{"month":"12","author":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse","full_name":"Fraisse, Christelle"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"title":"Supplementary Files for \"Pleiotropy modulates the efficacy of selection in Drosophila melanogaster\"","abstract":[{"lang":"eng","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."}],"date_published":"2018-12-19T00:00:00Z","citation":{"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>","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>","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>.","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>.","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>.","ieee":"C. Fraisse, “Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.’” Institute of Science and Technology Austria, 2018."},"ddc":["576"],"date_created":"2018-12-19T14:22:35Z","keyword":["(mal)adaptation","pleiotropy","selective constraint","evo-devo","gene expression","Drosophila melanogaster"],"doi":"10.15479/at:ista:/5757","article_processing_charge":"No","file":[{"relation":"main_file","file_id":"5758","checksum":"aed7ee9ca3f4dc07d8a66945f68e13cd","file_name":"FileS1.zip","creator":"cfraisse","access_level":"open_access","content_type":"application/zip","date_created":"2018-12-19T14:19:52Z","file_size":369837892,"date_updated":"2020-07-14T12:47:11Z"},{"creator":"cfraisse","file_name":"FileS2.zip","content_type":"application/zip","access_level":"open_access","date_created":"2018-12-19T14:19:49Z","date_updated":"2020-07-14T12:47:11Z","file_size":84856909,"file_id":"5759","relation":"main_file","checksum":"3592e467b4d8206650860b612d6e12f3"},{"checksum":"c37ac5d5437c457338afc128c1240655","relation":"main_file","file_id":"5760","file_size":881133,"date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:49Z","content_type":"text/plain","access_level":"open_access","file_name":"FileS3.txt","creator":"cfraisse"},{"file_name":"FileS4.txt","creator":"cfraisse","content_type":"text/plain","access_level":"open_access","date_created":"2018-12-19T14:19:49Z","file_size":883742,"date_updated":"2020-07-14T12:47:11Z","relation":"main_file","file_id":"5761","checksum":"943dfd14da61817441e33e3e3cb8cdb9"},{"checksum":"1c669b6c4690ec1bbca3e2da9f566d17","file_id":"5762","relation":"main_file","date_updated":"2020-07-14T12:47:11Z","file_size":2495437,"date_created":"2018-12-19T14:19:49Z","access_level":"open_access","content_type":"text/plain","creator":"cfraisse","file_name":"FileS5.txt"},{"date_created":"2018-12-19T14:19:50Z","file_size":15913457,"date_updated":"2020-07-14T12:47:11Z","file_name":"FileS6.txt","creator":"cfraisse","access_level":"open_access","content_type":"text/plain","checksum":"f40f661b987ca6fb6b47f650cbbb04e6","relation":"main_file","file_id":"5763"},{"file_id":"5764","relation":"main_file","checksum":"25f41e5b8a075669c6c88d4c6713bf6f","access_level":"open_access","content_type":"text/plain","creator":"cfraisse","file_name":"FileS7.txt","date_updated":"2020-07-14T12:47:11Z","file_size":2584120,"date_created":"2018-12-19T14:19:50Z"},{"date_updated":"2020-07-14T12:47:11Z","file_size":2446059,"date_created":"2018-12-19T14:19:50Z","access_level":"open_access","content_type":"text/plain","creator":"cfraisse","file_name":"FileS8.txt","checksum":"f6c0bd3e63e14ddf5445bd69b43a9152","file_id":"5765","relation":"main_file"},{"relation":"main_file","file_id":"5766","checksum":"0fe7a58a030b11bf3b9c8ff7a7addcae","content_type":"text/plain","access_level":"open_access","file_name":"FileS9.txt","creator":"cfraisse","file_size":100737,"date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:50Z"}],"publisher":"Institute of Science and Technology Austria","ec_funded":1,"_id":"5757","status":"public","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"has_accepted_license":"1","contributor":[{"first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse"},{"first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","orcid":"0000-0002-4579-8306"}],"oa":1,"file_date_updated":"2020-07-14T12:47:11Z","year":"2018","related_material":{"record":[{"status":"public","relation":"research_paper","id":"6089"}]},"type":"research_data","day":"19","oa_version":"Published Version","date_updated":"2024-02-21T13:59:18Z"}