> For the complete documentation index, see [llms.txt](https://cgps.gitbook.io/pathogenwatch/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/browsing-and-viewing-genomes/genome-reports.md).

# Viewing Genome Reports

## Genome Reports

Each genome has a detailed report associated with it, comprising its metadata and analysis outputs. The information in the report match the data in the Data Tables, with extra details added. The report can be accessed by clicking on the genome's name (leftmost column, purple) in the Data Tables.

The report includes detailed results for each tool run by Pathogenwatch, e.g. MLST or Genotyphi, along with metadata and assembly metrics such as N50. The version of each tool is also tagged, and a link to the original FASTA provided at the top. Most of the information in the report is also shown in the Data Tables.

To better understand the data included in the Genome Report, refer to the relevant [Analysis Tools](/pathogenwatch/technical-descriptions-of-analysis-tools.md) pages.

<figure><img src="/files/LTnedcHxg6RCnDxgaBkg" alt=""><figcaption><p>Example pages of a Genome Report</p></figcaption></figure>

{% hint style="info" %}
The Genome Report can be downloaded by clicking the download icon in the top left of the screen when the report is in view.&#x20;
{% endhint %}

<figure><img src="/files/XTJmI4i0Fs1ClNGVKQL9" alt=""><figcaption><p>Download Genome Report as PDF</p></figcaption></figure>

### Core genome-based neighbourhood searches

For species where a cgMLST scheme exists, the cgMLST-based clusters can be accessed from within the genome report. In these cases, a "Core Genome Clustering" section will appear in the report. The report's cluster section will be first need initialising by clicking the "Run clustering" button. This will begin a search for near neighbours according to within both yours and any public genomes, and create a set of single-linkage clusters according to the specified cgMLST allele similarity threshold. For details see the [Genomic Neighbourhood Search](/pathogenwatch/technical-descriptions-of-analysis-tools/trees-clustering-and-context-search/cgmlst-clustering.md) documentation.

Once the search is complete, the genomes clustered with the query genome are displayed in the interactive embedded cluster viewer. Below the clusters, a slide bar shows the number of linked genomes at different thresholds, up to the maximum of 50 differences. Selecting different thresholds will display the genomes at that threshold. The "View Clusters" button opens up the clustering in the "[Cluster Viewer](/pathogenwatch/how-to-use-pathogenwatch/genomic-neighbourhood-search/the-cluster-viewer.md)".

<figure><img src="/files/MekedqmXnxSN5zB4TZfE" alt=""><figcaption></figcaption></figure>