Processed SNP Data and Genomic Annotations for Cinnamomum

This dataset contains SNP variant data and population genomics analysis results derived from RNA-Seq data of Cinnamomum species. The processed VCF files and population genetics outputs include SNP annotations, allele frequency distributions, linkage disequilibrium analysis, and Fst calculations. These data were used in the study titled "[Your Manuscript Title]" and are made publicly available for further research and validation.

Included Files:

Processed SNP datasets in VCF format

SNP annotations and allele frequency tables

Population genomics analysis results (Fst, LD decay, AFS)

Usage:Researchers can use this dataset for comparative genomics, evolutionary studies, and population structure analysis of Cinnamomum species.

NCBI SRA Data

The raw RNA-Seq data used in this study were retrieved from the NCBI Sequence Read Archive (SRA) under the following accession numbers:

SRR10063926

SRR10063927

SRR10063928

SRR31477125

SRR31477126

SRR31477127

The datasets can be accessed via the NCBI SRA database: https://www.ncbi.nlm.nih.gov/sra 

Reference Genome

The reference genome used for alignment and variant calling was obtained from:

GenBank Accession: GCA_003546025.1

Available at: NCBI Genome Database

Variant Calling and Population Genetics Analysis Tools

The variant calling, SNP annotation, and population genetics analyses were performed using the following tools:

VCFtools: Danecek P, et al. (2011) "The variant call format and VCFtools." Bioinformatics. DOI: 10.1093/bioinformatics/btr330

PLINK: Purcell S, et al. (2007) "PLINK: a tool set for whole-genome association and population-based linkage analyses." American Journal of Human Genetics. DOI: 10.1086/519795