Total number of read pairs: Total number of read pairs that were assigned to this library in demultiplexing.
Fraction of read pairs with a valid barcode: Fraction of read pairs with barcodes that match the whitelist after barcode correction.
Q30 bases in Read 1: Fraction of read 1 bases with Q-score >= 30.
Q30 bases in Read 2: Fraction of read 2 bases with Q-score >= 30.
Q30 bases in Barcode: Fraction of cell barcode bases with Q-score >= 30.
Q30 bases in Sample Index: Fraction of sample index bases with Q-score >= 30.

Estimated number of cells: The total number of barcodes identified as cells.
Lower threshold on the number of fragments overlapping peaks per barcode to annotate barcode as cell: If the number of fragments (that passed all filters and overlap peaks) associated with a barcode is greater than this threshold (as determined by the cell calling algorithm), the barcode is annotated as cell.
Median fragments per cell: Among barcodes identified as cells, the median number of fragments per barcode.
Median fragments per non-cell barcode: Among barcodes not identified as cells, the median number of fragments per barcode.
Plots: (left) Knee plot of number of fragments overlapping peaks for all the barcodes in the library. This number is used to call cells.; (right) Histograms of number of fragments per cell barcode for non-cells and cells.

Plots: (left) Scatter plot of barcodes annotated as cells, colored by automatically computed clusters via graph clustering.; (right) Scatter plot of barcodes annotated as cells, colored by number of fragments in the barcode.

Fragments in nucleosome-free regions: Fraction of fragments (that passed all filters) of size smaller than 147 basepairs.
Fragments flanking a single nucleosome: Fraction of fragments (that passed all filters) of size between 147 and 294 basepairs.
Plots: Insert size distribution in linear scale.

Fraction of fragments overlapping any targeted region: The fraction of fragments (that passed all filters) overlapping targeted regions (transcription start sites, DNase hypersensitive regions, enhancer or promoter regions).
Fraction of fragments overlapping TSS: The fraction of fragments (that passed all filters) overlapping transcription start sites, as defined by the GENCODE basic annotation.
Fraction of fragments overlapping DNase HS regions: The fraction of fragments (that passed all filters) overlapping DNase hypersensitive regions, as defined by ENCODE (The ENCODE Project Consortium 2012).
Fraction of fragments overlapping enhancer regions: The fraction of fragments (that passed all filters) overlapping enhancer regions, as defined by the Ensembl Regulatory Build (Zerbino et al. 2015).
Fraction of fragments overlapping promoter regions: The fraction of fragments (that passed all filters) overlapping promoter regions, as defined by the Ensembl Regulatory Build (Zerbino et al. 2015).
Fraction of fragments overlapping blacklisted regions: The fraction of fragments (that passed all filters) overlapping blacklisted regions, as defined by ENCODE (The ENCODE Project Consortium 2012).
Fraction of fragments overlapping called peaks: The fraction of fragments (that passed all filters) overlapping the set of peaks called for the library.
Enrichment score of transcription start sites: The TSS profile is the summed accessibility signal (defined as number of cut sites per base) in a window of 2,000 bases around all the annotated TSSs, normalized by the minimum signal in the window. This metric reports the maximum value in the profile.
Fraction of total read pairs mapped confidently to genome (>30 mapq): Fraction of all the sequenced read pairs that mapped to the genome with high mapping quality. Includes unique and duplicate read pairs from any barcode.
Fraction of total read pairs that are unmapped and in cell barcodes: Fraction of all the sequenced read pairs that come from cell barcodes and could not be mapped to the genome with confidence.
Fraction of total read pairs in mitochondria and in cell barcodes: Fraction of all the sequenced read pairs that come from cell barcodes and map to the mitochondrial genome.
Plots: (left) TSS profile, as described above.; (right) Targeting scatter plot. Each dot represents a barcode. Horizontal axis is the barcode's number of fragments, vertical axis is the percentage of those fragments that overlap peaks. Non-cell and cell groups are represented with different colors.

Percent duplicates: Fraction of all the sequenced read pairs that come from cell barcodes and are deemed to be PCR duplicates due to alignment to the same genomic position as another read pair in the library.
Sequencing saturation: Estimated sequencing saturation of high-quality fragment pool. Computed as the ratio of observed unique read pairs to estimated library complexity.
Estimated bulk library complexity: Estimated complexity of the library given the observed unique read pairs when sequenced to current depth.
Plots: Observed per cell complexity as a function of downsampling rate in mean reads per cell.