Torrent Browser Analysis Report Guide

Torrent Suite Software space on Ion Community

Run Report Metrics Before Alignment

The Unaligned area in the Run Summary section provides before-alignment metrics. There are three sections in the Unaligned area:

ISP Density

ISP Summary

Read Length

Note: Click the magnifying glass icon in the run report to open a larger image.

ISP Density

This table describes the I on Sphere Particle (ISP) density metrics:

Metric	Description
Total Bases	Number of filtered and trimmed base pairs reported in the output BAM file.
Key Signal	Percentage of LiveISPs with a key signal that is identical to the library key signal.
Bead Loading	Percentage of chip wells that contain a live ISP. (T he percentage value considers only potentially addressable wells.)

The ISP Density image is is a pseudo-color image of the Ion Chip Plate showing percent loading across the physical surface.

Click on the image (or the magnify icon ) to open a larger version:

Key signal

Click the magnify icon in the Key Signal area to open the key incorporation graphs:

The key incorporation graph show the average signal readings for flows of the bases T, C, and A in the library key.

ISP Summary

In the lower rows, the percentages are relative to the total in the next higher row. The first row gives percentages of loaded wells and empty wells, relative to the number of potentially addressable wells on the chip.

This table describes the ISP s ummary metrics:

Metric	Description	Calculation
Total Reads	Total number of filtered and trimmed reads independent of length reported in the output BAM file.	(Not calculated)
Usable Sequence	The percentage of library ISPs that pass the polyclonal, low quality, and primer dimer filters.	Final Library ISPs / Library ISPs
Loading	Percentage of chip wells that contain a live ISP. (T he percentage value considers only potentially addressable wells.)	No. of Loaded ISPs / No. of potentially addressable wells
Empty Wells	Percentage of chip wells that do not contain an ISP. (The percentage value considers only potentially addressable wells.)	(No. of potentially addressable wells minus No. of Loaded ISPs) / No. of potentially addressable wells
Enrichment	Predicted number of Live ISPs that have a key signal identical to the library key signal. The Percent Enrichment value reported is the number of loaded ISPs that are Library ISPs, after taking out Test Fragment ISPs.	Library ISPs / (No. of Loaded ISPs minus TF ISPs)
No Template	Percentage of chip wells that do not contain a DNA template.	(No. of Loaded ISPs minus TF ISPs) minus (Library ISPs) / (No. of Loaded ISPs minus TF ISPs)
Clonal	Percentage of clonal ISPs (all library and Test Fragment ISPs that are not polyclonal). An ISP is clonal if all of its DNA fragments are cloned from a single original template. All the fragments on such a bead are identical (and they respond in unison as each nucleotide is flowed in turn across the chip).	No. of ISPs with single beads / No. of Live Wells
Polyclonal	Percentage of polyclonal ISPs ( ISPs carrying clones from two or more templates).	Polyclonal ISPs / Live ISPs
Final Library	Percentage of reads which pass all filters and which are recorded in the output BAM file. This value may be different from the Total Reads due to technicalities associated with read trimming beyond a minimal requirement resulting in Total Reads being slightly less than Final Library.	Final Library / Clonal ISPs
% Test Fragments	Percentage of Live ISPs with a key signal that is identical to the test fragment key signal.	Test Fragment ISPs /Clonal ISPs
% Adapter Dimer	Percentage of ISPs with an insert length of less than 8 bp.	Primer dimer ISPs /Clonal ISPs
% Low Quality	Percentage of ISPs with a low or unrecognizable signal.	Low quality ISPs /Clonal ISPs

Click the ISP Summary magnify icon to open a larger version with also a table of metrics:

These metrics are described in this table:

Metric	Description	Calculation
Addressable Wells	Total number of addressable wells.	(Not calculated)
With ISPs	Number (and percentage of addressable wells) of wells that were determined to be "positive" for the presence of an ISP within the well. "Positive"is determined by measuring the diffusion rate of a flow with a different pH. Wells containing ISPs have a delayed pH change due to the presence of an ISP slowing the detection of the pH change from the solution.	Wells with ISPs / Total Addressable Wells
Live	Number (and percentage of wells with ISPs) of wells that contained an ISP with a signal of sufficient strength and composition to be associated with the library or Test Fragment key. This value is the sum of the following categories: Test Fragment Library	Live ISPs / Wells with ISPs
Test Fragment	Number (and percentage of Live ISPs) of LiveISPs with a key signal that was identical to the Test Fragment key signal.	Test Fragment ISPs / Live ISPs
Library	Number (and percentage of Live ISPs) of LiveISPs with a key signal that was identical to the library key signal.	Library ISPs / Live ISPs
Library ISPs	Predicted number of Live ISPs that have a key signal identical to the library key signal (the same value as shown in the well information table on the right).	Library ISPs
Filtered: Polyclonal	ISPs carrying clones from two or more templates.	Polyclonal ISPs / Library ISPs
Filtered: Low quality	Low or unrecognizable signal.	Low quality ISPs / Library ISPs
Filtered: Primer dimer	Insert length of less than 8 bp.	Primer dimer ISPs / Library ISPs
Final Library ISPs	Number (and percentage of Library ISPs) of reads passing all filters, which are recorded in the output BAM file. This value may be different from the Total number of reads located in the Library Summary Section due to technicalities associated with read trimming beyond a minimal requirement resulting in Total number of reads being slightly less than Final Library Reads .	Final Library / Library ISPs

Read Length

This table describes the read length metrics:

Metric	Description
Mean Read Length	Average length, in base pairs, of called reads.
Median Read Length	Median length of called reads.
Mode Read Length	Mode length of called reads.

The read length histogramis a histogram of the trimmed lengths of all reads present in the output files.

Click on the histogram to open a larger version:

Icon

For more information on filtering and trimming, please see Technical Note - Filtering and Trimming .

Contents

Torrent Browser Analysis Report Guide

Run Report Metrics

Run Metrics Overview

Run Report Metrics Before Alignment

Run Report Metrics on Aligned Reads

Compare Multiple Run Reports

Barcode Reports

Test Fragment Report

Report Information

Output Files

Plugin Summary

Run the Installed Plugins

Assembler SPAdes Plugin

Coverage Analysis Plugin

ERCC Analysis Plugin

FileExporter Plugin

FilterDuplicates Plugin

IonReporterUploader Plugin

See The Ion Reporter™ Software Integration Guide

Run RecognitION Plugin

SampleID Plugin

TorrentSuiteCloud Plugin

Torrent Variant Caller Plugin

Torrent Variant Caller Parameters

Example Torrent Variant Caller Parameter File

Torrent Variant Caller Output

The Command-Line Torrent Variant Caller

Ion Reporter™ Software Features Related to Variant Calling

Integration with TaqMan® and PCR

Classic Run Reports