Bases ≥ Q30

• ID: yield_bp_q30
• Description: The number of bases in short paired-end sequencing high quality reads, primary alignments, achieving a base quality score of 30 or greater (Phred scale). Duplicated reads and clipped bases are included. No minimum mapping quality is imposed.
• Implementation details: In the NPM-sample-QC reference implementation it is computed using GATK Picard’s CollectQualityYieldMetrics, reporting the PF_Q30_BASES field. Only high quality bases from primary alignments are considered. No filter on duplicated reads, clipped bases or mapping qualiy is applied.
• Type: Integer (eg. 102984371235)
• Functionally equivalent implementations:
  • NPM sample qc
  • ICGC-ARGO dnaalnqc
  • DRAGEN v3.7.6. Extracted from [sample-id].mapping_metrics.csv, key name: MAPPING/ALIGNING SUMMARY,,Q30 bases