Reanalysis of public WES data SRR4088561 for RAG1-associated severe combined immunodeficiency using Galaxy

Educational-diagnostic Galaxy WES reanalysis of public SRA run SRR4088561, focused on SCID-associated genes and the RAG1 c.2308G>A, p.E770K / p.Glu770Lys variant. The deposit contains quality-control outputs, annotation summaries, filtered SCID-panel tables, RAG1 variant annotation files, depth checks and workflow documentation. The analysis was performed in Galaxy and includes read quality control, adapter trimming, mapping to GRCh38/hg38, BAM preparation, FreeBayes variant calling, SnpEff and VEP annotation, SCID-panel filtering and local depth assessment of the RAG1 p.E770K position. This is an educational and portfolio-oriented reanalysis, not a clinically validated diagnostic report. The detected RAG1 p.E770K variant has low local coverage in this analysis (DP=2; AD=0,2), so it requires cautious interpretation and independent validation.