ERDDAP > info > bcodmo_dataset_998738_v1

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	FGDC, ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
		data	graph		files	public	[CviMVP Experiment - Parents genotypes] - SNP genotypes of Eastern oysters (Crassostrea virginica) from wild and hatchery populations along U.S. Atlantic and Gulf coasts (collected 2022), used as broodstock in a field experiment (2023–2025) (CAREER: Evaluation of machine learning algorithms for understanding and predicting adaptation to multivariate environments with a Model Validation Program (MVP))		M	background			BCO-DMO	bcodmo_dataset_998738_v1

The Dataset's Variables and Attributes

Row Type	Variable Name	Attribute Name	Data Type	Value
attribute	NC_GLOBAL	cdm_data_type	String	Other
attribute	NC_GLOBAL	Conventions	String	COARDS, CF-1.6, ACDD-1.3
attribute	NC_GLOBAL	creator_email	String	info at bco-dmo.org
attribute	NC_GLOBAL	creator_name	String	BCO-DMO
attribute	NC_GLOBAL	creator_url	String	https://www.bco-dmo.org/
attribute	NC_GLOBAL	doi	String	10.26008/1912/bco-dmo.998738.1
attribute	NC_GLOBAL	infoUrl	String	https://osprey.bco-dmo.org/dataset/998738
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	license	String	The data may be used and redistributed for free but is not intended for legal use, since it may contain inaccuracies. Neither the data Contributor, ERD, NOAA, nor the United States Government, nor any of their employees or contractors, makes any warranty, express or implied, including warranties of merchantability and fitness for a particular purpose, or assumes any legal liability for the accuracy, completeness, or usefulness, of this information.
attribute	NC_GLOBAL	sourceUrl	String	(local files)
attribute	NC_GLOBAL	summary	String	This dataset contains SNP genotype and metadata for broodstock (parent) Eastern oysters (Crassostrea virginica) used in a multi-year common garden field experiment (2023–2025) as part of the project "CAREER: Evaluation of machine learning algorithms for understanding and predicting adaptation to multivariate environments with a Model Validation Program (MVP)" (NSF award #2043905 to Dr. Katie Lotterhos). The goal of the broader project is to assess the ability of machine learning algorithms (MLAs) to predict adaptation of organisms from their DNA sequences. Broodstock were sourced from six wild populations along the U.S. Atlantic and Gulf coasts and two hatchery selection lines. These parents were used in spawning treatments that included monocultures of each population or line, as well as two polyculture (mixed) treatments. The resulting juvenile oysters were deployed at two common garden sites in the Chesapeake Bay (Lewisetta, VA and York River, VA) and monitored over two years. Mortality and phenotype data were collected at six-month intervals to assess fitness across spawn treatments and garden sites, providing a field-based validation of MLA predictions. Broodstock were genotyped on a 200K ThermoFisher Affymetrix Axiom SNP array derived from a 600K array (Gómez-Chiarri et al., 2015; Guo et al., 2023; Modak et al., 2021; Puritz et al., 2024) and aligned to the haplotig-masked C. virginica reference genome (C_virginica-3.0, GCA_002022765.4). The data are archived as two files: (1) a SNP genotype matrix with processed, imputed genotype calls per individual in 0/1/2 integer format (homozygous reference, heterozygous, homozygous alternate), and (2) a SNP metadata file with per-locus information including SNP identifiers, genomic positions, gene annotations, Gene Ontology terms, and population genetic statistics from OutFLANK outlier detection (FST, expected heterozygosity, p-values, q-values, and outlier flags).
attribute	NC_GLOBAL	title	String	[CviMVP Experiment - Parents genotypes] - SNP genotypes of Eastern oysters (Crassostrea virginica) from wild and hatchery populations along U.S. Atlantic and Gulf coasts (collected 2022), used as broodstock in a field experiment (2023–2025) (CAREER: Evaluation of machine learning algorithms for understanding and predicting adaptation to multivariate environments with a Model Validation Program (MVP))
