RNA Expanded Metrics

RNA 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	Description	Units
PCT_CHIMERIC_READS	Percentage of reads that are aligned as two segments which map to nonconsecutive regions in the genome.	%
PCT_ON_TARGET_READS	Percentage of reads that cross any part of the target region versus total reads. A read that partially maps to a target region is counted as on target.	%
SCALED_MEDIAN_GENE_COVERAGE	Median of median base coverage of genes scaled by length. An indication of median coverage depth of genes in the panel.	Count
TOTAL_PF_READS	Total number of reads passing filter.	Count
GENE_MEDIAN_COVERAGE	The median coverage depth of all genes in the panel.	Count
GENE_ABOVE_MEDIAN_CUTOFF	Number of genes above the median coverage cutoff.	Count
PER_GENE_MEDIAN_COVERAGE	Median deduped coverage across each gene (available in Logs_Intermediates only)	Count
PCT_SOFT_CLIPPED_BASES	percentage of based that were not used for alignment but retained as part of the alignment file	%
RNA_PCT_030_BASES	Average percentage of bases ≥ Q30. A prediction of the probability of an incorrect base call (Q‑score). Troubleshooting: An indicator of sequencing run quality, low Q30 across all samples on a run could be the result of run overclustering.	%