DNA Expanded Metrics

DNA expanded metrics are provided for information only. They can be informative for troubleshooting but are provided without explicit specification limits and are not directly used for sample quality control. For additional guidance, contact Illumina Technical Support.

Metric (Unit)	Description
TOTAL_PF_READS (count)	Total number of reads that pass filter.
MEAN_FAMILY_SIZE (count)	The sum of the reads in each UMI family divided by the number of families after correction, collapsing, and filtering on supporting reads.
MEDIAN_TARGET_COVERAGE (count)	Median depth across all the unique loci occurring in all regions of the manifest file.
PCT_CHIMERIC_READS (%)	Percent of total number of non-supplementary, non-secondary, and passing QC reads after alignment to the whole genome sequence.
PCT_READ_ENRICHMENT (%)	Percentage of reads that have overlapping sequence with the target regions defined in the sample manifest.
PCT_USABLE_UMI_READS (%)	Percentage of reads that have valid UMI sequences associated with them.
MEAN_TARGET_COVERAGE (count)	Mean depth across all the unique loci defined in the manifest file.
PCT_ALIGNED_READS (%)	Proportion of aligned reads that are non-supplementary, non-secondary and pass QC versus aligned reads that are non-supplementary, non-secondary, mapped and pass QC.
PCT_CONTAMINATION_EST (%)	Percentage contamination estimation. The contamination level is computed by taking 2.0 * the average of the adjusted allele frequencies of all variants that were selected. The adjusted alllele frequency is either the actual allele frequency of the variant if it is less than 0.5, or 1 -allele frequency if it is greater than or equal to 0.5.
PCT_TARGET_0.4X_MEAN (%)	Parentage of target (all locations in manifest) reads that have a coverage depth of greater the 0.4x the mean target coverage depth (see definition above).
PCT_TARGET_100X (%)	Percent target bases (bases in manifest) with fragment coverage > 100X.
PCT_TARGET_250X	Percent target bases (bases in manifest) with fragment coverage > 250X.
PCT_TARGET_50X	Percent target bases (bases in manifest) with fragment coverage > 50X.