Data from: Linkage disequilibrium and inversion-typing of the Drosophila melanogaster Genome Reference Panel

Houle D, Marquez EJ

Date Published: June 12, 2015

DOI: http://dx.doi.org/10.5061/dryad.06jt7

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title LD205results.zip
Downloaded 6 times
Description List of all SNP pairs in Freeze 2 of the Drosophila Genome Reference Panel with linkage disequilbirium r^2>0.5. Minor allele count of the focal SNP must be >=5.
Download LD205results.zip (860.3 Mb)
Details View File Details
Title HouleMarquezSASfiles
Downloaded 39 times
Description This zip archive contains: Gcorrlimits.SAS. A SAS file that calculates limits on which range of minor allele frequencies can be correlated at r^2>=0.5. CalcHighCorr.SAS A SAS file that calculates the genotypic r^2 between sites that could be correlated at a particular r^2 value. gcorrexampledata.sas7bdat - as SAS format data set with sample data for CalcHighCorr.SAS.
Download HouleMarquezSASfiles.zip (174.9 Kb)
Details View File Details
Title HouleMarquezF3_PCscores
Downloaded 6 times
Description Supplemental File S3. Inversion-typing of DGRP lines for the three common inversions In(2L)t, In(2R)NS, and In(3R)Mo, and heterozygosity of chromosome regions. For each inversion: the column beginning PC1sc is the score on Principal component 1 for variants between inversion breakpoints and in disequilibrium with large number of distant sites; (see text for explanation) . Pred is the inversion type predicted based on the PC1 scores (1=homozygous inversion, 0.5 Standard/inversion heterozygote, 0= homozygous Standard). CDL is the combined assignments of inversion-type from Langley et al. 2012 and Corbett-Detig & Hartl 2012 (1=homozygous inversion, 0= not a homozygote for the inversion, blank=not scored). Huang indicates the assignements from Huang et al. 2014 (0= homozygous Standard, 0.5= homozygous ST/INV, 1=homozygous inversion), blank= not scored), Heterozygosity columns are the average heterozygosity for chromsome segments defined by inversion breakpoints, plus the X and arm 3L. Heterozygosities were calculated from sites with no more than 5 missing calls in the 205 lines, and omit regions within 10kb of inversion breakpoints.
Download HouleMarquezF3_PCscores.csv (22.62 Kb)
Details View File Details

When using this data, please cite the original publication:

Houle D, Marquez EJ (2015) Linkage disequilibrium and inversion-typing of the Drosophila melanogaster Genome Reference Panel. G3: Genes - Genomes - Genetics 5(8): 1695-1701. http://dx.doi.org/10.1534/g3.115.019554

Additionally, please cite the Dryad data package:

Houle D, Marquez EJ (2015) Data from: Linkage disequilibrium and inversion-typing of the Drosophila melanogaster Genome Reference Panel. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.06jt7
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: