# Visualize

This section presents a visualization of the variant in the genome with supporting annotations and surrounding variants.

## Available Tracks

* **Reference** — Reference genome base pair proportions when zoomed out. Base pair letters and amino acids for a given reading frame when zoomed in.
* **Genes** — RefSeq gene track. Blue indicates the - strand and red indicates the + strand. Click a gene to show the reading frame of the selected transcript for the variant (amino acid and position).
* **Protein Domains** — Displays protein domains from UniProt. Blue indicates the - strand and red indicates the + strand.
* **Small variants** — Small variants shown with the reference allele on top and the two alt alleles below.
* **Structural variants** — Structural variants with VCF filter PASS by chromosomal position. The legend to the right of the genome view identifies the events (translocation, inversion, deletion, insertion, and tandem duplication). Translocations begin at the karyogram at the top of the track and connect to chromosomes identified at the bottom of the track.
* **Coverage and copy number variants** — The depth of coverage by chromosomal position. Data points are color-coded by presence of copy number variant calls. The legend identifies the events (gain, gain LOH, neutral LOH, loss, and no call). Hovering over a region will highlight the copy number variant call and clicking provides variant details.
* **B-allele ratio** — The minor allele frequency by chromosomal position.
* **BAMs** — Displays read tracks for each sample (i.e. DNA, RNA, tumor, or normal) aligned in the given region showing substitutions and clipping. Reads can optionally be color-coded and grouped by read strand, first-of-pair, and pair orientation.

> Track availability depends on the VCFs provided by the secondary analysis pipeline.
>
> For example,
>
> * If there's no structural variant VCF provided, then the structural variant track will not be available.
> * If there's no absolute copy number provided in the VCF, then the copy number variant track will not be available.

## Navigation

* To pan, use the pan controls at the top of the section, or click and drag one of the tracks left or right.
* To zoom, use the zoom controls at the top of the section, or hold ctrl and scroll with your mouse or trackpad.


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