---
_id: '5757'
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."
article_processing_charge: No
author:
- first_name: Christelle
  full_name: Fraisse, Christelle
  id: 32DF5794-F248-11E8-B48F-1D18A9856A87
  last_name: Fraisse
  orcid: 0000-0001-8441-5075
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>
  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>.
  ieee: C. Fraisse, “Supplementary Files for ‘Pleiotropy modulates the efficacy of
    selection in Drosophila melanogaster.’” Institute of Science and Technology Austria,
    2018.
  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>.
  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>.
  short: C. Fraisse, (2018).
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
date_created: 2018-12-19T14:22:35Z
date_published: 2018-12-19T00:00:00Z
date_updated: 2024-02-21T13:59:18Z
day: '19'
ddc:
- '576'
department:
- _id: BeVi
- _id: NiBa
doi: 10.15479/at:ista:/5757
ec_funded: 1
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has_accepted_license: '1'
keyword:
- (mal)adaptation
- pleiotropy
- selective constraint
- evo-devo
- gene expression
- Drosophila melanogaster
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '291734'
  name: International IST Postdoc Fellowship Programme
publisher: Institute of Science and Technology Austria
related_material:
  record:
  - id: '6089'
    relation: research_paper
    status: public
status: public
title: Supplementary Files for "Pleiotropy modulates the efficacy of selection in
  Drosophila melanogaster"
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...