Cells detected
The number of barcodes associated with partitions containing cells
Median effective reads per MB
Median over cells of the number of reads per cell with mapping quality at least 30 and not duplicate divided by the genome size in megabases
Median unmapped fraction per cell
Median over cells of the fraction of reads per cell that are not mapped to the genome
Reads from cells
Total number of reads from cells
Mean mapped de-duplicated reads per cell
Mean over cells of the number of non-duplicate reads per cell with mapping quality at least 30
Median duplicate fraction per cell
Median over cells of the fraction of reads per cell with mapping quality at least 30 and are marked duplicates. Note that these include both PCR duplicates and duplicates created by the sequencer
Median average ploidy
Median over cells of the estimated average ploidy per cell
MAPD quartiles
Quartiles of the MAPD per cell distribution. MAPD is a measure of coverage dispersion that correlates with the ability to detect copy number variation. This metric depends on sequencing depth. See the documentation for more details
DIMAPD quartiles
Quartiles of the DIMAPD per cell distribution. DIMAPD is a measure of coverage dispersion derived from MAPD and is independent of sequencing depth. See the documentation for more details
Average ploidy quartiles
Quartiles of the Average ploidy per cell distribution
Fraction of noisy cells
Fraction of cells in the dataset that have high values of DIMAPD or where the copy number estimation procedure may be unreliable
Fraction of Q30 bases
The fraction of total bases with quality score at least 30 for read 1 (or read 2)
Total reads
Total number of sequencing reads
Total mapped de-duplicated reads
Total number of reads that have mapping quality at least 30 and are not duplicates
Fraction mapped de-duplicated reads
Total mapped de-duplicated reads / total reads
Fraction of reads with valid barcodes
The fraction of reads that could be confidently associated with a valid barcode
Fraction of reads not in cell barcodes
The fraction of reads with a valid barcode that are associated with empty partitions without a cell