{"action":"opened","issue":{"url":"https://api.github.com/repos/REGOVAR/QRegovar/issues/128","repository_url":"https://api.github.com/repos/REGOVAR/QRegovar","labels_url":"https://api.github.com/repos/REGOVAR/QRegovar/issues/128/labels{/name}","comments_url":"https://api.github.com/repos/REGOVAR/QRegovar/issues/128/comments","events_url":"https://api.github.com/repos/REGOVAR/QRegovar/issues/128/events","html_url":"https://github.com/REGOVAR/QRegovar/issues/128","id":296900762,"number":128,"title":"Precision about ExAC displayed columns","user":{"login":"Oodnadatta","id":5510283,"avatar_url":"https://avatars2.githubusercontent.com/u/5510283?v=4","gravatar_id":"","url":"https://api.github.com/users/Oodnadatta","html_url":"https://github.com/Oodnadatta","followers_url":"https://api.github.com/users/Oodnadatta/followers","following_url":"https://api.github.com/users/Oodnadatta/following{/other_user}","gists_url":"https://api.github.com/users/Oodnadatta/gists{/gist_id}","starred_url":"https://api.github.com/users/Oodnadatta/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Oodnadatta/subscriptions","organizations_url":"https://api.github.com/users/Oodnadatta/orgs","repos_url":"https://api.github.com/users/Oodnadatta/repos","events_url":"https://api.github.com/users/Oodnadatta/events{/privacy}","received_events_url":"https://api.github.com/users/Oodnadatta/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-02-13T21:59:48Z","updated_at":"2018-02-13T21:59:48Z","closed_at":null,"author_association":"OWNER","body":"## Screenshot from Regovar\r\n![image](https://user-images.githubusercontent.com/5510283/36174758-91d4daa2-110d-11e8-9005-20c2bbfc4017.png)\r\n\r\n## ExAC information\r\nFrom [ExAC Browser FAQ](http://exac.broadinstitute.org/faq)\r\n\r\n### About populations\r\nPopulation abbreviation | Population\r\n ------------ | -------------\r\nAFR | African/African American\r\nAMR | Latino\r\nEAS | East Asian\r\nFIN | Finnish\r\nNFE | Non-Finnish European\r\nSAS | South Asian\r\nOTH | Other\r\n\r\n### About Adj_Maf\r\n> Why does the allele frequency (AF) found in the ExAC VCF differ from the AF shown on the browser?\r\n> The AF shown in the VCF is AC/AN. The browser however shows the adjusted allele frequency (AC_adj/AN_adj). The raw counts (AC and AN) refer to the total number of chromosomes with this allele, and total that were able to be called (whether reference or alternate), respectively. Thus, the allele frequency is AC/AN. However, for more stringent applications, we **adjusted the allele count to only include individuals with genotype quality (GQ) >= 20 and depth (DP) >= 10**, which we term AC_adj (and correspondingly, AN_adj for total number of chromosomes from individuals with those criteria regardless of genotype call). \r\n\r\nThen, \"Adj_Maf\" stands for \"**adjusted minor allelle frequency**\"."}}
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