Coverage Analysis metrics

Coverage metrics are included in a Quality Control report 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.

Coverage analysis metric

Description

Sample Name

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

Barcode

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 non-uniquely mapped can have equally well-aligned reads that are mapped to multiple locations, and are typically mapped randomly to one.

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. An example of a read that is not counted is as follows: If a read overlaps a targeted region on a region that includes a flanking sequence that is aligned, due to poor matching of 5' bases of the read, the read is not counted.

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 if their (5') mapping location being sufficiently close to the end of the amplicon region, taking the read direction (mapping strand) into account.

Uniformity

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.