yield_bp_q30

metrics.yield_bp_q30(mqc, biosample_id)

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 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.