DOI: 10.5061/dryad.xsj3tx9nk
title: SNP data (DArTseq) for population genomics of Araucaria bidwillii

description: We took Araucaria bidwillii leaf DNA samples from a total of 31 sites and
 171 samples, representing 3 sites from a northern population in the
 Australian Wet Tropics and 28 sites from a southern population in
 Southeast Queensland, Australia. SNP data was obtained from
 genotyping-by-sequencing platform Divesity Arrays Technology (DArTseq) and
 the resultant dataset has not been processed for quality control.
description: # Araucaria bidwillii genomic data (DArTseq)
 [https://doi.org/10.5061/dryad.xsj3tx9nk](https://doi.org/10.5061/dryad.xsj3tx9nk) Unprocessed SNP dataset of Araucaria bidwillii. ## Description of the data and file structure Data format: SNP data in 2 Rows Format. Each allele scored in a binary fashion ("1"=Presence and "0"=Absence). Heterozygotes are therefore scored as 1/1 (presence for both alleles/both rows). Missing data denoted as "-".   | **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 |