Data for: Variant filters using segregation information improve mapping of nectar-production genes in sunflower (Helianthus annuus L.)
Genotypic Data (VCFs):All VCF files contain imputed, biallelic SNPs derived from the same population but differ in the filtering strategies applied.Approach1_...vcf.gz: Filtered using hard thresholds (minQ ≥ 100, max Missing ≤ 0.75, MAF ≥ 0.05, inferred single copy).Approach2_...vcf.gz: Applies the same hard filters as Approach 1, with an additional Chi-Square filter (p-value ≤ 0.1).Approach3_...vcf.gz: Filtered using only a Chi-Square filter (p-value ≤ 0.1) on imputed, biallelic SNPs.Phenotypic Data (XLSX):nectar_phenotype.xlsx: Contains phenotypic measurements for the population, including individual identifiers (ID) and nectar volume data (nectar_mm_T, nectar_mm).
Complete Metadata
| @type | dcat:Dataset |
|---|---|
| accessLevel | public |
| bureauCode |
[
"005:18"
]
|
| contactPoint |
{
"fn": "Smart, Brian, C.",
"hasEmail": "mailto:brian.smart@ndsu.edu"
}
|
| description | <ul><li><b>Genotypic Data (VCFs):</b><ul><li>All VCF files contain imputed, biallelic SNPs derived from the same population but differ in the filtering strategies applied.</li><li><code>Approach1_...vcf.gz</code>: Filtered using hard thresholds (minQ ≥ 100, max Missing ≤ 0.75, MAF ≥ 0.05, inferred single copy).</li><li><code>Approach2_...vcf.gz</code>: Applies the same hard filters as Approach 1, with an additional Chi-Square filter (p-value ≤ 0.1).</li><li><code>Approach3_...vcf.gz</code>: Filtered using <i>only</i> a Chi-Square filter (p-value ≤ 0.1) on imputed, biallelic SNPs.</li></ul></li><li><b>Phenotypic Data (XLSX):</b><ul><li><code>nectar_phenotype.xlsx</code>: Contains phenotypic measurements for the population, including individual identifiers (<code>ID</code>) and nectar volume data (<code>nectar_mm_T</code>, <code>nectar_mm</code>).</li></ul></li></ul><p></p> |
| distribution |
[
{
"@type": "dcat:Distribution",
"title": "nectar_phenotype.xlsx",
"format": "xlsx",
"mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
"downloadURL": "https://ndownloader.figshare.com/files/54026390"
},
{
"@type": "dcat:Distribution",
"title": "Approach2_Imputed_biallelic_singleCopy_minQ100_maxM0.75_maf0.05_ChiSquareFilterP0.1.vcf",
"format": "vcf",
"mediaType": "text/plain",
"downloadURL": "https://ndownloader.figshare.com/files/54026393"
},
{
"@type": "dcat:Distribution",
"title": "Approach3_Imputed_biallelicSNPs_ChiSquareFilterP0.1.vcf.gz",
"format": "gz",
"mediaType": "application/gzip",
"downloadURL": "https://ndownloader.figshare.com/files/54026396"
},
{
"@type": "dcat:Distribution",
"title": "Approach1_Imputed_biallelic_singleCopy_minQ100_maxM0.75_maf0.05.vcf.gz",
"format": "gz",
"mediaType": "application/x-gzip",
"downloadURL": "https://ndownloader.figshare.com/files/54026399"
}
]
|
| identifier | 10.15482/USDA.ADC/28886726.v1 |
| keyword |
[
"Genome sequencing",
"Genomic techniques",
"Sunflower",
"crop genetics",
"data management"
]
|
| license | https://creativecommons.org/publicdomain/zero/1.0/ |
| modified | 2025-05-27 |
| programCode |
[
"005:040"
]
|
| publisher |
{
"name": "Agricultural Research Service",
"@type": "org:Organization"
}
|
| temporal | 2019-04-14/2025-04-14 |
| title | Data for: Variant filters using segregation information improve mapping of nectar-production genes in sunflower (Helianthus annuus L.) |
