9.0 Outputs & Results

This section describes the INDUCE-seq Analysis output reports and visualisations.

Background

The On-Demand INDUCE-seq Solution excludes an amplification step in order to capture breaks in their true proportion. One INDUCE-seq read is therefore equivalent to one digital readout of a break. The propensity of a genomic location to break can be expressed as the frequency of DSBs at that location within the cell population.

INDUCE-seq Analysis detects breaks at single base-pair resolution to accurately resolve endonuclease-induced breaks within a large background of endogenous breaks. The high frequency of breaks at a target location serves as a diagnostic readout of gene editing by an endonuclease, compared to the endogenous break landscape, for both on- and off-target editing.

Output sections

Section	Description
Report	High-level summary HTML file per run.
Output Structure	Full directory tree of all output files.
QC Plots	Sample and library quality control reports.
Breakends	Per-read genomic break coordinates.
Breakcounts	Merged and counted break sites per sample.
Summary TSVs	Tabular summary of all non-singleton break sites per condition.
Nomination Lists	Frequency- and homology-based candidate break sites.
Homology-Based Outputs	Mismatch plots for guide-homologous break sites.
Breaksite Plots	Per-base resolution strand-resolved break visualisations.
Break Count Frequencies Plot	Distribution of break counts across all samples in a run.