# Genome view tab

The Genome view tab is a powerful feature designed to give users a clear, visual overview of the genome and chromosomes in their cases. This feature is especially useful for analyzing large Copy Number Variation (CNV) events and regions of homozygosity/loss of heterozygosity (ROH/LOH) across the genome, providing intuitive filtering and interactive insights for researchers and clinicians.

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### **What is the Genome view tab?**

The Genome View tab is a dedicated section within the Case Page for Whole Genome Sequencing (WGS), Whole Exome Sequencing (WES), and Array data. This tab offers a graphical visualization of genomic data, focusing on CNV and LOH/ROH analysis for proband cases. Users can access this tab directly from the Case Page.

### **Key features**

**Chromosome ideogram**

The chromosome ideogram offers a visual representation of all 23 human chromosomes, with CNV and LOH/ROH events highlighted for intuitive analysis. Here's what you can expect:

Variant types:

* Deletions (DEL): Marked in red, displayed to the left of the chromosome.
* Duplications (DUP): Marked in blue, displayed to the right of the chromosome.
* LOH/ROH (Regions of Homozygosity/Loss of Heterozygosity): Marked in gold, displayed over the chromosome.

{% hint style="info" %}
**Note**: Variants with no coverage or reference (Ref) are excluded.
{% endhint %}

Filtering Options:

* Users can filter segments by size, using a range selector with the following options: 50 bp,1 KB, 10 KB, 50 KB, 100 KB, 1 MB, 10 MB, Max (no filter).
* The default filter is set from 50 KB to Max.

{% hint style="info" %}
**Note**: Only the 500 largest variants are displayed in this tab.
{% endhint %}

Hover and Click Interactions:

* Hovering over a variant displays
  * Chromosome number, start and end positions, and size (e.g., chr1:100000-200000 (100 KB))
  * Cytoband range (e.g., p12.3 - q11.2) based on ISCN nomenclature
  * Variant type (DEL/DUP/LOH/ROH)
  * Number of genes affected
* Clicking on a chromosome refines the genome view below to that chromosome.
* Clicking on a variant opens a detailed Variant Page where many actions and further review can be made.
* Legend: A clear legend explains color coding and icons for DEL, DUP, and LOH/ROH variants for quick reference.

### Genome viewer

The genome viewer provides a deeper dive into the genomic data through three interactive tracks:

* Log R / TNS Track:
  * Displays copy number intensity data using values from the TNS BigWig file or LogR bedgraph.
  * Y-axis ranges from -3 to 3, with increments of 0.4.
  * X-axis displays the genome (whole genome view) or chromosome segments (whole chromosome view).
* BAF Track:
  * Displays B Allele Frequency (BAF) data using values from the BAF BigWig file or BAFbedgraph.
  * Y-axis ranges from 0 to 1, with increments of 0.1.
  * X-axis aligns with the Log R track.
* ROH Track:
  * Indicates regions of homozygosity for further analysis.

Zoom and navigation

* Default View: Displays the entire genome.
* Zoom-In Options: Users can zoom in to view individual chromosomes by clicking on them.
* Interactive Navigation: Clickable chromosomes on the ideogram allow seamless switching between views.