (European ancestry), there are 3.57M auto+X SNPs and 0.58M INDELs in 2.71Gb confident regions [reference] with an ins:del ratio 0.99. These give you an idea of relative short INDELs.
  For indels longer than 50bp, I would highly recommend to read this paper by Chaisson et al. This call set is constructed from the whole-genome assembly of the CHM1 genome. It is far more comprehensive and probably more accurate than all the other call sets. The following is Table 1 from the paper:
  
  I have to say that the high ins-to-del ratio is surprising to me, but this is what the data tells us. I have done a similar analysis and reached a similar ratio.
  PS: These numbers are essentially from one haplotype. They will be higher for a diploid sample.
  EDIT: some numbers in the original post are wrong.
  
  user77: One of the 2015 papers from the 1000 genomes project has a nice figure (figure 1) showing the size distribution of medium to large sized insertions and deletions:
  
  From another 2015 1000 genomes paper, one can see that the absolute number of smaller indels is much larger, though an exact size range isn't given (as far as I saw). If you really want to know that, just download the most recent 1000 genomes VCF file(s) and compute the exact median size and/or distribution that you want.
  
original_text: 146: <p>My understanding is that indels are from 1bp to 10Kb, and a healthy genome has ~400K-500K Indels. Surely most of these are small. </p>
  
  <p>What is the distribution of insertion sizes in a healthy human genome? What is the distribution of deletion sizes? What is an average ratio of insertions:deletions? </p>
  
  <p>I have not found a definitive reference.</p>
   37: <p>Genome-In-A-Bottle (GIAB; version 3.3.2) contains 3.21M SNPs on auto+X chromosomes and 0.51M INDELs in 2.58Gb confident regions. The ins:del ratio is 0.92. On the CHM1-CHM13 pacbio assembly (European ancestry), there are 3.57M auto+X SNPs and 0.58M INDELs in 2.71Gb confident regions [<a href="https://rdcu.be/232R" rel="nofollow noreferrer">reference</a>] with an ins:del ratio 0.99. These give you an idea of relative short INDELs.</p>
  
  <p>For indels longer than 50bp, I would highly recommend to read <a href="https://www.nature.com/nature/journal/v517/n7536/full/nature13907.html" rel="nofollow noreferrer">this paper</a> by Chaisson et al. This call set is constructed from the whole-genome assembly of the CHM1 genome. It is far more comprehensive and probably more accurate than all the other call sets. The following is Table 1 from the paper:</p>
  
  <p><a href="https://i.stack.imgur.com/om410.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/om410.png" alt="CHM1-SVs"></a></p>
  
  <p>I have to say that the high ins-to-del ratio is surprising to me, but this is what the data tells us. I have done a similar analysis and reached a similar ratio.</p>
  
  <p>PS: These numbers are essentially from one haplotype. They will be higher for a diploid sample.</p>
  
  <p>EDIT: some numbers in the original post are wrong.</p>
   77: <p>One of the <a href="https://www.nature.com/nature/journal/v526/n7571/full/nature15394.html" rel="noreferrer">2015 papers from the 1000 genomes project</a> has a nice figure (figure 1) showing the size distribution of medium to large sized insertions and deletions:</p>
  
  <p><a href="https://i.stack.imgur.com/bFMCX.jpg" rel="noreferrer"><img src="https://i.stack.imgur.com/bFMCX.jpg" alt="enter image description here"></a></p>
  
  <p>From <a href="https://www.nature.com/nature/journal/v526/n7571/full/nature15393.html" rel="noreferrer">another 2015 1000 genomes paper</a>, one can see that the absolute number of smaller indels is much larger, though an exact size range isn't given (as far as I saw). If you really want to know that, just download <a href="ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/" rel="noreferrer">the most recent 1000 genomes VCF file(s)</a> and compute the exact median size and/or distribution that you want.</p>
  