{"action":"created","issue":{"url":"https://api.github.com/repos/meren/anvio/issues/364","repository_url":"https://api.github.com/repos/meren/anvio","labels_url":"https://api.github.com/repos/meren/anvio/issues/364/labels{/name}","comments_url":"https://api.github.com/repos/meren/anvio/issues/364/comments","events_url":"https://api.github.com/repos/meren/anvio/issues/364/events","html_url":"https://github.com/meren/anvio/issues/364","id":155320527,"number":364,"title":"SNV types in anvi-gen-variability-profile output","user":{"login":"tdelmont","id":8332889,"avatar_url":"https://avatars.githubusercontent.com/u/8332889?v=3","gravatar_id":"","url":"https://api.github.com/users/tdelmont","html_url":"https://github.com/tdelmont","followers_url":"https://api.github.com/users/tdelmont/followers","following_url":"https://api.github.com/users/tdelmont/following{/other_user}","gists_url":"https://api.github.com/users/tdelmont/gists{/gist_id}","starred_url":"https://api.github.com/users/tdelmont/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tdelmont/subscriptions","organizations_url":"https://api.github.com/users/tdelmont/orgs","repos_url":"https://api.github.com/users/tdelmont/repos","events_url":"https://api.github.com/users/tdelmont/events{/privacy}","received_events_url":"https://api.github.com/users/tdelmont/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"meren","id":197307,"avatar_url":"https://avatars.githubusercontent.com/u/197307?v=3","gravatar_id":"","url":"https://api.github.com/users/meren","html_url":"https://github.com/meren","followers_url":"https://api.github.com/users/meren/followers","following_url":"https://api.github.com/users/meren/following{/other_user}","gists_url":"https://api.github.com/users/meren/gists{/gist_id}","starred_url":"https://api.github.com/users/meren/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/meren/subscriptions","organizations_url":"https://api.github.com/users/meren/orgs","repos_url":"https://api.github.com/users/meren/repos","events_url":"https://api.github.com/users/meren/events{/privacy}","received_events_url":"https://api.github.com/users/meren/received_events","type":"User","site_admin":false},"milestone":null,"comments":1,"created_at":"2016-05-17T17:49:00Z","updated_at":"2016-05-18T00:26:12Z","closed_at":null,"body":"Hi, I very slowly realize that some \"SNV\" types are difficult to extract from the current report tables of NTs (anvi'o 2.0.0)\r\n\r\nI suggest to classify positions into 4 categories (I think those 4 represent the entire panel but might have missed extra-ones so far):\r\n\r\n1- stable in the metagenome and consistent with the reference sequence (e.g., genome). Departure is currently \"0\". This is not a SNV.\r\n\r\n2- stable in the metagenome but different from the reference genome. Departure is currently very close to \"1\". This is not a SNV either, but provides information regarding distances between references sequences and metagenomic data. Preliminary results suggest it might represent an important index in the future.\r\n\r\n3- variable with one nucleotide/aa consistent with the reference sequence. Departure is ranges from close to \"0\" to close to \"1\". This is the classic SNV!\r\n\r\n4- variable without being consistent with the reference sequence. Departure is currently close to \"1\". This is not a SNV from the reference sequence perspective, but a SNV from the metagenomic perspective... So it might need a distinct naming?\r\n\r\nAt this point, it is not easy for me to differentiate types 2 and type 4 from the table. Missing might be a column providing the frequency of the most abundant NT (named n1 in the anvi'o publication). Or, in the best case scenario, a column with position type from 1 to 4 would be great, no? If this can be processed during profiling. \r\n\r\nHope it is not too confusing. I think adding those columns will improve the user's ability to inventory genomic heterogeneity types in environmental surveys.\r\n\r\nTom"},"comment":{"url":"https://api.github.com/repos/meren/anvio/issues/comments/219893030","html_url":"https://github.com/meren/anvio/issues/364#issuecomment-219893030","issue_url":"https://api.github.com/repos/meren/anvio/issues/364","id":219893030,"user":{"login":"meren","id":197307,"avatar_url":"https://avatars.githubusercontent.com/u/197307?v=3","gravatar_id":"","url":"https://api.github.com/users/meren","html_url":"https://github.com/meren","followers_url":"https://api.github.com/users/meren/followers","following_url":"https://api.github.com/users/meren/following{/other_user}","gists_url":"https://api.github.com/users/meren/gists{/gist_id}","starred_url":"https://api.github.com/users/meren/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/meren/subscriptions","organizations_url":"https://api.github.com/users/meren/orgs","repos_url":"https://api.github.com/users/meren/repos","events_url":"https://api.github.com/users/meren/events{/privacy}","received_events_url":"https://api.github.com/users/meren/received_events","type":"User","site_admin":false},"created_at":"2016-05-18T00:26:12Z","updated_at":"2016-05-18T00:26:12Z","body":"I will re-introduce n1n2_ratio which will address all of these, in conjunction with the departure of consensus metric."}}