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10x Genomics
Chromium Single Cell ATAC

Summary Metrics

The cellranger-atac count pipeline outputs summary.csv which contains a number of key metrics in text, csv format. Below are the definitions of the reported metrics. When the metric is species specific, a value is reported for each species in multi-species experiments. When a metric is not computed by the pipeline, likely because of insufficient information or divison by zero, it is not reported in the summary.csv.

MetricDescriptionIs Species Specific
median_fragments_per_cellMedian fragments per cell barcode.True
median_per_cell_total_library_complexityEstimated median per cell library complexity.False
median_per_cell_unique_fragments_at_50000_RRPCMedian unique fragments per cell after downsampling to 50K raw reads per cell.True
median_per_cell_unique_fragments_at_30000_RRPCMedian unique fragments per cell after downsampling to 30K raw reads per cell.True
frac_cut_fragments_in_peaksFraction of transposition events in peaks.False
frac_fragments_nfrFragments in nucleosome-free regions.False
frac_fragments_nucFragments flanking a single nucleosome.False
frac_fragments_nfr_or_nucFragments in nucleosome-free or single-nucleosome regions.False
frac_fragments_overlapping_targetsFraction of fragments overlapping any targeted region.True
frac_fragments_overlapping_peaksFraction of fragments overlapping called peaks.True
tss_enrichment_scoreEnrichment score of transcription start sites.False
bc_q30_bases_fractQ30 bases in Barcode.False
r1_q30_bases_fractQ30 bases in Read 1.False
r2_q30_bases_fractQ30 bases in Read 2.False
si_q30_bases_fractQ30 bases in Sample Index.False
frac_waste_no_barcodeFraction of read pairs with invalid barcodes.False
frac_waste_overall_nondupFraction of total read pairs that are non-duplicate and wasted read pairs.False
frac_waste_non_cell_barcodeFraction of total read pairs in non-cell barcodes.False
frac_waste_chimericFraction of total read pairs that are improper pairs or map to a supplementary contig and are in cell barcodes.False
frac_waste_mitochondrialFraction of total read pairs in mitochondria and in cell barcodes.False
frac_waste_unmappedFraction of total read pairs that are unmapped and in cell barcodes.False
frac_waste_lowmapqFraction of total read pairs that have low mapping quality and are in cell barcodes.False
frac_waste_duplicatePercent duplicates.False
frac_waste_totalFraction of total read pairs wasted (either have invalid barcodes or in non cell barcodes, or did not pass filters).False
total_usable_fragmentsTotal number of read pairs in cell barcodes passing all filters.False
frac_mapped_confidentlyFraction of total read pairs mapped confidently to genome (>30 mapq).False
num_fragmentsTotal number of read pairs.False
cellranger-atac_versionSoftware version used to run the pipeline.False
cells_detectedNumber of barcodes identified as cells.False
annotated_cellsEstimated number of cells.True
observed_doublet_rateObserved multiplet rate.False
inferred_doublet_rateInferred multiplet rate.False