DOI: 10.5061/dryad.sqv9s4ncc
title: Single nucleotide polymorphism (SNP) genotypes of Cashmere goat (Capra hircus) populations from Mongolia

description: This dataset comprises comprehensive data on Genetic characterization of
 cashmere goat (Capra hircus) populations in Mongolia, collected over a
 period of 2020-2022.  From the 14 populations, 1256 goats were
 genotyped using Axiom Goat 60K SNP. The dataset is structured into text
 document, including eight populations were recognised as ‘breed’ (ATU,
 ULU, ZBL, ERK, ZJE, BDU, GGS, UBR), two populations had the status of
 ‘strain/line’ (GLU, BUU), and four populations were local populations
 without breed or strain status (MSK, KHU, TSK, TEU). Data values included
 12 out of 14 populations were categorized into three socio-economic
 regions, according to their geographical reference. Populations GGS and
 UBR were categorized into the same ‘region’ called ‘Outliers.  
 The dataset offers substantial reuse potential for researchers focusing on
 animal breeding and genetics, particularly in Genitic diversity analysis.
 The data is stored in text format, allowing for easy integration with
 common statistical and analytical tools. Metadata accompanying the dataset
 provides detailed descriptions of each variable, facilitating its use by a
 broad audience.   Ethical considerations were carefully addressed
 during data collection, ensuring compliance with  ethical
 standards. Access to the dataset is not governed by any licensing
 agreements, ensuring that usage aligns with ethical and legal standards.
 Potential users are not encouraged to review the accompanying
 documentation to understand the limitations and appropriate use cases for
 this dataset.
description: The data set contains raw Affymetrix (Axiom Goat 60K SNP array)
 single nucleotide polymorphism (SNP) genoptypes, used for genetic
 characterization of 14 cashmere goat populations in Mongolia. The data set
 consists of 41007 SNP genotypes for 1256 goats in nucleotide ACGT coding.
 The missing genotypes are denoted as "---".
 The following goat populations of Mongolia are
 represented: 
 <strong>Breeds</strong> Alai Ulaan
 (ATU), Ulgiin Ulaan (ULU), Zavkhan Buural (ZBL), Erchim Khar (ERK), Zalaa
 Jinst Edren (ZJE), Bayandelger Ulaan (BDU), Govi Gurvan Saikhan (GGS),
 Uuliin Bor (UBR); Lines: (Galshar Ulaan (GLU) and Bumbugur Ulaan
 (BUU) <strong>Local
 populations</strong> Mungun Sort Khar (MSK),
 Khuvchiin Ulaan (KHU), Tsagaan Ovoo Khar (TSK) and Teeliin Ulaan
 (TEU).
description: # Single nucleotide polymorphism (SNP) genotypes of Cashmere goat (*Capra
 hircus*) populations from Mongolia ## Description of the data and file
 structure The descriptions of the columns are as follows: * *probeset_id*:
 The Affymetrix unique identifier for the set of probes used to detect a
 particular Single Nucleotide Polymorphism (SNP). * *Columns starting with
 "MNG_GAU"*: Individual identification of genotyped goats *
 *Affy_SNP_ID*: The Affymetrix unique identifier for the set of probes used
 to detect a particular SNP. * *Chr_id*: The chromosome on which the SNP is
 located * *Start*: The nucleotide base start position where the SNP is
 found. The genomic coordinates given are in relation to the current genome
 version and may shift as subsequent genome builds are released. * *Stop*:
 The nucleotide base stop position where the SNP is found. The genomic
 coordinates given are in relation to the current genome version and may
 shift as subsequent genome builds are released. * *Strand*: Genomic strand
 that the SNP resides on. * *dbSNP_RS_ID*: The dbSNP ID that corresponds to
 this probe set or SNP. * *Flank*: The nucleotide sequence surrounding the
 SNP. This is a 33-mer sequence with 16 nucleotides on either end of the
 SNP position. The alleles at the SNP position are provided in the
