Percent reads properly paired
- ID: pct_reads_properly_paired
- Description: The percentage of short paired-end sequencing high quality, properly paired reads, primary alignments, mapped on GRCh38 assembly. Duplicated reads 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 properly paired reads mapped on GRCh38 assembly. Duplicated reads are included. No mapping qualiy is applied.
- Type: Float 2 decimal precision (eg. 98.33)
- 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,,Properly paired reads