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Data for: Variant filters using segregation information improve mapping of nectar-production genes in sunflower (Helianthus annuus L.)

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DataCite Commons2025-05-27 更新2025-06-14 收录
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https://agdatacommons.nal.usda.gov/articles/dataset/Data_for_Variant_filters_using_segregation_information_improve_mapping_of_nectar-production_genes_in_sunflower_Helianthus_annuus_L_/28886726
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资源简介:
<b>Genotypic Data (VCFs):</b>All VCF files contain imputed, biallelic SNPs derived from the same population but differ in the filtering strategies applied.<code>Approach1_...vcf.gz</code>: Filtered using hard thresholds (minQ ≥ 100, max Missing ≤ 0.75, MAF ≥ 0.05, inferred single copy).<code>Approach2_...vcf.gz</code>: Applies the same hard filters as Approach 1, with an additional Chi-Square filter (p-value ≤ 0.1).<code>Approach3_...vcf.gz</code>: Filtered using <i>only</i> a Chi-Square filter (p-value ≤ 0.1) on imputed, biallelic SNPs.<b>Phenotypic Data (XLSX):</b><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>).

<b>基因型数据(VCFs(Variant Call Format文件)):</b>所有VCF文件均包含源自同一群体的经填充的双等位基因单核苷酸多态性(Single Nucleotide Polymorphisms, SNPs),仅所采用的过滤策略存在差异。<code>Approach1_...vcf.gz</code>:采用硬过滤阈值进行过滤(最低质量值minQ ≥ 100、最大缺失率max Missing ≤ 0.75、最小等位基因频率(Minor Allele Frequency, MAF)≥ 0.05,且推断为单拷贝)。<code>Approach2_...vcf.gz</code>:采用与方法1一致的硬过滤规则,并额外添加卡方(Chi-Square)过滤(p值(p-value)≤0.1)。<code>Approach3_...vcf.gz</code>:仅对经填充的双等位基因单核苷酸多态性(SNPs)采用卡方(Chi-Square)过滤(p值(p-value)≤0.1)进行筛选。<b>表型数据(XLSX):</b><code>nectar_phenotype.xlsx</code>:包含该群体的表型测量数据,其中包含个体标识符<code>ID</code>以及花蜜体积数据<code>nectar_mm_T</code>与<code>nectar_mm</code>。
提供机构:
Ag Data Commons
创建时间:
2025-05-27
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