Chloropyron molle single nucleotide polymorphism genotype data from Contra Costa, Napa, and Solano Counties, California, USA
This dataset contains 253 samples from 11 occurrences of Chloropyron molle subsp. molle, and 3 occurrences of Chloropyron molle hispidum. Genomic markers were generated from ddRAD loci and analyzed using the Stacks v2.60 pipeline. The genotypes for all samples are provided in a VCF file with 40,707 independent loci . A companion sample data file is provided with sample names, and occurrence designations, and other data. These files may be opened and edited in a text editor program, such as Notepad (PC) or BBEdit (Mac). The .vcf file can be loaded into the Stacks population program to calculate genetic diversity statistics, or loaded into R, using vcfR, for further analysis.
Complete Metadata
| accessLevel | public |
|---|---|
| bureauCode |
[
"010:12"
]
|
| contactPoint |
{
"fn": "U.S. Geological Survey, Western Ecological Research Center",
"@type": "vcard:Contact",
"hasEmail": "mailto:gs-b-werc_data_management@usgs.gov"
}
|
| description | This dataset contains 253 samples from 11 occurrences of Chloropyron molle subsp. molle, and 3 occurrences of Chloropyron molle hispidum. Genomic markers were generated from ddRAD loci and analyzed using the Stacks v2.60 pipeline. The genotypes for all samples are provided in a VCF file with 40,707 independent loci . A companion sample data file is provided with sample names, and occurrence designations, and other data. These files may be opened and edited in a text editor program, such as Notepad (PC) or BBEdit (Mac). The .vcf file can be loaded into the Stacks population program to calculate genetic diversity statistics, or loaded into R, using vcfR, for further analysis. |
| distribution |
[
{
"@type": "dcat:Distribution",
"title": "Digital Data",
"format": "XML",
"accessURL": "https://doi.org/10.5066/P13TAP3G",
"mediaType": "application/http",
"description": "Landing page for access to the data"
},
{
"@type": "dcat:Distribution",
"title": "Original Metadata",
"format": "XML",
"mediaType": "text/xml",
"description": "The metadata original format",
"downloadURL": "https://data.usgs.gov/datacatalog/metadata/USGS.67633cd0d34ebad02167e80f.xml"
}
]
|
| identifier | http://datainventory.doi.gov/id/dataset/USGS_67633cd0d34ebad02167e80f |
| keyword |
[
"Grizzly Bay",
"San Pablo Bay",
"Suisun Bay",
"USGS:67633cd0d34ebad02167e80f",
"abundance",
"adaptation",
"annual plant",
"biota",
"habitat suitability",
"population structure",
"remediation",
"restoration",
"sea level rise",
"sea-level change",
"single nucleotide polymorphisms"
]
|
| modified | 2025-07-11T00:00:00Z |
| publisher |
{
"name": "U.S. Geological Survey",
"@type": "org:Organization"
}
|
| spatial | -122.3513, 38.0056, -121.9511, 38.2316 |
| theme |
[
"Geospatial"
]
|
| title | Chloropyron molle single nucleotide polymorphism genotype data from Contra Costa, Napa, and Solano Counties, California, USA |
