Data from: Double-digest RAD Sequencing using Ion Proton semiconductor platform (ddRADseq-ion) with non-model organisms

Recknagel H, Jacobs A, Herzyk P, Elmer KR

Date Published: March 19, 2015

DOI: http://dx.doi.org/10.5061/dryad.7tb72

 

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Title Table_1
Downloaded 8 times
Description Table_1 contains the locus sequences and coded genotypes of each individual used to recreate genomic composition of the Alpine x Baltic cross and their offspring. SNPs that were fixed between parents (following standard genetic mapping procedure) were used in the Structure analysis. Each individual contains two columns per locus with their genotype. Numbers refer to the four different DNA bases: A = 1, C = 2, G = 3, T = 4. 0 = missing data.
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Title Table_2
Downloaded 2 times
Description Table_2 contains all the locus sequences (sheet 1: ‘Locus sequences’) and SNP information (sheet 2: ‘Genotypes’) that were used for the inference of phylogenetic relationships of Arctic charr and European whitefish.
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Title Library1_SNPs
Downloaded 9 times
Description Sequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').
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Title Library2_SNPs
Downloaded 1 time
Description Sequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').
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Title Library3_SNPs
Downloaded 3 times
Description Sequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').
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Title Library4_SNPs
Downloaded 6 times
Description Sequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').
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Title Library5_SNPs
Downloaded 2 times
Description Sequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').
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Title Library6_SNPs
Downloaded 1 time
Description Sequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').
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Title Library7_SNPs
Downloaded 3 times
Description Sequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').
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Title Library8_SNPs
Downloaded 8 times
Description Sequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').
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Title Library9_SNPs
Downloaded 4 times
Description Sequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').
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Title Library10_SNPs
Downloaded 3 times
Description Sequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').
Download Library10_SNPs.xlsx (1.159 Mb)
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Title Library11_SNPs
Downloaded 3 times
Description Sequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').
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Title Library12_SNPs
Downloaded 28 times
Description Sequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').
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Title Library13_SNPs
Downloaded 1 time
Description Sequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').
Download Library13_SNPs.xlsx (409.6 Kb)
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Title RAxML_treefile
Downloaded 3 times
Description The tree file contains three Arctic charr and three European whitefish individuals from different localities in Europe
Download RAxML_treefile.tre (284 bytes)
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Title Replicate_1_genotypes_8x
Downloaded 3 times
Description Input file for estimation of the SNP error rate. The R script to analyse this file is provided by Mastretta-Yanes et al. (2014).
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Title Replicate_1_genotypes_16x
Downloaded 4 times
Description Input file for estimation of the SNP error rate. The R script to analyse this file is provided by Mastretta-Yanes et al. (2014).
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Title Replicate_2_genotypes_8x
Downloaded 4 times
Description Input file for estimation of the SNP error rate. The R script to analyse this file is provided by Mastretta-Yanes et al. (2014).
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Title Replicate_2_genotypes_16x
Downloaded 3 times
Description Input file for estimation of the SNP error rate. The R script to analyse this file is provided by Mastretta-Yanes et al. (2014).
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When using this data, please cite the original publication:

Recknagel H, Jacobs A, Herzyk P, Elmer KR (2015) Double-digest RAD Sequencing using Ion Proton semiconductor platform (ddRADseq-ion) with non-model organisms. Molecular Ecology Resources 15(6): 1316–1329. http://dx.doi.org/10.1111/1755-0998.12406

Additionally, please cite the Dryad data package:

Recknagel H, Jacobs A, Herzyk P, Elmer KR (2015) Data from: Double-digest RAD Sequencing using Ion Proton semiconductor platform (ddRADseq-ion) with non-model organisms. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.7tb72
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