> For the complete documentation index, see [llms.txt](https://docs.omics.ai/products/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.omics.ai/products/workbench/variant-interpreter/reviewing-variants/paralogs.md).

# Paralogs

Some medically important genes sit in **segmental duplications**, regions with a near-identical copy (a paralog) elsewhere in the genome. Short reads struggle to tell the gene apart from its look-alike. Long reads, with specialized analysis (Paraphase), can separate them so variants are assigned to the correct gene. The Paralogs tab surfaces these paralog-resolved calls, one row per gene or region.

## Clinically relevant regions

The **Clinically Relevant** dropdown in the toolbar narrows the table to the curated set of Paraphase genes with an established clinical definition:

* **Clinical**: the curated regions: SMN1, RCCX, PMS2, STRC, IKBKG, NCF1, NEB, F8, and CFC1.
* **Other**: every other region Paraphase reports.

The tab opens with **Clinical** checked. Click **Clear**, or check both options, to see every region.

## The candidate table

| Column                  | Description                                                             |
| ----------------------- | ----------------------------------------------------------------------- |
| **User Classification** | The classification assigned by a reviewer. This column can't be hidden. |
| **Gene / Region**       | The Paraphase gene-family region, shown exactly as called (e.g. SMN1).  |
| **Total CN**            | The total copy number of the gene family for this region.               |
| **Haplotypes**          | The number of haplotypes assembled.                                     |
| **Two-Copy Haplotypes** | Haplotypes present in two copies.                                       |
| **Linked Haplotypes**   | Haplotypes that could be linked across the region.                      |
| **Fusions**             | Fusion events between the gene and its paralog.                         |
| **Genome Depth**        | The sample's mean sequencing depth across the genome.                   |
| **Region Depth**        | The median sequencing depth in this region.                             |
| **Heterozygous Sites**  | Heterozygous sites found in the region.                                 |
| **Homozygous Sites**    | Homozygous sites found in the region.                                   |

**Sample Sex** is available from the **Columns** dropdown. The table is sorted by **Gene / Region** by default. You can sort on every column except **Fusions**.

## Filters

The filter drawer offers:

* **User Classification**: Pathogenic, Likely Pathogenic, VUS, Likely Benign, Benign.
* **Clinically Relevant**: Clinical or Other. This facet mirrors the toolbar dropdown.
* **Sample Sex**: Male or Female.
* Numeric ranges for **Total CN**, **Genome Depth**, **Region Depth (Median)**, **Haplotypes**, **Two-Copy Haplotypes**, **Linked Haplotypes**, **Heterozygous Sites**, **Homozygous Sites**, **Sites for Phasing**, and **Het Sites Not Phased**.

Paralog rows are keyed by gene or region rather than position, so there are no Gene, Chromosome, or Position filters.

## The paralog detail

Opening a row shows summary cards for the region:

* **Paralog Summary**: region, total copy number, sample sex, and the numbers of assembled, two-copy, and linked haplotypes.
* **Sequencing Depth**: median depth and 80th percentile.
* **Phasing Sites**: the sites used for phasing, heterozygous and homozygous sites, and heterozygous sites not used in phasing.
* **Region-Specific Details** and **Fusions**, where the caller reports them.

## The paralog haplotype explorer

The **Paralog haplotype explorer** shows each assembled haplotype and the paralog-specific variants (PSVs) that tell the gene apart from its paralog. Use it to confirm which gene each haplotype belongs to, and to spot gene conversion.

### Views and colour modes

* **Grid** (default): a matrix with one row per haplotype and one column per PSV site.
* **Genomic**: the same haplotypes as lanes along a position ruler, so you can see where the sites fall in the region.

Colour the cells by:

* **Allele state** (default): whether each site matches the reference archetype, carries the alternate (paralog) base, or another base state.
* **Conversion**: highlights sites that look like the other gene (gene conversion) and private bases (candidate de novo). This mode needs per-gene haplotype data; when that is missing it is unavailable.

Hover a site to see its details in the readout strip above the chart. Open **Legend / key** for the meaning of each cell colour and badge.

### Haplotype badges

Each haplotype row carries badges:

* the gene it is assigned to;
* **2-copy**, when the haplotype is present twice;
* **conversion → GENE:n** and **n private**, in **Conversion** mode;
* **▸ n reads**, the reads supporting it.

### Reviewing a haplotype's reads

1. Click a haplotype row. A panel lists the reads supporting it, split into **unique** and **ambiguous** reads.
2. Review each read's PSV pattern to confirm the haplotype is well supported.
3. Close the panel with **✕**.

## How to review

1. Start from the **Clinical** regions.
2. Check **Total CN** and the haplotype counts against what's expected for the gene.
3. Open a region and use the haplotype explorer to confirm that each haplotype is attributed to the intended gene rather than its paralog. Switch to **Conversion** to look for gene conversion.
4. [Classify](/products/workbench/variant-interpreter/classifying-variants.md) the finding so it can be included in the [report](/products/workbench/variant-interpreter/generating-a-report.md).

{% hint style="info" %}
Paralog calls are not included in the Summary tab's priority findings. Review this tab directly for cases where a segmental-duplication gene is relevant to the phenotype.
{% endhint %}

## Background: phasing

Phasing determines which variants sit together on the same physical copy of a chromosome (the same haplotype). Long-read data phases variants across long distances, which is what lets the Interpreter resolve compound heterozygotes and attribute calls to the correct paralog. For how phase is used to tell cis from trans, see [Haplotype phase (cis/trans)](/products/workbench/variant-interpreter/reviewing-variants/haplotype-phase.md).


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation by asking a question.

Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters:

```
GET https://docs.omics.ai/products/workbench/variant-interpreter/reviewing-variants/paralogs.md?ask=<question>&goal=<user_goal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case.

The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.