Data from: SNPs to discriminate different classes of hybrid between wild Atlantic salmon and aquaculture escapees

Pritchard VL, Erkinaro J, Kent MP, Niemelä E, Orell P, Lien S, Primmer CR

Date Published: July 5, 2016

DOI: http://dx.doi.org/10.5061/dryad.dg8f3

 

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Title Bayescan_Fdist2.tar.gz
Downloaded 21 times
Description This archive contains files used by Pritchard et al. (2016) for Fst outlier analyses: Index.txt - index of SNPs. Bayescan*.in - Bayescan input files, SNPs in index order. Fdist*.in -Fdist2 input files, SNPs in index order. datacal.c; fdist2.c; Original_README_fdist2 - Fdist2 source code & information. R_code_for_analysing_Fdist2_output.txt - modified R code from Lotterhos & Whitlock (2014). See README file in archive for further information.
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Title Genotyping_allelotyping.tar.gz
Downloaded 25 times
Description This archive contains the following data files for Pritchard et al. (2016): B_allele_freq_Naatamo_pools.csv: Uncorrected B allele frequencies for the Naatamo pools. B_allele_freq_New_Teno_pools.csv: Uncorrected B allele frequencies for the New Teno mainstem pools. B_allele_freq_Teno_Finnmark_pools.csv: Uncorrected B allele frequencies for the old Teno and Finnmark pools. B_allele_freqs_all_pops.csv: Corrected B allele frequencies for all populations. Individuals_and_pooling.csv: Details of genotyped individuals. Pritchardetal_genotypes.map; Pritchardetal_genotypes.ped: Individual genotypes in PLINK format. See README file in archive for further information.
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Title Simupop_code.tar.gz
Downloaded 14 times
Description This archive contains Python code for simulating populations using the package simuPOP, plus additional data files, used in Pritchard et al. (2016): *.py: code for simulating test or reference individuals. Estimated_allele_frequencies.csv: estimated frequencies of the 200 discriminatory alleles, from Table S3. Allele_frequencies_for_simulations.csv: adjusted allele frequencies used for simulations, from Table S3. See README file in archive for further information.
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Title Hybrid_class_assignment.tar.gz
Downloaded 8 times
Description This archive contains code used for hybrid class assignments, and hybrid class assignment results for Pritchard et al. (2016): Code_for_hybrid_class_assigments.txt: code used to generate NewHybrids and Structure input files and parse results. Folder "Extra_required_files" contains text files required by the above code. Folder "Results" contains hybrid class assignment results. See README file in archive for further information.
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Title Code_and_data_for_figures.tar.gz
Downloaded 7 times
Description This archive contains the ggplot2 code and data files required for making all the figures in Pritchard et al. (2016): Code_for_ggplot.txt contains annotated ggplot code for making figures. See README file in archive for further information.
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Title PPC_correction.tar.gz
Downloaded 11 times
Description This archive (700MB) contains the following data files for Pritchard et al. (2016), used for calculating and applying the PPC correction: R_code for_PPC_correction.txt: Annotated R code for calculating PPC correction coefficients from data in CALL.txt and INT.txt. CALL.txt: File of genotype calls. INT2.txt: File of A and B allele probe intensities. PPC_correction_coefficients.csv: PPC correction coefficients returned for each SNP. See README file in archive for further information.
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When using this data, please cite the original publication:

Pritchard VL, Erkinaro J, Kent MP, Niemelä E, Orell P, Lien S, Primmer CR (2016) Single nucleotide polymorphisms to discriminate different classes of hybrid between wild Atlantic salmon and aquaculture escapees. Evolutionary Applications 9(8): 1017-1031. http://dx.doi.org/10.1111/eva.12407

Additionally, please cite the Dryad data package:

Pritchard VL, Erkinaro J, Kent MP, Niemelä E, Orell P, Lien S, Primmer CR (2016) Data from: SNPs to discriminate different classes of hybrid between wild Atlantic salmon and aquaculture escapees. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.dg8f3
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