Percent reads mapped

• ID: pct_reads_mapped
• Description: The percentage of short paired-end sequencing high quality reads, primary alignments, mapped on GRCh38 assembly. 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 samtools stats, reporting the percentage of reads mapped on GRCh38 assembly. Duplicated reads are included. No mapping qualiy is applied.
• Type: Float 2 decimal precision (eg. 99.78)
• 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,,Mapped reads