Data from: Congruent population structure across paralogous and non-paralogous loci in Salish Sea chum salmon (Oncorhynchus keta)

Waples RK, Seeb JE, Seeb LW

Date Published: April 26, 2017

DOI: http://dx.doi.org/10.5061/dryad.kq652

 

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Title linkage map
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Description Tab-delimited text file giving the linkage group (LG) and cM (centiMorgan) position of each SNP. The remaining columns give different identifiers for the positions. "Contig" = aligned reference contig. "resolved_locus" = genetic locus, for non-duplicated loci this is the contig. For paralogous loci, multiple loci are associated with a contig. "stacks_CatID" and "stacks_SNP" give the identifiers given by the Stacks program. "LEPname" gives the locus identifier given by the LEPmap program.
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Title Genome scan summary statistics
Downloaded 12 times
Description Tab-delimited text file giving summary statistics for each locus. See the README for column descriptions.
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Download README.txt (807 bytes)
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Title Stacks Haplotypes.tsv file
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Description "Haplotypes" file produced by Stacks, in text format. See Stacks documentation.
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Title non_paralogs.map
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Description Locus list (in PLINK .map format) of non-paralogous loci. Associated with non_paralogous.ped
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Title non_paralogs.ped
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Description Genotype data (in PLINK .ped format) for non-paralogous loci. For use with the non_paralogs.map file.
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Title complete.dom.map
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Description Locus list for the dominance-coded data set with both non-paralogous and paralogous loci (in PLINK .map format).
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Title complete.dom.txt
Downloaded 6 times
Description non-delimited text file with Genotype data for dominance-coded genotypes at paralogous and non-paralogous loci. Each genotype takes one character: 1 = present, 0 = absent, 9 = missing. One row per locus, loci are given in complete.dom.map. One column per individual, individuals are listed in non_paralogs.ped.
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When using this data, please cite the original publication:

Waples RK, Seeb JE, Seeb L (2017) Congruent population structure across paralogous and non-paralogous loci in Salish Sea chum salmon (Oncorhynchus keta). Molecular Ecology 26(16): 4131–4144. http://dx.doi.org/10.1111/mec.14163

Additionally, please cite the Dryad data package:

Waples RK, Seeb JE, Seeb LW (2017) Data from: Congruent population structure across paralogous and non-paralogous loci in Salish Sea chum salmon (Oncorhynchus keta). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.kq652
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