{"citation":{"ama":"Fraisse C. Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” 2018. doi:<a href=\"https://doi.org/10.15479/at:ista:/5757\">10.15479/at:ista:/5757</a>","apa":"Fraisse, C. (2018). Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:/5757\">https://doi.org/10.15479/at:ista:/5757</a>","ista":"Fraisse C. 2018. Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/at:ista:/5757\">10.15479/at:ista:/5757</a>.","chicago":"Fraisse, Christelle. “Supplementary Files for ‘Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.’” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/at:ista:/5757\">https://doi.org/10.15479/at:ista:/5757</a>.","short":"C. Fraisse, (2018).","mla":"Fraisse, Christelle. <i>Supplementary Files for “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.”</i> Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/at:ista:/5757\">10.15479/at:ista:/5757</a>.","ieee":"C. Fraisse, “Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.’” Institute of Science and Technology Austria, 2018."},"date_published":"2018-12-19T00:00:00Z","ec_funded":1,"_id":"5757","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"abstract":[{"text":"File S1. Variant Calling Format file of the ingroup: 197 haploid sequences of D. melanogaster from Zambia (Africa) aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S2. Variant Calling Format file of the outgroup: 1 haploid sequence of D. simulans aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S3. Annotations of each transcript in coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pn (# of non-synonymous polymorphic sites); Ds (# of synonymous divergent sites); Dn (# of non-synonymous divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S4. Annotations of each transcript in non-coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pu (# of UTR polymorphic sites); Ds (# of synonymous divergent sites); Du (# of UTR divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S5. Annotations of each transcript in coding regions with SNPGenie: Ps (# of synonymous polymorphic sites); πs (synonymous diversity); Ss_p (total # of synonymous sites in the polymorphism data); Pn (# of non-synonymous polymorphic sites); πn (non-synonymous diversity); Sn_p (total # of non-synonymous sites in the polymorphism data); Ds (# of synonymous divergent sites); ks (synonymous evolutionary rate); Ss_d (total # of synonymous sites in the divergence data); Dn (# of non-synonymous divergent sites); kn (non-synonymous evolutionary rate); Sn_d (total # of non-\r\nsynonymous sites in the divergence data); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S6. Gene expression values (RPKM summed over all transcripts) for each sample. Values were quantile-normalized across all samples.\r\n\r\nFile S7. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for coding sites, excluding variants below 5% frequency.\r\n\r\nFile S8. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for non-coding sites, excluding variants below 5%\r\nfrequency.\r\n\r\nFile S9. Final dataset with all covariates, ⍺ EWK , ωA EWK and deleterious SFS for coding sites obtained with the Eyre-Walker and Keightley method on binned data and using all variants.","lang":"eng"}],"type":"research_data","file":[{"checksum":"aed7ee9ca3f4dc07d8a66945f68e13cd","relation":"main_file","access_level":"open_access","creator":"cfraisse","file_name":"FileS1.zip","content_type":"application/zip","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:52Z","file_size":369837892,"file_id":"5758"},{"date_updated":"2020-07-14T12:47:11Z","file_id":"5759","file_size":84856909,"date_created":"2018-12-19T14:19:49Z","relation":"main_file","checksum":"3592e467b4d8206650860b612d6e12f3","content_type":"application/zip","file_name":"FileS2.zip","access_level":"open_access","creator":"cfraisse"},{"file_id":"5760","file_size":881133,"date_created":"2018-12-19T14:19:49Z","date_updated":"2020-07-14T12:47:11Z","content_type":"text/plain","access_level":"open_access","creator":"cfraisse","file_name":"FileS3.txt","checksum":"c37ac5d5437c457338afc128c1240655","relation":"main_file"},{"date_updated":"2020-07-14T12:47:11Z","file_id":"5761","date_created":"2018-12-19T14:19:49Z","file_size":883742,"relation":"main_file","checksum":"943dfd14da61817441e33e3e3cb8cdb9","content_type":"text/plain","file_name":"FileS4.txt","access_level":"open_access","creator":"cfraisse"},{"date_updated":"2020-07-14T12:47:11Z","file_size":2495437,"date_created":"2018-12-19T14:19:49Z","file_id":"5762","relation":"main_file","checksum":"1c669b6c4690ec1bbca3e2da9f566d17","file_name":"FileS5.txt","creator":"cfraisse","access_level":"open_access","content_type":"text/plain"},{"checksum":"f40f661b987ca6fb6b47f650cbbb04e6","relation":"main_file","creator":"cfraisse","access_level":"open_access","file_name":"FileS6.txt","content_type":"text/plain","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:50Z","file_size":15913457,"file_id":"5763"},{"relation":"main_file","checksum":"25f41e5b8a075669c6c88d4c6713bf6f","file_name":"FileS7.txt","creator":"cfraisse","access_level":"open_access","content_type":"text/plain","date_updated":"2020-07-14T12:47:11Z","file_size":2584120,"date_created":"2018-12-19T14:19:50Z","file_id":"5764"},{"relation":"main_file","checksum":"f6c0bd3e63e14ddf5445bd69b43a9152","content_type":"text/plain","file_name":"FileS8.txt","access_level":"open_access","creator":"cfraisse","date_updated":"2020-07-14T12:47:11Z","file_id":"5765","date_created":"2018-12-19T14:19:50Z","file_size":2446059},{"file_id":"5766","date_created":"2018-12-19T14:19:50Z","file_size":100737,"date_updated":"2020-07-14T12:47:11Z","content_type":"text/plain","file_name":"FileS9.txt","access_level":"open_access","creator":"cfraisse","relation":"main_file","checksum":"0fe7a58a030b11bf3b9c8ff7a7addcae"}],"has_accepted_license":"1","author":[{"orcid":"0000-0001-8441-5075","last_name":"Fraisse","first_name":"Christelle","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"}],"day":"19","doi":"10.15479/at:ista:/5757","month":"12","article_processing_charge":"No","date_updated":"2024-02-21T13:59:18Z","title":"Supplementary Files for \"Pleiotropy modulates the efficacy of selection in Drosophila melanogaster\"","file_date_updated":"2020-07-14T12:47:11Z","status":"public","keyword":["(mal)adaptation","pleiotropy","selective constraint","evo-devo","gene expression","Drosophila melanogaster"],"related_material":{"record":[{"status":"public","relation":"research_paper","id":"6089"}]},"project":[{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"contributor":[{"last_name":"Fraisse","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala","first_name":"Gemma"},{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"ddc":["576"],"oa_version":"Published Version","oa":1,"date_created":"2018-12-19T14:22:35Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","publisher":"Institute of Science and Technology Austria"}