BCO-DMO ERDDAP
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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/ (external link)
attribute NC_GLOBAL doi String 10.26008/1912/bco-dmo.998738.1
attribute NC_GLOBAL infoUrl String https://osprey.bco-dmo.org/dataset/998738 (external link)
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\nfor legal use, since it may contain inaccuracies. Neither the data\nContributor, ERD, NOAA, nor the United States Government, nor any\nof their employees or contractors, makes any warranty, express or\nimplied, including warranties of merchantability and fitness for a\nparticular purpose, or assumes any legal liability for the accuracy,\ncompleteness, 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

 
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