vcf files with raw and filtered SNPs of 24 samples of Posidonia oceanica

These files contain single nucleotide polymorphism (SNP) datasets derived from whole-genome resequencing of 24 Posidonia oceanica samples. Genomic DNA was sequenced using the Illumina platform (150 bp paired-end reads) and aligned against the P. oceanica reference genome Po_2 version 1.0 (NCBI assembly accession GCA_037176725.1). Raw SNP discovery was performed using the snpArcher pipeline (https://snparcher.readthedocs.io/en/latest/). Variant filtering was subsequently conducted with bcftools v1.16 (https://samtools.github.io/bcftools/bcftools.html) using custom parameters to retain high-confidence polymorphisms. Filtering steps included: a) Removal of insertions/deletions (indels) and non-biallelic variants.b) etention of SNPs with per-sample sequencing depth between 8 and 30 reads (FORMAT/DP > 8 and FORMAT/DP < 30).c) Exclusion of low-quality variants (QUAL > 30).d) Removal of variants with more than 10% missing data across samples (F_MISSING < 0.1).e) Retention of variants with a minor allele count (MAC) ≥ 2 across the dataset.f) Retention of variants with a mean sequencing depth greater than 10 across all samples (MEAN(FORMAT/DP) > 10).g) To reduce redundancy caused by linkage disequilibrium (LD), an additional SNP set was generated by LD pruning using PLINK v2.0.0-a.6.2LM (https://www.cog-genomics.org/plink/2.0/). Pruning was performed with the --indep-pairwise algorithm using a 50 kb window size, 5 SNP step size, and r² threshold of 0.2. Because the dataset contained fewer than 50 samples, the --bad-ld option was used to allow LD calculations under these conditions. The three files correspond to: 1) Raw SNP dataset obtained directly from the snpArcher variant-calling pipeline. 2) Filtered SNP dataset containing high-confidence, biallelic SNPs after applying filters for variant quality, sequencing depth, missing data, and minor allele count. This file also includes the LD-pruned SNP dataset, generated after removing linked markers to reduce redundancy due to linkage disequilibrium. 3) Sample metadata file (Excel format) containing detailed information for the 24 Posidonia oceanica samples, including sampling information and associated metadata used in this study.