- Total reads
- Total number of sequencing reads
- Read length
- The median number of alignable bases in read 1 (or read 2)
- Fraction of Q30 bases
- The fraction of total bases with quality score at least 30 for read 1 (or read 2)
- Reads with valid barcodes
- The number of reads that could be confidently associated with a valid barcode
- Cells detected
- The number of barcodes associated with partitions containing cells
- Reads from cells
- The number of reads with a valid barcode that are associated with cell-containing partitions
- Total mapped de-duplicated reads in cells
- Total number of reads that have mapping quality at least 30 and are not duplicates that are associated with cell-containing partitions
- Median duplicate fraction per cell
- Median over cells of the fraction of duplicate reads
- 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 average ploidy
- Median of the average ploidy per cell distribution
- Median estimated CNV resolution per cell
- The approximate size of copy number events (in Mb) that can be profiled accurately in single cells based on the sequencing depth and library quality, as determined by a theoretical model
- 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 genome mappable
- The fraction of 20kb bins of the genome that are at least 70% mappable