variable	Affx_ID		String
attribute	Affx_ID	long_name	String	Affx_id
attribute	Affx_ID	units	String	unitless
variable	AX_ID		String
attribute	AX_ID	long_name	String	Ax_id
attribute	AX_ID	units	String	unitless
variable	Chromosome		int
attribute	Chromosome	actual_range	int	1, 10
attribute	Chromosome	long_name	String	Chromosome
attribute	Chromosome	units	String	unitless
variable	Position		int
attribute	Position	actual_range	int	591, 104128119
attribute	Position	long_name	String	Position
attribute	Position	units	String	unitless
variable	FST		float
attribute	FST	actual_range	float	-0.0409, 0.9754
attribute	FST	long_name	String	Fst
attribute	FST	units	String	unitless
variable	He		float
attribute	He	actual_range	float	0.0894, 0.5
attribute	He	long_name	String	He
attribute	He	units	String	unitless
variable	pvalues		float
attribute	pvalues	actual_range	float	9.375E-7, 0.9999
attribute	pvalues	long_name	String	Pvalues
attribute	pvalues	units	String	unitless
variable	pvaluesRightTail		float
attribute	pvaluesRightTail	actual_range	float	4.688E-7, 0.9999
attribute	pvaluesRightTail	long_name	String	Pvaluesrighttail
attribute	pvaluesRightTail	units	String	unitless
variable	qvalues		float
attribute	qvalues	actual_range	float	9.345E-4, 0.6295
attribute	qvalues	long_name	String	Qvalues
attribute	qvalues	units	String	unitless
variable	OutlierFlag		String
attribute	OutlierFlag	long_name	String	Outlierflag
attribute	OutlierFlag	units	String	unitless
variable	gene_id		String
attribute	gene_id	long_name	String	Gene_id
attribute	gene_id	units	String	unitless
variable	gene_description		String
attribute	gene_description	long_name	String	Gene_description
attribute	gene_description	units	String	unitless
variable	go_ids		String
attribute	go_ids	long_name	String	Go_ids
attribute	go_ids	units	String	unitless
variable	go_terms		String
attribute	go_terms	long_name	String	Go_terms
attribute	go_terms	units	String	unitless
variable	SNPType		String
attribute	SNPType	long_name	String	Snptype
attribute	SNPType	units	String	unitless
variable	Tile_Std		int
attribute	Tile_Std	actual_range	int	0, 1
attribute	Tile_Std	long_name	String	Tile_std
attribute	Tile_Std	units	String	unitless
variable	Tile_max		int
attribute	Tile_max	actual_range	int	0, 1
attribute	Tile_max	long_name	String	Tile_max
attribute	Tile_max	units	String	unitless
variable	Tile_v3		int
attribute	Tile_v3	actual_range	int	1, 1
attribute	Tile_v3	long_name	String	Tile_v3
attribute	Tile_v3	units	String	unitless
variable	Replicates		int
attribute	Replicates	actual_range	int	2, 4
attribute	Replicates	long_name	String	Replicates
attribute	Replicates	units	String	unitless
variable	Rank		int
attribute	Rank	actual_range	int	2000, 31611
attribute	Rank	long_name	String	Rank
attribute	Rank	units	String	unitless
variable	Group		String
attribute	Group	long_name	String	Group
attribute	Group	units	String	unitless
variable	organism		String
attribute	organism	long_name	String	Organism
attribute	organism	units	String	unitless
variable	cust_id		String
attribute	cust_id	long_name	String	Cust_id
attribute	cust_id	units	String	unitless
variable	on_oystercv		String
attribute	on_oystercv	long_name	String	On_oystercv
attribute	on_oystercv	units	String	unitless
variable	mutID		String
attribute	mutID	long_name	String	Mutid
attribute	mutID	units	String	unitless
variable	chrom_position		float
attribute	chrom_position	actual_range	float	1.000068, 10.32639
attribute	chrom_position	long_name	String	Chrom_position
attribute	chrom_position	units	String	unitless
variable	scaffold		String
attribute	scaffold	long_name	String	Scaffold
attribute	scaffold	units	String	unitless
variable	Sequence		String
attribute	Sequence	long_name	String	Sequence
attribute	Sequence	units	String	unitless
variable	thinned_dataset		String
attribute	thinned_dataset	long_name	String	Thinned_dataset
attribute	thinned_dataset	units	String	unitless

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.