**** 18 Nov 2012 **** RAD sequencing data for 5 populations of westslope cutthroat trout with introgression from rainbow trout - for details on sample preparation and analysis see Hohenlohe et al. (2013) Genomic patterns of introgression in rainbow and west slope cutthroat trout illuminated by overlapping paired-end RAD sequencing. Molecular Ecology in press - final manuscript and other information available at: http://webpages.uidaho.edu/hohenlohe/publications.html Files: 1) Raw Data (nicola.tar.gz, dutch.tar.gz, meadow.tar.gz, lowhay.tar.gz, tepee.tar.gz) -- 5 tar.gz folders of reads in fastq format, one population per folder. These have been sorted by barcode into individuals and filtered for quality using the Stacks component process_radtags.pl. For each individual, there is a file of forward reads and one of reverse reads (pairs in the same order), plus a file of remainder reads filtered from further analysis. Populations are as follows (see Hohenlohe et al 2013 for more information): - Nicola lat 48.556 long -114.345 - Dutch lat 48.657 long -114.070 - Meadow lat 48.655 long -114.235 - Lower Hay lat 48.795 long -114.289 - Tepee lat 48.887 long -114.401 2) RAD contigs (FinalContigs120611.fa) -- One fasta file of 77,141 contigs, one assembled at each RAD locus as described in Hohenlohe et al. (2013). Genotypes at SNPs were based on alignments of raw reads (files above) to this reference. Contig names provide the RAD locus ID from Stacks analysis and the length of the contig. 3) SNP genotypes (genotyped_121009.txt) -- This file gives SNP genotypes at each of the 3180 diagnostic SNPs (see Hohenlohe et al 2013 for details). Each line corresponds to one SNP. The first column is the contig name (from 2 above), second column is the SNP position in the contig, and remaining 94 columns are genotypes coded as W (homozygous westslope cutthroat trout), H (heterozygote), R (homozygous rainbow trout), or 0 (missing genotype). Columns are in order of populations, omitting some individuals that were screened for low coverage: - Meadow (individuals 1-11, 13-19) - Lower Hay (individuals 1-20) - Dutch (individuals 1-18) - Nicola (individuals 2-22) - Tepee (individuals 1-17)