Run report metrics before alignment

To assess the sequencing run, you can review the quality metrics for the unaligned reads. Primary pipeline processing, basecalling, and signal processing generate these metrics. The following prealignment metrics are provided in the run report. Access the run report in the Torrent Suite™ Software using the Data tab.

Number	Metric	Description
1	Total Bases	The number of filtered and trimmed base pairs reported in the output BAM file.
2	Key Signal	The average signal for all library ISPs with library key (TCAG).
3	ISP Loading	The percentage of chip wells that contain an Ion Sphere Particle (ISP). The percentage value considers only addressable wells.
4	ISP Loading Density	A visual representation of well loading distribution on the chip surface. Red color indicates areas of high loading and blue indicates areas of low loading.
5	Total Reads	The total number of filtered and trimmed reads independent of length reported in the output BAM file.
6	Usable Reads	The percentage of library ISPs that pass the polyclonal, low quality, and primer-dimer filters. This percentage is calculated by dividing final library ISPs by library ISPs.
7	ISP Summary-Loading	The percentage of chip wells that contain an ISP. The percentage value considers addressable wells.
8	ISP Summary-Enrichment	The predicted number of live ISPs that have a key signal identical to the library key signal or test fragment (TF) key signal. The Percent Enrichment value reported is the number of loaded wells with live ISPs that are Library ISPs or TF ISPs. This number is calculated by dividing wells with live ISPs by the number of wells loaded with ISPs.
9	ISP Summary-Clonality	The percentage of clonal ISPs (all library and TF ISPs that are clonal, not polyclonal). An ISP is clonal if all of its DNA fragments are cloned from a single original template. All the fragments on such an ISP are identical and they respond in unison as each nucleotide is flowed in turn across the chip. This percentage is calculated by dividing the number of ISPs with a single DNA template by the number of live wells.
10	ISP Summary-Final Library	The percentage of reads, which pass all filters, and which are recorded in the output BAM file. This value can be different from the Total Reads due to technicalities associated with read trimming beyond a minimal requirement that results in Total Reads being slightly less than Final Library.
11	Mean Read Length	The average length, in base pairs, of called reads.
12	Median Read Length	The median length, in base pairs, of called reads.
13	Mode Read Length	The mode length, in base pairs, of called reads.
14	Read Length Histogram	The read length histogram is a histogram of the trimmed lengths of all reads present in the output files.

Table 1. Additional metrics are shown when you click the magnifying glass icon in the run report.
Metric	Description
Empty Wells	Percentage of chip wells that do not contain an ISP. The percentage value considers only potentially addressable wells. The percentage is calculated by the number of potentially addressable wells, minus the number of loaded ISPs, divided by the number of potentially addressable wells.
No Template	Percentage of chip wells that do not contain a DNA template. This percentage is calculated by the number of loaded ISPs minus TF ISPs divided by the number of loaded ISPs plus TF ISPs.
Polyclonal	Percentage of polyclonal ISPs (ISPs carrying clones from two or more templates). A high polyclonal percentage indicates that library input is too high and should be titrated down. Enrichment does not filter out polyclonal ISPs, it removes only template-negative ISPs. This percentage is calculated by dividing polyclonal ISPs by live ISPs.
Final Library	Percentage of reads that pass all filters and are recorded in the output BAM file. This value can be different from the Total Reads due to specifications associated with read trimming beyond a minimal requirement resulting in Total Reads being slightly less than Final Library. This percentage is calculated by dividing final library ISPs by clonal ISPs.
% Test Fragments	Percentage of live ISPs with a key signal that is identical to the test fragment (TF) key signal. This percentage is calculated by dividing TF ISPs by clonal ISPs.
% Adapter Dimer	Percentage of ISPs with an insert length of less than 8 bp. This percentage is calculated by dividing primer‑dimer ISPs by clonal ISPs.
% Low Quality	Percentage of ISPs with a low or unrecognizable signal. This percentage is calculated by dividing low quality ISPs by clonal ISPs.
Addressable Wells	Total number of wells on the chip minus excluded wells.
With ISPs	Number (and percentage) of addressable 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. This percentage is calculated by dividing the number of wells with ISPs by total addressable wells.

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Run report metrics before alignment