Coverage Analysis metrics

Coverage metrics are included in a Quality Control report and can be added to a final report template if the coverageAnalysis plugin was run in Torrent Suite™ Software, before data was transferred to and analyzed in Ion Reporter™ Software. These metrics describe the level of sequence coverage for target genomic regions.

To download a report that contains the metrics, click the Download link in the Coverage Report column of an open Quality Control report. To create a final report template, see Final reports.

Coverage analysis metric


Sample Name

The name of the sample, as it was entered into the Planned Run for Torrent Suite™ Software.


The name of the specific barcode in the barcode kit that was used for the sequencing run.

Mapped Reads

The total number of reads that were mapped to the reference in Torrent Suite™ Software.

Reads that are not uniquely mapped can have equally well-aligned reads that are mapped to multiple locations. Such reads are typically mapped randomly to one location.

On Target

The total number of reads that were mapped in the target regions file to any targeted region of the reference in Torrent Suite™ Software.

A read is on target only if at least one aligned base overlaps with a target region. For example, a read is not counted if the read overlaps a targeted region on a region that includes a flanking sequence that is aligned. In this case the read is not counted due to poor matching of 5' bases.

Mean Depth

The summary statistics for reads that are assigned to specific amplicons. Each sequence read is assigned to exactly one of the amplicons specified by the targets file. Reads are assigned to particular amplicon targets based on whether the (5') mapping location is sufficiently near the end of the amplicon region, taking into account the read direction (mapping strand).


The percentage of bases in all targeted regions (or whole‑genome) that is covered by at least 20% of the average base coverage depth reads.

Cumulative coverage is linearly interpolated between nearest integer base read depths.