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# Summary Metrics

The cellranger vdj pipeline outputs metrics_summary.csv which contains a number of key metrics about the barcoding and sequencing process. Conventions for these metrics:

• In some cases there is a metric for each chain type. We only show one.
• "Cells" refers to T or B cells.
• References to quality scores exclude very low quality/no-call (Q ≤ 2) bases.
Type Name                           Description
int Estimated Number of Cells The number of barcodes estimated to correspond to GEMs containing cells. See VDJ Cell Calling Algorithm.
int Mean Read Pairs per Cell Number of input read pairs divided by the estimated number of cells.
int Number of Cells With Productive V-J Spanning Pair Number of cell barcodes for which at least one productive sequence was found for each of TRA and TRB (or heavy and light chains, for Ig).
int Number of Read Pairs Total number of read pairs that were assigned to this library in demultiplexing.
float Valid Barcodes Fraction of reads with barcodes that match the whitelist after barcode correction.
float Q30 Bases in Barcode Fraction of cell barcode bases with Q-score ≥ 30.
float Q30 Bases in RNA Read 1 Fraction of read 1 bases with Q-score ≥ 30. (Likewise for read 2.)
float Q30 Bases in Sample Index Fraction of sample index bases with Q-score ≥ 30.
float Q30 Bases in UMI Fraction of UMI bases with Q-score ≥ 30.
float Reads Mapped to Any V(D)J Gene Fraction of reads that partially or wholly map to a V(D)J gene segment.
float Reads Mapped to TRA Fraction of reads that map partially or wholly to a TRA gene segment.
int Mean Used Read Pairs per Cell Mean number of read pairs used in assembly per cell barcode. These reads must have a cell barcode, map to a V(D)J gene, and have a UMI with sufficient read support, counted after subsampling.
float Fraction Reads in Cells Number of reads with cell barcodes divided by the number of reads with valid barcodes.
float Median TRA UMIs per Cell Median number of UMIs assigned to a TRA contig per cell.
float Paired Clonotype Diversity Effective diversity of the paired clonotypes, computed as the Inverse Simpson Index of the clonotype frequencies. A value of 1 indicates a minimally diverse sample - only one distinct clonotype was detected. A value equal to the estimated number of cells indicates a maximally diverse sample.
float Cells With TRA Contig Fraction of cell barcodes with at least one TRA contig annotated as a full or partial V(D)J gene.
float Cells With CDR3-annotated TRA Contig Fraction of cell barcodes with at least one TRA contig where a CDR3 was detected.
float Cells With V-J Spanning Contig Fraction of cell barcodes with at least one full-length contig.
float Cells With V-J Spanning TRA Contig Fraction of cell barcodes with at least one full-length TRA contig.
float Cells With Productive TRA Contig Fraction of cell barcodes with at least one full-length TRA contig that is productive.
float Cells With Productive V-J Spanning Pair Fraction of cell barcodes with at least one contig for each chain of the receptor pair that is productive.