> For the complete documentation index, see [llms.txt](https://cmo-ci.gitbook.io/access-quality-control-v1/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cmo-ci.gitbook.io/access-quality-control-v1/on-target-coverage.md).

# On Target Coverage

Confirming adequate coverage of ACCESS genomic targets

![](https://2763969089-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-M52gq1rRSDQOKMQGEuR%2F-M9Z39Nd7c6cJRknLQBm%2F-M9Z5Mowo5yqREbp8s7I%2FScreen%20Shot%202020-06-11%20at%2011.57.04%20AM.png?alt=media\&token=91fbd651-2589-42e6-8148-0529f84542ab)

**Theoretical Method**

Unlike other coverage metrics from this report which report coverage for bait regions, this graph shows the coverage of actual genomic target regions of the ACCESS A panel 

**Technical Methods**

* Tool Used:
  * Marianas
  * Waltz CountReads
  * aggregate\_bam\_metrics.sh
  * tables\_module.py
  * plots\_module.r
* Input
  * Duplex Bams
  * pool A bed file
* Output
  * waltz\_duplex\_a\_exon\_level\_files (directory of Pool A Exon Targets QC results)
  * waltz-coverage.txt

**Interpretations**

Coverage in this graph should be slightly higher than for the probe-level coverage results, as the calculation is limited to a smaller window of the histogram of coverage values. This metric is relevant for analysts who are more interested in coverage for a particular gene rather than coverage of the baits used to target that gene.