
# Title of Dataset: GBS(DArTseq) genotyping scores for 478 rye accessions

the data set contains genotyping scores for 378 diverse rye accessions of different improvement status and worldwide origin.GBS genotyping (DArTseq) was performed at Diversity Array Technology Pty Ltd., Bruce ACT, Australia (http://diversityarrays.com) on DNA isolated from leaf tissue. Genome complexity reduction involved PstI-HpaII digestion. Two adaptors corresponding to two different restriction enzyme (RE) overhangswere used in ligation. The PstI-compatible adapter was designed
to include Illumina flowcell attachment sequence, sequencing primer sequence and ‘‘staggered’’, varying length barcode region. Sequences generated from each lane were processed using proprietary DArT analytical pipeline. These genotyping scores were used for calculation of diversity indices, population structure analyses, clustering analysis and detection of selective sweeps.

## Description of the data and file structure


File type: SNP		
file type: mapping		
"description: SNP 1 Row Mapping Format: ""0"" = Reference allele homozygote, ""1"" = SNP allele homozygote, ""2""= heterozygote and ""-"" = double null/null allele homozygote (absence of fragment with SNP in genomic representation)"		
		
		
Metadata columns in the file:		
AlleleID		Unique identifier for the sequence in which the SNP marker occurs
AlleleSequence		In 1 row format: the sequence of the Reference allele. In 2 rows format: the sequence of the Reference allele is in the Ref row, the sequence of the SNP allele in the SNP row
AvgCountRef		The sum of the tag read counts for all samples, divided by the number of samples with non-zero tag read counts, for the Reference allele row
AvgCountSnp		The sum of the tag read counts for all samples, divided by the number of samples with non-zero tag read counts, for the SNP allele row
AvgPIC		The average of the polymorphism information content (PIC) of the Reference and SNP allele rows
CallRate		"The proportion of samples for which the genotype call is either ""1"" or ""0"", rather than ""-"" "
CloneID		Unique identifier for the sequence in which the SNP marker occurs
FreqHets		The proportion of samples which score as heterozygous.
FreqHomRef		The proportion of samples which score as homozygous for the Reference allele
FreqHomSnp		The proportion of samples which score as homozygous for the SNP allele
OneRatioRef		"The proportion of samples for which the genotype score is ""1"", in the Reference allele row"
OneRatioSnp		"The proportion of samples for which the genotype score is ""1"", in the SNP allele row"
PICRef		The polymorphism information content (PIC) for the Reference allele row
PICSnp		The polymorphism information content (PIC) for the SNP allele row
RepAvg		The proportion of technical replicate assay pairs for which the marker score is consistent
SNP		In 2 rows format: this column is blank in the Reference row, and contains the base position and base variant details in the SNP row. In 1 row format: contains the base position and base variant details
SnpPosition		The position (zero indexed) in the sequence tag at which the defined SNP variant base occurs
TrimmedSequence		Same as the full sequence, but with removed adapters in short marker tags
		
Blast columns (each column starting with is):		
AlnCnt_		Total count of aligning markers / tags with selection criteria described below
AlnEvalue_		E value of the best alignment to an existing model genome
ChromPos_		Position(s) on contig(s) with the best alignment of marker / tag to an existing model genome
Chrom_		Contig(s) with the best alignment of marker / tag to an existing model genome, "n/a" = not available
Blast alignment parameters:		
E-value: 5e-5		
Min sequnence % identity: 70		
		
Aligned to the following blast databases:		
Model reference: Rye_Lo7_2018_v1p1p1		
		
Header rows:		
1		genotype name

## Sharing/access Information
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