Cell Ranger DNA 1.0 (latest), printed on 02/23/2019
cell barcode/non-cell barcode: Each barcode labels a partition but not every partition contains a cell. A small fraction of reads are associated with empty partitions and this is a consequence of imperfections in the library creation process, sequencing and barcode error correction. A small minority of detected barcodes will be cells, but these barcodes will contain the majority of the reads.
copy number (CNV): the number of copies of a given genomic region that are present in a sample. A normal diploid cell has copy number 2 for most genomic regions on the autosomes.
duplicates: Duplicates are reads that came from the same cell and map to the same position, and arise as a consequence of either sequencing or PCR amplification.
group: A collection of cells within the hierarchical tree. The copy number profile for a group is computed from reads across all cells in that group.
heterogeneity: The fraction of cells in the group that have a different copy number than the plurality copy number for that group, with copy numbers binned into either 0, 1, 2, 3, 4, or >4. As a greater fraction of cells come into agreement, this value goes to 0. Undefined for single cells.
mappability: for a given region of the genome, the fraction of simulated reads from the region that map back to the region with mapping quality at least 30. A genomic interval is considered mappable if at least 90% of the interval is mappable.
mean ploidy: The mean estimated copy number over all primary contigs for a given cell or group of cells.
MAPD/DIMAPD: MAPD is a measure of unevenness of sequencing coverage calculated at 500 kb resolution. DIMAPD is a depth-independent measure of MAPD and measures the unevenness of the underlying library at 500 kb resolution. See Interpreting Output Metrics for more information.
noisy cell: Each cell is labeled with a noisy flag that captures both the uncertainty that the cell’s absolute ploidy scaling is the correct one, as well as whether the cell's read-count profile has a statistically greater variability than other cells in the sample. See Interpreting Output for more information.
pipestance: See Pipestance Structure.
event resolution: The smallest copy number event size that can be detected with 90% sensitivity and 90% positive predictive value. The event resolution changes as a function of sequencing depth—lower sequencing depth increases the event resolution and prevents detection of small CNVs. For an approximately diploid human sample, at a sequencing depth of 750,000 read-pairs per cell (1.5 million reads per cell), the event resolution is 2 megabases for single cell CNV detection, and 200 kilobases for groups of 10 or more cells. Refer to the Single Cell vs Bulk page for more details.
tree: For Single Cell DNA, a hierarchical agglomerative clustering tree. Note, this tree does not represent any kind of intentional phylogenetic inference. See Clustering Cells for more information.
unmappable: see mappability.