> 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/distribution-of-access-panel-a-coverage-values.md).

# Distribution of ACCESS panel A coverage values

Ensure consistent coverage across ACCESS bait (or “probe”) regions

![](https://2763969089-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-M52gq1rRSDQOKMQGEuR%2F-M9Z39Nd7c6cJRknLQBm%2F-M9Z66kvDfnNGvCCiuKm%2FScreen%20Shot%202020-06-11%20at%2012.00.22%20PM.png?alt=media\&token=01f4df9a-5529-4992-aa7d-f1443222b577)

**Theoretical Method**

Coverage of each genomic region in the ACCESS panel is grouped on a per-sample basis, and a distribution of these values is plotted. Each sample is normalized by the median coverage value of that sample to align all peaks with one another and correct for sample-level differences. 

**Technical Methods**

* Tool Used:
  * Waltz CountReads
  * aggregate\_bam\_metrics.sh
  * tables\_module.py
  * plots\_module.r
* Input
  * Collapsed, unfiltered bam
  * ACCESS pool A bed file
* Output
  * intervals-coverage-sum.txt (one per bam type / pool combination)
  * coverage\_per\_interval.txt (one per sample / bam type / pool combination)
  * coverage\_per\_interval\_A\_targets\_All\_Unique.txt (this is used for graph above)
    *  ~~(DMP specific format?)~~

**Interpretations**\
Each distribution should be unimodal, apart from a second peak on the low end due to X chromosome mapping from male samples. Narrow peaks are indicative of evenly distributed coverage across all bait regions. Wider distributions indicate uneven read distribution, and may be correlated with a large GC bias. Note that the provided bed file lists start and stop coordinates of ACCESS design probes, not the actual genomic target regions.

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