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).
Resources
4 resources available
-
nectar_phenotype.xlsx
XLSX -
Approach2_Imputed_biallelic_singleCopy_minQ100_maxM0.75_maf0.05_ChiSquareFilterP0.1.vcf
VCF -
Approach3_Imputed_biallelicSNPs_ChiSquareFilterP0.1.vcf.gz
GZ -
Approach1_Imputed_biallelic_singleCopy_minQ100_maxM0.75_maf0.05.vcf.gz
GZ
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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.) |
