# MSI The DRAGEN microsatellite instability status (MSI) module assesses microsatellite sites for evidence of microsatellite instability, relative to a set of baseline normal samples that are based on Jensen– Shannon (JS) distance (an information entropy metric). In total, there are 2343 selected MSI sites with 6 or 7 single nucleotide repeats in the panel. For MSI sites with 500 or more spanning duplex collapsed reads, JS distance is calculated using a test sample vs baseline normal samples, and then any two baseline normal samples. If the JS distance is significantly higher in the test sample vs baseline normal with p-value ≤ 0.01 and the JS distance difference is ≥ 0.02, the site is considered unstable. The final MSI score aggregates all JS distance across all unstable sites. The input is the BAM file from the DNA alignment and read collapsing step, and the output is an MSI metric file. --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://help.tso500software.illumina.com/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-methods/msi.md?ask= ``` The question should be specific, self-contained, and written in natural language. 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.