Gp-pat-1 SNPs Associated with Virulence on GpaV_vrn

A 16.4 KB dataset by Arno S. Schaveling, last updated on 2026-05-06. It provides an overview of four single nucleotide polymorphisms (SNPs) located inside the coding sequence of the Gp-pat-1 gene, previously associated with virulence on GpaV_vrn. The dataset includes SNP positions on two genome scaffolds, amino acid changes, and association analysis p-values.

Use Cases

• Validate SNP associations with virulence based on FDR-corrected p-values from AMPOP02 and AMPOP10 analyses.
• Map genetic variants to amino acid changes based on the ref_aa and alt_aa columns.
• Compare SNP positions across different genome assemblies (Rookmaker and D383 scaffolds).
• Annotate functional consequences of SNPs based on the provided annotation field.

Strengths

• Provides FDR-corrected p-values from two distinct association analyses (AMPOP02 and AMPOP10).
• Includes mapping of SNPs to amino acid positions and changes, linking genotype to potential phenotype.
• Positions are provided on two different genome scaffolds (Rookmaker and D383) for cross-reference.
• Dataset is openly available under a CC-BY-4.0 license.

Limitations

• Row count is unknown, which may limit suitability assessment.
• Column-level documentation is absent; field semantics must be inferred after download.
• The dataset's 16.4 KB size indicates a very limited scope, containing only four specific SNPs.

Provenance

Source

figshare

Collection Method

Likely derived from genome-wide association studies (GWAS) on nematode populations.

Time Range

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Freshness

Last updated 2026-05-06 17:39:10; freshness should be verified.

Geography

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