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 summary 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. (The percentage value considersonly 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 thathave 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 ISPsminus 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 in 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 Live ISPs 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 Live ISPs 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 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