 brackets. * *Allele_A*: Allele A following the naming convention (see
 details below). * *Allele_B*: Allele B following the naming convention
 (see details below). * *Associated_Gene*: Associations (if any) with human
 genes by comparing the genomic locations of the SNPs to genomic alignments
 of human mRNA sequences * *Ordered_Alleles*: A list of alleles
 alphabetically ordered by abstract allele code. * *affy_snp_id*: The
 Affymetrix unique identifier for the set of probes used to detect a
 particular SNP * *CR*: Call rate (CR) is the percentage of samples with a
 genotype call other than "No Call" for the SNP. * *FLD*:
 Fisher's Linear Discriminant (FLD) is a measure of the cluster
 quality of a probeset. * *HomFLD*: HomFLD is a version of FLD computed for
 the homozygous genotype clusters. HomFLD is undefined for probesets
 without two homozygous clusters. * *HetSO*: Heterozygous Strength Offset
 measures how far the heterozygous cluster center sits above the homozygous
 cluster centers in the Size dimension (Y position). * *HomRO*: Homozygote
 Ratio Offset is the distance to zero in the Contrast dimension (X
 position) from the center of the homozygous cluster that is closest to
 zero. * *Nclus*: The number of genotype clusters. * *n_AA*: The number of
 AA calls. * *n_AB*: The number of AB calls. * *n_BB*: The number of BB
 calls. * *n_NC*: The number of NoCall calls, including NoCall_1 (haploid).
 * *hemizygous*: Hemizygous flag is 1 if the probeset measures chromsome Y
 or mitochondrial DNA, indicating that diploid genotypes are not possible.
 Otherwise the flag is 0. * *gender_metrics*: Also knowns a s "sex
 metrics". The metrics are calculated by sex depending on the
 chromosomes. What is displayed is restricted to the sex in the sex_metrics
 column. For chromosomes MT and CP: all sexes, no splitting by sex.
 Chromosome X: all metrics on females, some metrics on males. Chromosome Y:
 all metrics on males, a small number of metrics on females. *
 *ConversionType*: Probeset classification * *BestProbeset*: BestProbeset
 flag is available when multiple probesets are mapped to the same SNP
 (affy_snp_id) by a ps2snp file. A probeset is selected based on the
 priority order of the conversion types. BestProbeset flag is 1 when it is
 the best or only probeset for a SNP. Otherwise the flag is 0. *
 *BestandRecommended*: BestandRecommended flag is 1 if BestProbeset is 1
 and the ConversionType belongs to the Recommended set of conversion types.
 Otherwise the flag is 0. * *HomHet*: HomHet flag is 1 if, when two diploid
 genotype clusters are present, one cluster is homozygous and the other is
 heterozygous. Otherwise the flag is 0. * *MinorAlleleFrequency*: The
 proportion of the less frequent allele. * *H.W.p-Value*: Hardy Weinberg
 p-value significance measure * *Call Modified*: Call Modified flag is True
 if any calls for this probeset are changed since the batch results were
 first created. If no calls are changed the flag is False. ### A-B SNP
 naming convention the following naming convention is used to assign allele
 nucleotide bases to the "Abstract" allele codes "A"
 and "B": 1. SNPs are fixed on the forward strand of the
 design-time reference genome. 2. For AT or CG SNPs (SNP alleles are A/T or
 C/G), the alleles are named in alphabetical order (A and C are the
 "A" alleles, in these cases); 3. For non-AT and non-CG SNPs,
 allele A is A or T, allele B is C or G; 4. For indels, allele A is -,
 allele B is the insertion. 5. For multi-base alleles, the alleles are
 named in alphabetical order. (For [AGT/TTA], AGT would be "Allele
 A". For [GGT/TTA], GGT would be "Allele A".) More
 information in the "Probeset summary table definitions" chapter
 of Axiom Analysis Suite USER GUIDE. ## Code/Software The data was prepared
 using the Axiom Analysis Suite.