A Torrent Suite™ Software run report contains statistics and quality metrics for your run. From a run report you can do the following:

• Review pre-alignment metrics such as bead loading, Ion Sphere™ Particle (ISP) density, total number of reads, filtering numbers, and mean read length

• Review alignment metrics such as total aligned bases, average coverage, and mean raw accuracy

• Download the result set

• Manually run a plugin on the run results

• Review the planned run settings

• Review the test fragments used with this run and test fragment quality metrics

• Review Chef Summary

• Review Calibration Report

• Review analysis information and Torrent Suite™ Software versions

• Review the analysis log

• Generate a zip file for technical support

A run report is divided into the following main areas:

• Report header - Use this section to download the run report or summary in PDF format, to review the planned run settings for the run, to reanalyze the run, and to upload the run report output files to Ion Reporter™ Software. Also, change to a different result set for the same sample and use links to move to the Output Files or Plugin Summary sections of the run report.

• Barcode Summary - For barcoded runs, a barcode summary table appears above the Plugin Summary area.

• Unaligned - Metrics taken before alignment, including bead loading, ISP density and other metrics, read and filtering metrics, and read length.

• Aligned - Metrics on the aligned reads.

• Plugin Previews - Summary output of completed plugins (only if supported by the plugins that executed on this analysis).

• Output Files - Download read files for both before alignment and after alignment. Full-chip Ion Proton™ analyses only offer the download of aligned reads.

• Plugin Summary - Links to plugin reports and allows you to run plugins manually on a completed sequencing run.

• Test Fragments - Displays information about the performance of each test fragment included in the experiment.

• Chef Summary - Displays Ion Chef™ templating results.

• Calibration Report - Displays pre-base calibration and calibration arguments.

• Analysis Details - Displays a set of information about the sequencing run environment. For example, run date, sample name, chip type, instrument name, barcode set, and so on.

• Support - Displays a link to the report log and a link to generate information for technical support.

• Software Version - Displays the version of Torrent Suite™ Software and its modules.