16 research outputs found
TASSLEgeno15239Ind237vfinal_genotype.hmp
The input file of genotypes for the program TASSLE which was used to perform the univariate GWAS for this study
Genotypes
Genotypes: Individual genotypes for each sample at each of the 19,703 loci. Sample ID is population abbreviation (see Table 1) followed by "xXXX", where XXX is a three digit numerical identifier
Mantel-Hecht-Moran FST full matrices
Input files for Mantel test between Hecht Fst values and Moran et al. (2013) Fst values. Each set of Fst values are included in full matrix format in separate tabs of the Excel file. See Table S2 for corresponding triangular matrices and results of Mantel tests
Hardy Weinberg equilibrium
Hardy Weinberg equilibrium: Locus summary by population including estimates of the genotyping success rate (GSR), the P-value from a chi-square test of the deviation from Hardy-Weinberg Equilibrium (HWE, * reported is the raw uncorrected p-value, the Bonferroni threshold p-value for 19,703 comparisons at α=0.05 level is 0.05/19703 = 0.00000254), the observed heterozygosity (Ho), the expected heterozygosity based on HWE (He), and the minor allele (Q) frequency (MAF). Populations are numbered according to Table 1, and the colored font corresponds to the lineage of the population (blue, North Coastal Lineage; red, South Coastal Lineage; green, Interior Columbia River Stream-Type Lineage)
PCA-adegenet_neutralSNPs
Input file for PCA in adgenet for all populations; 5,007 putatively adaptive SNP