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9.3 QC Plots

QC reports are in the QC/ folder. Only plots for which QC metrics were provided will be generated.

Interacting with plots

  • Hover over data points to view exact values and percentages.
  • Legend click to hide or show a metric.
  • Download as PNG using the camera icon (upper-right corner).
  • Pan / Zoom using the corresponding toolbar icons.
  • Reset axis to return to the initial view.

Lab metrics plots

File Description Target
*_gDNA_yield_ng_barchart.html gDNA yield (ng) per sample. ≥ 100 ng
*_gDNA_yield_ng_grouped_barchart.html Average gDNA yield per condition with range. ≥ 100 ng
*_gDNA_yield_ng_v_library_yield_ng_scatter.html Correlation of gDNA yield vs library yield. —
*_gDNA_library_yield_ng_barchart.html Library yield (ng) per sample. —
*_library_yield_ng_grouped_barchart.html Average library yield (ng) per condition with range. —
*_qPCR_conc_pM_barchart.html Library concentration (pM) per sample. ≥ 0.2 pM
*_qPCR_conc_pM_grouped_barchart.html Average library concentration (pM) per condition with range. ≥ 0.2 pM

Break metrics plots

File Description
*_absolute_breaks_barchart.html Absolute break counts per sample.
*_normalised_absolute_breaks_per_ng_of_dna_yield_barchart.html Break counts normalised by ng gDNA per sample.
*_absolute_breaks_grouped_barchart.html Absolute break counts grouped by condition.
*_normalised_absolute_breaks_per_ng_of_dna_yield_grouped_barchart.html Normalised break counts grouped by condition.
*_absolute_breaks_v_qPCR_conc_pM_scatter.html Correlation of absolute break numbers vs qPCR concentration (pM).
*_read_loss.html Read counts at each filtering stage: total, mapped, properly paired, duplicated, MAPQ-filtered. Expected: > 75% primary reads.
*_read_loss.xlsx Same data as above in tabular format.

Example gDNA yield bar chart showing per-sample gDNA yield (ng) grouped by condition

FastQC

Available for both raw and trimmed FASTQ files. Review trimmed output where possible.

Metric Description Expected value
%Dups Percentage of duplicate reads. < 5%
%GC Average GC content. ~40% (human genomes)
Seqs Total reads (millions). If the sum across replicates for one condition is < 0.1 million, a library preparation error may have occurred. This also appears as a warning in the analysis validation report. —

FastQC plots available

  • Sequence Counts — bar chart of read counts per sample.
  • Sequence Quality Histogram — mean quality score per base position. Expected post-trimming: Phred > 30 for all positions.
  • Per Sequence Quality Scores — read count distribution by average quality score.
  • Per Base Sequence Content — base percentages at each position. Note: failure of this metric is expected given the non-random nature of DSBs; the first few bases may not match the expected ~40% GC content.
  • Per Sequence GC Content — distribution should form a smooth peak centred at ~40%.
  • Per Base N Content — expected value near 0%.
  • Sequence Length Distribution — slight length reduction post-trimming is expected. Trimming to < 75% of read length is unusual.
  • Sequence Duplication Levels — relative duplication level per sequence.
  • Overrepresented Sequences — count of overrepresented sequences per library.
  • Adapter Content — cumulative percentage of adapter sequences by position.
  • Status Checks — green (normal), orange (slightly abnormal), red (very unusual).