Chicken Pangenome Graph Resources with Structural Variant Genotypes

1,962 chickens have structural variant genotypes in a VCF file with complete FORMAT annotations. The 10.9 GB collection includes pangenome graphs, pan-transcriptome annotations, and cross-platform SV data for 30 broilers from short- and long-read resequencing. Xinting Yang published this dataset under CC-BY-4.0 in April 2026.

Use Cases

• Constructing and analyzing pangenome graphs based on the provided vg format resources.
• Studying structural variant genotypes and allele frequencies across 1,962 chicken samples.
• Comparing structural variant calls from short-read (NGS) and long-read (TGS) sequencing technologies using the 30-sample cross-platform data.
• Mapping gene-level transcription start sites (TSS) for molecular QTL (molQTL) analysis using the provided pangenome graph coordinates.
• Annotating functional elements on a pangenome graph coordinate system using the provided BED file.

Strengths

• Includes structural variant genotypes for a large cohort of 1,962 chickens.
• Provides cross-platform validation data for 30 broilers sequenced with both NGS and TGS technologies.
• Contains multiple coordinated resources (graphs, annotations, genotypes) in a 10.9 GB package.
• Offers complete FORMAT annotations (GQ, DP, AD) in the VCF files for genotype quality assessment.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment for some analyses.
• The description does not specify the geographic or breed origin of the chicken samples, which may reflect source bias.

Provenance

Source

Xinting Yang

Collection Method

Likely generated from resequencing data (short-read NGS and long-read PacBio HiFi) and pangenome construction pipelines like PSVCP.

Freshness

Last updated 2026-04-24 08:26:23; freshness should be verified.