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. | % |
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