Data from: Genome-wide selection components analysis in a fish with male pregnancy

Flanagan SP, Jones AG

Date Published: January 18, 2017

DOI: http://dx.doi.org/10.5061/dryad.5c1tj

 

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Title Archive of code
Description This is the archived GitHub repository containing the code used to analyze the data in this paper.
Download //zenodo.org/badge/latestdoi/51270799 (0 bytes)
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Title Variant Call File
Downloaded 5 times
Description In this file are the SNP data for all loci and all individuals, output by Stacks' populations module. The README file contains the population map that assigns each individual to a group (FEM = females, OFF = offspring, NPM = non pregnant males, PRM = pregnant males)
Download batch_1.vcf (531.9 Mb)
Download README.txt (9.232 Kb)
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Title Input file for likelihood ratio tests
Downloaded 6 times
Description This file was used as input for the likelihood ratio tests. The columns are: Chromosome, Position, Individual ID, Genotype (Format: Allele 1, Allele 2), Likelihood of AA, Likelihood of Aa, Likelihood of aa. Genotypes were generated by Stacks and the Stacks hard calls were given a likelihood of 1. The other two genotype likelihoods were set to 0.000001.
Download pipefish_input_full.LLm.txt (688.2 Mb)
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Title Supplemental simulation output
Downloaded 2 times
Description The output from the various runs of the simulation model described in the supplement are in this compressed folder.
Download sca_simulation_output.tar.gz (14.91 Mb)
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Title Variant Call File with inferred maternal alleles
Downloaded 1 time
Description This is a file containing the original genotypes and the inferred maternal alleles. The maternal alleles were generated from the Stacks Variant Call File output (archived here as Variant Call File) using the program infer_mat_vcf. This file was generated by merge_vcfs.R.
Download biallelic_merge.vcf (145.9 Mb)
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When using this data, please cite the original publication:

Flanagan SP, Jones AG (2017) Genome-wide selection components analysis in a fish with male pregnancy. Evolution 71(4): 1096–1105. http://dx.doi.org/10.1111/evo.13173

Additionally, please cite the Dryad data package:

Flanagan SP, Jones AG (2017) Data from: Genome-wide selection components analysis in a fish with male pregnancy. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.5c1tj
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