QC metrics

QC metrics for tumor mutational burden are listed at the top of Analysis Visualization in the TMB tab when you visualize analysis results with Ion Reporter™ Software.

QC metric

Definition

Number of bases used in calculating TMB

Number of bases used as a denominator for Tumor Mutational Burden calculation. Only the number of bases with sufficient base coverage are used in the calculation. You can also select only the exonic regions covered by the panel to be used instead of all the genomic regions.

Number of variant calls

The number of variants that are identified in the sample. Value is reported in the statistic.txt file as Total Variant Count.

For more information, see View the tumor mutational burden statistics.

Deamination score

Deamination is reported as the Estimated SNP proportion consistent with Deamination (low allele frequency C:G>T:A SNVs). The deamination score is can be used to determine the quality of the FFPE sample. For more information on how to minimize the impact of high deamination on a Tumor Mutational Burden score, see Reduce the impact of deamination in low-quality FFPEs.

A deamination QC status of PASS/FAIL is also reported. The threshold for this QC can be adjusted in the analysis workflow parameter settings. For more information, see Annotation parameters.