Library Sequencing Data Processing Workflow File

For each repair outcome category, sgRNA enrichment was evaluated by comparing outcome frequencies between individual sgRNAs and nontargeting controls using Fisher’s exact test. Both left-tailed (depletion) and right-tailed (enrichment) p-values were computed together with the corresponding log₂ fold change (log₂FC). sgRNAs with ≤10 reads or without detectable mutations were excluded.To derive gene-level significance, sgRNAs were ranked globally based on direction-specific p-values and log₂FCs. For depletion analysis, sgRNAs showing negative log₂FCs and smaller left-tailed p-values were prioritized, while inconsistent entries were penalized. The same strategy was mirrored for enrichment analysis. Robust Rank Aggregation (RRA) was applied to these ranked lists to compute gene-level RRA scores. Statistical significance was assessed through 20,000 random permutations to generate empirical p-value distributions.To integrate results from the sg3 and sg81 libraries, shared genes were retained, and combined log₂FC values were calculated using outcome-frequency–weighted averages. Corresponding one-tailed p-values were transformed into z-scores, merged by weighted averaging, and back-transformed into integrated p-values. Genes with |log₂FC| > 0.5 and combined p