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10x Genomics
Chromium Single Cell Gene Expression

Antibody Metrics

Cell Ranger computes sequencing quality and application results metrics on each supported library, which currently are Antibody Capture, CRISPR Guide Capture, and Custom (user-defined assays that are neither Antibody nor CRISPR). These metrics will be computed and displayed only when one of these library types was used. This page describes Antibody Capture libraries metrics for QC of the library prep and sequencing of antibody libraries, which appear in the metrics_summary.csv file and on the web_summary.html page.

MetricDescription
Antibody: Number of ReadsTotal number of reads.
Antibody: Mean Reads per CellThe total number of reads divided by the number of barcodes associated with cell-containing partitions.
Antibody: Valid BarcodesFraction of reads with a cell-barcode found in or corrected to one that is found in the whitelist.
Antibody: Fraction Reads in
Barcodes with High UMI Counts
Fraction of reads lost after removing barcodes with unusually high UMI counts, which may have been formed by antibody aggregates. Applies only to reads in "Antibody Capture" input library.
Antibody: Sequencing SaturationFraction of antibody library reads originating from an already-observed UMI. This is a function of library complexity and sequencing depth. More specifically, this is a ratio where: the denominator is the number of reads with a recognized antibody barcode, valid cell-barcode, and valid UMI, and the numerator is the subset of those reads that had a non-unique combination of (cell-barcode, UMI, antibody barcode).
Antibody: Q30 Bases in BarcodeFraction of cell barcode bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.
Antibody: Q30 Bases in Antibody ReadFraction of bases from the read containing the antibody barcode with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator. This is Read 2 for the Single Cell 3' v3 and Single Cell 5' chemistries.
Antibody: Q30 Bases in Sample IndexFraction of sample index bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.
Antibody: Q30 Bases in UMIFraction of UMI bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.
Antibody: Fraction Antibody ReadsFraction of reads that contain a recognized antibody barcode
Antibody: Fraction Antibody
Reads Usable
Fraction of reads that contain a recognized antibody barcode, a valid UMI, and a cell-associated barcode.
Antibody: Antibody Reads
Usable per Cell
Number of antibody reads usable divided by the number of cell-associated barcodes.
Antibody: Fraction Unrecognized
Antibody
Among all reads, the fraction with an unrecognizable antibody barcode
Antibody: Antibody Reads in CellsAmong reads with a recognized antibody barcode, a valid UMI, and a valid barcode, the fraction associated with cell-containing partitions.
Antibody: Median UMIs per CellMedian UMIs per Cell (summed over all recognized antibody barcodes).