9.2 Output Structure

All outputs are written under the execution name in the specified results folder.

Primary Outputs

Primary_Outputs/
├── Breakcounts/              # Sites where adjacent breaks were merged and counted
├── Break_Site_Plots/         # Per-base break distribution plots for each non-singleton nominated site
├── Break_Site_Summary_Tables/# Summary of all non-singleton break sites per condition with metadata
├── Homology/                 # Observed break sites intersected with in silico-predicted guide-homologous sequences
├── Nomination_Lists/         # Break sites nominated as putatively induced (frequency- and/or homology-based)
├── report.html               # Run summary — START HERE
└── Sample_Report/            # Per-condition summary of results

QC

QC/
├── Break_Metrics/            # Absolute break counts, normalised counts, and breaks vs library concentration
├── FastQC/
│   ├── Raw_FastQC/           # FastQC quality assessment on raw FASTQ files
│   ├── Trimmed/              # FastQC quality assessment on trimmed FASTQ files
│   └── Trimming/             # Trimming quality assessment
├── Lab_Metrics/              # gDNA yield, library yield, and library concentration plots
├── Mapping/                  # Read loss breakdown (primary reads, unmapped, MAPQ-filtered)
└── Trimming/                 # Per-sample trimming report

sample_manifest_combined.valid.csv — combined sample and nuclease manifest used for the run.

Secondary Outputs

Secondary_Outputs/
├── Bedfiles/                 # Reads converted from FASTQ to BED format
├── Breakcount_Frequencies/   # Unique break counts per break-class for each condition (table + interactive plot)
├── Breakends/                # Genomic coordinates and strand for each break
├── Region_Exclusions_List/   # Genomic regions excluded from analysis
├── Sample_Thresholds/        # Per-sample break count thresholds (TSV)
└── Sequence_Mapping/
    ├── *.bam                 # Mapped reads (primary only, MAPQ ≥ 30)
    ├── pre-filter_flagstat/  # Summary statistics for unfiltered BAM files
    ├── post-filter_flagstat/ # Summary statistics for filtered BAM files
    └── Unfiltered_BAMs/      # Unfiltered mapped reads

Sample Thresholds

The TSV files in Sample_Thresholds/ contain the break count above which the control condition is predicted to produce fewer than 1 site. Sites above this threshold in the treated sample are less likely to be explained by endogenous processes and more likely to be induced by the treatment. Each file includes a threshold with upper and lower bounds.