Data from: Genome-wide analysis of SNPs is consistent with no domestic dog ancestry in the endangered Mexican wolf (Canis lupus baileyi)

READMEPlease read for more information and md5 checksums for the contents of this data repository.MW raw dataRaw fluorescence data from the BeadChip analysis. This is RAW, UNPROCESSED data.MW_raw_data.tar.gzMexican Wolf unprocessed genotypesRaw, Mexican wolf genotypes prior to any filtering in the standard PLINK format.MW.pedMexican wolf raw SNP locationsRaw, Mexican wolf SNP locations prior to any filtering in the standard PLINK format.MW.mapMexican Wolf Sample SpreadsheetA simple excel spreadsheet to convert sample IDs between BeadChip IDs, studbook numbers, and museum numbersMW-Samples.xlsxMexican wolf cleaned genotypes PEDThis file contain the filtered set of genotypes and sample information for the 84 samples (83 Mex Wolves and 1 domestic dog). See Table 1 in the manuscript. The format is in the standard PLINK ped format.MW.clean.pedMexican wolf cleaned genotypes MAPThis file contains the SNP position data in the Plink 'map' format for the 62219 SNPs after filtering. See Table 1 in the manuscriptMW.clean.mapMERGED set of genotypes PEDThis file contains the unfiltered set of genotypes and sample information for the 1094 samples (89 Mex Wolves + 371 gray wolves + 634 domestic dogs). See Table 1 in the manuscript. The format is in the standard PLINK ped format.MERGED.pedMERGED set of SNPs MAPThis file contains the SNP position data in the Plink 'map' format for the 169066 SNPs before filtering. See Table 1 in the manuscriptMERGED.mapMERGED clean set of genotypes PEDThis file contains the filtered set of genotypes and sample information for the 1021 samples (88 Mex Wolves + 299 gray wolves + 634 domestic dogs). See Table 1 in the manuscript. The format is in the standard PLINK ped format.MERGED.clean.pedMERGED clean set of SNPs MAPThis file contains the SNP position data in the Plink 'map' format for the 118287 SNPs after filtering. See Table 1 in the manuscriptMERGED.clean.mapMERGED clean pruned set of genotypes PEDThis file contains the filtered set of genotypes and sample information for the 1021 samples (88 Mex Wolves + 299 gray wolves + 634 domestic dogs). See Table 1 in the manuscript. The format is in the standard PLINK ped format.MERGED.clean.pruned.pedMERGED clean pruned set of SNPs MAPThis file contains the SNP position data in the Plink 'map' format for the 74876 SNPs after filtering and LD pruning. See Table 1 in the manuscriptMERGED.clean.pruned.mapLampLD 3-way local admixture results and phased genotypesThis file, once unpacked, contains the results of the local ancestry analysis using LAMP-LD v1.3. In addition to the numerous output files, there is a folder for each of the 38 chromosomes. Each chromosome's folder contains the LAMP-LD results. Most importantly, for each chromosome the phased genotypes generated using Beagle are found in the files chr#_phased.txt. I recommend following the code described at the GitHub page https://github.com/rfitak/Mexican_Wolf_SNPs to know exactly what each of the files represents.LampLD-3way.tar.gz