A project-aware and contamination-aware re-evaluation of host-unmapped reads in public Silene latifolia sequencing data

This archive contains derived tables, supplementary materials, figures, metadata, and representative command examples supporting a project-aware and contamination-aware re-evaluation of host-unmapped reads in public Silene latifolia sequencing datasets. The associated study reanalyzed 2,686 public S. latifolia SRA runs from multiple BioProjects. After fastp quality control and BWA-MEM2-based host subtraction, 801,976,057 reads remained unmapped, corresponding to 5.49% of reads before fastp filtering and 5.50% of reads retained after fastp filtering. The residual fraction varied by BioProject and library design. The archive includes tables summarizing host-unmapped read fractions, BioProject-level summaries, PRJNA907022 sensitivity analyses, Kraken2/MEGAHIT/BLASTn summaries of Viridiplantae-classified residual reads, contamination-aware genus-level interpretation tables, figure files, software version information, database metadata, and representative command examples. The NCBI nt database used for BLASTn validation was downloaded on 30 May 2026. These files are intended to support transparency and reproducibility. They should not be interpreted as raw sequencing data. Raw sequencing reads remain available from the NCBI Sequence Read Archive under the run accessions and BioProjects listed in the included metadata tables. The derived results should be interpreted cautiously because the original public datasets were not generated as a controlled microbiome experiment and because the residual-read fraction is project-skewed, taxonomically mixed, and contamination-sensitive.