Output from Target Region Coverage Analysis
Two outputs are produced from the Target Region Coverage Analysis tool:
- Target region coverage track: Target regions annotated with coverage metrics from the individual samples and statistics across all samples. In the table view, fields for which values did not pass the defined threshold will be highlighted. This makes it possible to quickly spot both poor samples that have multiple failing targets and poor target regions that fail across samples. The latter may be indicative of failing primers.
- Annotation coverage track: This output is produced only if an annotation track is provided. The track table view lists cross-sample statistics for each annotation (e.g. gene) that have at least one overlapping target region. Annotations with no overlapping target region are not displayed.
Target region coverage track
The target region coverage track includes the following annotations:
- Target region length: Length of the target region.
- Metric, min: Sample minimum of the selected metric observed for this target region.
- Metric, max: Sample maximum of the selected metric observed for this target region.
- Metric, mean: Sample mean of the selected metric observed for this target region.
- Metric, median: Sample median of the selected metric observed for this target region.
- Metric, std dev: Sample standard deviation of the selected metric observed for this target region.
- Percentage of samples passing threshold: Percentage of samples for which the metric is equal to or above the threshold.
- Individual per-region statistics track metrics: One column per input track with the individual sample metrics.
- Annotation column: Overlapping annotation (Gene, CDS, mRNA). This column is only present if an annotation track was provided.
Annotation coverage track
The annotation coverage track provides combined statistics for target regions overlapping the same annotation region. If the target regions correspond to exons and a gene track is selected as annotation track, all exons within a gene are combined and statistics are reported per gene. For each sample, the metric values from overlapping target regions are combined to a single metric value. The selected metric dictates how values are combined: Min coverage values are combined by taking the minimum, Max coverage values are combined by taking that maximum and Mean coverage and GC% values are combined as a weighted average, where each target region is weighted by its length. Median coverage values are combined by calculating the median of the values, however, it should be noted that this is different from calculating the median of all base position coverage values contained in the set of target regions.The annotation coverage track includes the following annotations:
- Target regions: Number of overlapping target regions.
- Target region length: Cumulative length of overlapping target regions.
- Metric, min: Sample minimum of the selected metric observed for this annotation region.
- Metric, max: Sample maximum of the selected metric observed for this annotation region.
- Metric, mean: Sample mean of the selected metric observed for this annotation region.
- Metric, median: Sample median of the selected metric observed for this annotation region.
- Metric, std dev: Sample standard deviation of the selected metric observed for this annotation region.
- Individual per-annotation statistics track metrics: One column per input track with the individual sample metrics.