> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/genome-overview/ideogram-mode.md).

# Ideogram mode

**Ideogram** is the default mode of the [**Genome View** tab](/emedgene/emedgene-analyze-manual/reviewing_a_case/genome-overview.md). It shows a genome ideogram and a genome viewer for reviewing copy number variants (CNVs) and loss of heterozygosity or regions of homozygosity (LOH/ROH) in the proband:

* The genome ideogram marks CNV and LOH/ROH events on every chromosome.
* The genome viewer shows the data tracks for the whole genome or for a single chromosome.

The **Ideogram** mode is available for whole genome sequencing (WGS), whole exome sequencing (WES), and array cases.

<div data-with-frame="true"><figure><img src="https://4225924541-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F2YO86ZgkG5vXGkBAMT71%2Fuploads%2FVOa91eTNTQ5ZUIi71SEo%2Fv41_genome_view.png?alt=media&#x26;token=b6d6bd86-26ea-4e64-ac67-435ea6989f38" alt="Genome View tab in Ideogram mode"><figcaption><p><strong>Genome View</strong> tab in <strong>Ideogram</strong> mode.</p></figcaption></figure></div>

## Genome ideogram

The ideogram shows chromosomes 1–22, X, and Y, and marks CNV and LOH/ROH events on each chromosome.

* **Deletions (DEL)** appear in <mark style="color:red;">red</mark>, to the left of the chromosome.
* **Duplications (DUP)** appear in <mark style="color:blue;">blue</mark>, to the right of the chromosome.
* **LOH/ROH** events appear in <mark style="color:yellow;">yellow</mark>, over the chromosome.

{% hint style="info" %}
Variants with no coverage and reference calls are excluded from the ideogram.
{% endhint %}

### Filter events by size

Use the **Variant size filter** to show only events within a size range.

The available values are `50 bp`, `1 KB`, `10 KB`, `50 KB`, `100 KB`, `1 MB`, `10 MB`, and `Max`, which sets no upper limit. The default range is `50 KB` to `Max`.

The ideogram shows only the 500 largest variants.

### Explore events

Hover over an event to view:

* Chromosome, start and end positions, and size, for example `chr1:100000-200000 (100 KB)`
* Cytoband range in ISCN nomenclature, for example `p12.3–q11.2`
* Event type: **DEL**, **DUP**, or **LOH/ROH**
* Number of affected genes

Select an event to open its **Variant page**.

## Genome viewer

The genome viewer under the ideogram shows the data tracks for the proband. The tracks that appear depend on the case type and on the visualization files in the case. For the file types and how to supply them, see Visualization files.

| Track                  | Case types          |
| ---------------------- | ------------------- |
| **Log R Ratio**        | Array               |
| **TNS**                | WGS                 |
| **B-Allele Frequency** | WGS, WES, and array |
| **LOH/ROH**            | WGS, WES, and array |

All tracks share the X-axis, which shows the genomic region in view.

By default, the genome viewer shows the whole genome. To show a single chromosome, select that chromosome in the ideogram. To return to the whole-genome view, select an empty area of the tab.

## Learn more

<table data-view="cards"><thead><tr><th></th><th></th><th></th></tr></thead><tbody><tr><td><strong>Genome View tab</strong></td><td>Learn about the two modes of the <strong>Genome View</strong> tab and how to switch between them.</td><td><i class="fa-arrow-up-right-from-square">:arrow-up-right-from-square:</i> <a href="/emedgene/emedgene-analyze-manual/reviewing_a_case/genome-overview.md">Learn more</a></td></tr><tr><td><strong>Colocation map mode</strong></td><td>Review colocation data for the whole genome in TruPath cases.</td><td><i class="fa-arrow-up-right-from-square">:arrow-up-right-from-square:</i> <a href="/emedgene/emedgene-analyze-manual/reviewing_a_case/genome-overview/colocation-map-mode.md">Learn more</a></td></tr></tbody></table>


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