> 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/illumina-trupath-genome/data-visualizations-and-analysis/visualize-data-in-dragen-reports.md). # Visualize Data in DRAGEN Reports This page describes how to visualize Short-Tandem Repeats (STR) Data and Multi-Region Joint Detection (MRJD) Outputs in DRAGEN Reports. ### Proximity Plots DRAGEN‑Reports includes a TruPath‑specific manifest to generate reports for TruPath WGS analysis. The manifest file, trupath/germline\_wgs.json, is located in the /opt/dragen-reports/manifests directory. In addition to the standard QC metrics and visualizations provided in DRAGEN WGS reports, the TruPath report includes an additional `Proximity` tab highlighting metrics and visualizations specific to TruPath proximity‑enabled analysis, including: * `Model Fit` – Root mean square error indicating how well the proximity model fits the data. * `Q25 Proximity Rate` – Percentage of read pairs with at least one neighbor above Q25. * `Q25 Proximity Coverage` – Average autosomal coverage of read pairs with link quality above Q25. * `P75 Template Size` – Size of linked template molecules at the 75th percentile. * `Phase Block NG50` – Size of the smallest phasing block required to cover at least 50% of the genome. The `Proximity` tab also includes several visualizations summarizing proximity‑specific characteristics, including: The distribution of template genomic lengths from `.wgs_template_gdist.csv`, as sorted by template size. This log-scaled plot should show a steady increase in linked template molecule sizes from less than 1 kilobase to 100 kilobases or more in length.

The genomic coverage of variant phasing blocks by minimum block size, from `.phase_blocks.gtf`. This plot shows the association between possible minimum phase-block sizes on the log-scaled X-axis, with the total number of non-overlapping genomic bases covered by those selected phase-blocks on the Y-axis. This plot should have a small vertical discontinuity at the minimum phase-block size (around 4kb), followed by a smooth downward curve as stricter minimum phase-block sizes remove more data from the analysis.

The distribution of templates by the number of subpairs they contain, using data from `.wgs_template_subpairs.csv`. This log-scaled plot should show a steady downward slope to the right with a long right-skew, representing the very longest templates. Some variance is expected as the Y-axis falls towards 10 templates and below, due to the small number of molecules involved.

### Short Tandem Repeats (STR) Visualization via REViewer DRAGEN-Reports includes additional tables and visualizations that benefit from the additional proximity information provided by TruPath analysis. The report includes plots generated by [REViewer](https://github.com/illumina/REViewer) for selected loci, which use TruPath results to show the alignments of reads around difficult-to-analyze short tandem repeat (STR) regions such as FMR1, FXN, and HTT.

### Multi-Region Joint Detection Viewer for Paralogous Regions MRJD results are integrated into DRAGEN Reports. For sample‑level reports, MRJD results are available under the **Paralogs** tab. The **Paralog Sets** table provides an overview of each paralogous region analyzed, including the estimated total copy number. Selecting a region opens the **Paralogous Regions** view, which displays haplotype‑resolved variant calls within each paralogous regions. The "Paralogous Regions" view provides visualization of the haplotype-resolved variant calls within each paralogous region. The following example shows the MRJD phased variant calls for *PMS2-PMS2CL*. In this visualization, dark orange indicates the alternative allele at a reference difference site between paralogous regions, light orange indicates the reference allele at a reference difference site, and gray indicates a non‑reference difference site variant. Blocks of light orange represent allele segments likely derived from the primary region in a paralog set, usually containing a functional gene of interest such as **PMS2**. Blocks of dark orange represent segments from other members of the paralog set and often contain related pseudogenes, such as **PMS2CL**. Blocks of gray denote sequence regions that have diverged from all known members of the paralog set. ![MRJD DRAGEN reports Example](https://2122546113-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FCiFAstZpxWHpI6k3vTvF%2Fuploads%2Fgit-blob-05cdbb8bfa0e06da6d9d6183985a4208143891dc%2Fmrjd_dragen_reports_example.png?alt=media) --- # 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://help.bioinsight.illumina.com/illumina-trupath-genome/data-visualizations-and-analysis/visualize-data-in-dragen-reports.md?ask=&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.