Answers.Body: <p>I'll stick my neck out and simply state that allopatry alone would account for the pattern you are observing. Thus populations can exihibit variation in allelic profiles, particularly where Mendellian inheritance is operating (i.e. higher eukaryotes), singly due to geographic isolation.</p>
  <p>This represents the Meyers view of population genetics and would account for variation within neutral theory, e.g. silent mutations. Obviously I'm guessing the populations were selected by geographic foci in generating the allelic frequencies.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-10-14T02:33:29.103Z
Answers.LastActivityDate: 2020-10-14T02:33:29.103Z
Answers.UserDisplayName: M__
Body: <p>Sometimes dbSNP reports very different allele frequencies for different large-scale genome projects e.g. between 1000 Genomes and GnomAD</p>
  <p><a href="https://www.ncbi.nlm.nih.gov/snp/rs11822440#frequency_tab" rel="nofollow noreferrer">rs11822440</a> 1000Genomes A=0.4629    C=0.5371 GnomAD A=0.99997   T=0.00003</p>
  <p><a href="https://www.ncbi.nlm.nih.gov/snp/rs28531832#frequency_tab" rel="nofollow noreferrer">rs28531832</a> 1000Genomes T=0.4379    C=0.5621 GnomAD T=0.99993   A=0.00007</p>
  <p><a href="https://www.ncbi.nlm.nih.gov/snp/rs78931618#frequency_tab" rel="nofollow noreferrer">rs78931618</a> 1000Genomes A=0.7334    C=0.2666 GnomAD A=0.9999    T=0.0001</p>
  <p><a href="https://www.ncbi.nlm.nih.gov/snp/rs75716913#frequency_tab" rel="nofollow noreferrer">rs75716913</a> 1000Genomes T=0.9006    C=0.0994 GnomAD T=0.99149   A=0.00851</p>
  <p>Is this an issue with one or other of these projects data processing? Is something else going on here biologically or technically that might cause this?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-10-13T13:47:03.597Z
Comments.Text: do you know what populations were used to calculate the gnomad frequencies?
Comments.UserDisplayName: user438383
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-10-13T16:08:36.983Z
Comments.Text: These are SNP frequencies - its not the same thing as whole genome GC content. What we are looking at here is selection pressure at given SNPs
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-10-13T16:25:19.797Z
Comments.Text: @user438383 the pattern is consistently different between projects in global and sub-populations e.g. African, European
Comments.UserDisplayName: afaulconbridge
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-10-13T16:26:43.713Z
Comments.Text: @Michael these are the same SNPs with different frequencies for different projects - but both on "normal human" so I would be surprised if there is that much selection via recruitment.
Comments.UserDisplayName: afaulconbridge
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-10-13T16:32:21.417Z
Comments.Text: The other thing - have you double checked you are comparing the same genome build between the two (i.e. gnomad is gr38 and 1kg is gr37)?
Comments.UserDisplayName: user438383
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-10-13T16:42:43.513Z
Comments.Text: allopatry .. it happens
Comments.UserDisplayName: M__
Tags: <snp><1000genomes>
Title: dbnSNP frequency anomalies
ThreadText: # dbnSNP frequency anomalies
  
  (Asked by: username_0 on 2020-10-13)
  
  Sometimes dbSNP reports very different allele frequencies for different large-scale genome projects e.g. between 1000 Genomes and GnomAD
  
  [rs11822440](https://www.ncbi.nlm.nih.gov/snp/rs11822440#frequency_tab) 1000Genomes A=0.4629 C=0.5371 GnomAD A=0.99997 T=0.00003
  
  [rs28531832](https://www.ncbi.nlm.nih.gov/snp/rs28531832#frequency_tab) 1000Genomes T=0.4379 C=0.5621 GnomAD T=0.99993 A=0.00007
  
  [rs78931618](https://www.ncbi.nlm.nih.gov/snp/rs78931618#frequency_tab) 1000Genomes A=0.7334 C=0.2666 GnomAD A=0.9999 T=0.0001
  
  [rs75716913](https://www.ncbi.nlm.nih.gov/snp/rs75716913#frequency_tab) 1000Genomes T=0.9006 C=0.0994 GnomAD T=0.99149 A=0.00851
  
  Is this an issue with one or other of these projects data processing? Is something else going on here biologically or technically that might cause this?
  
  **Tags:** snp, 1000genomes
  
  > **Comments:**
  > **username_1**: do you know what populations were used to calculate the gnomad frequencies?  
  > **username_2**: These are SNP frequencies - its not the same thing as whole genome GC content. What we are looking at here is selection pressure at given SNPs  
  > **username_0**: @username_1 the pattern is consistently different between projects in global and sub-populations e.g. African, European  
  > **username_0**: @Michael these are the same SNPs with different frequencies for different projects - but both on "normal human" so I would be surprised if there is that much selection via recruitment.  
  > **username_1**: The other thing - have you double checked you are comparing the same genome build between the two (i.e. gnomad is gr38 and 1kg is gr37)?  
  > **username_2**: allopatry .. it happens  
  
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  ## 1 answers
  
  ### Answer by username_2 on 2020-10-14. Score: 1
  
  I'll stick my neck out and simply state that allopatry alone would account for the pattern you are observing. Thus populations can exihibit variation in allelic profiles, particularly where Mendellian inheritance is operating (i.e. higher eukaryotes), singly due to geographic isolation.
  
  This represents the Meyers view of population genetics and would account for variation within neutral theory, e.g. silent mutations. Obviously I'm guessing the populations were selected by geographic foci in generating the allelic frequencies.
  
  
  ---
  
  