SNP data (DArTseq) for population genomics of Araucaria bidwillii
Data files
May 02, 2024 version files 50.70 MB
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README.md
5.39 KB
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Report_DAra21-6523_SNP_2.csv
50.70 MB
Abstract
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.
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 |