MSI parameters

Note: MSI parameters are available only for analysis workflows that will be released after Ion Reporter™ Software 5.12.

Parameter name

Description

Main tab

MSI Marker Regions

The MSI Marker regions file contains information about the genomic position of the MSI markers, and additional information that is used by the MSI detection algorithm. It is blank by default until the release of analysis workflows that are designed for use with MSI detection.

MSI Baseline File

Select an MSI baseline file—this file contains baseline information that is used if the spike-in that is used does not meet the RMC performance threshold that is set for the sequencing run.

MSI Marker Threshold

The MSI Marker Score (Forward or Reverse) above which the marker will be considered in the Total Marker Score (Forward or Reverse)

Minimal MSI Marker Coverage

The minimum number of filter reads per direction that is required for an MSI Marker Score (Forward or Reverse) to be calculated

MSI-High Threshold

The MSI score above which a sample is considered MSI-High. This score is reported in analysis results. [1]

MSS Threshold

The MSI score below which a sample will report MSS in analysis results. [2]

1 If the MSI Score falls between the MSI-High Threshold and the MSS Threshold, a No Call is reported in the analysis results.
2 If the MSI Score falls between the MSI-High Threshold and the MSS Threshold, a No Call is reported in the analysis results.