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10x Genomics
Chromium Single Cell Immune Profiling

Cell Ranger2.1, printed on 11/05/2024

Summary Metrics

Cell Ranger pipelines output key metrics in text format. Below are the definitions of the reported metrics.

"cellranger vdj" Metrics Definitions

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

Type Name Description
int Estimated Number of Cells The number of barcodes estimated to be associated with cells that express targeted V(D)J transcripts. A barcode is cell-associated if it has a contig with at least 2 UMIs with sufficient read support.
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 (TRA, TRB) Pair Number of cell barcodes for which at least 1 sequence was found for each of TRA and TRB. Both sequences must have an annotated CDR3, must be predicted to be productive, and must span the beginning of the 5′ end of the V region to the 3′ end of the J region.
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, excluding very low quality/no-call (Q <= 2) bases from the denominator.
float Q30 Bases in RNA Read 1 Fraction of RNA read 1 bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.
float Q30 Bases in RNA Read 2 Fraction of RNA read 2 bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.
float Q30 Bases in Sample Index Fraction of sample index bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.
float Q30 Bases in UMI Fraction of UMI bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.
float Reads Mapped to Any V(D)J Gene Fraction of reads that partially or wholly map to any germline V(D)J gene segment.
float Reads Mapped to TRA Fraction of reads that map partially or wholly to a germline TRA gene segment.
float Reads Mapped to TRB Fraction of reads that map partially or wholly to a germline TRB gene segment.
int Mean Used Read Pairs per Cell Mean number of read pairs used in assembly per cell-associated barcode. These reads must have a cell-associated barcode, map to a V(D)J gene, and have a UMI with sufficient read support. This value is counted after subsampling to a fixed N50 reads per UMI (See Assembly Subsampling Rate).
float Assembly Subsampling Rate Fraction of usable (assemblable) reads retained for assembly. The assembler uniformly subsamples reads to achieve a target N50 reads per UMI. If multiple gem groups were given as input, this is the weighted average across all gem groups, where each gem group is weighted by its total number of reads with a valid barcode and UMI.
float Fraction Reads in Cells Number of reads with cell-associated 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 Median TRB UMIs per Cell Median number of UMIs assigned to a TRB 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-associated barcodes with at least one TRA contig annotated as a full or partial V(D)J gene.
float Cells With TRB Contig Fraction of cell-associated barcodes with at least one TRB contig annotated as a full or partial V(D)J gene.
float Cells With CDR3-annotated TRA Contig Fraction of cell-associated barcodes with at least one TRA contig where a CDR3 was detected.
float Cells With CDR3-annotated TRB Contig Fraction of cell-associated barcodes with at least one TRB contig where a CDR3 was detected.
float Cells With V-J Spanning Contig Fraction of cell-associated barcodes with at least one contig spanning the 5′ end of the V region and the 3′ end of the J region.
float Cells With V-J Spanning TRA Contig Fraction of cell-associated barcodes with at least one contig spanning the 5′ end of the V region and the 3′ end of the J region for TRA.
float Cells With V-J Spanning TRB Contig Fraction of cell-associated barcodes with at least one contig spanning the 5′ end of the V region and the 3′ end of the J region for TRB.
float Cells With Productive TRA Contig Fraction of cell-associated barcodes with at least one contig that spans the 5′ end of the V region and the 3′ end of the J region for TRA, has a start codon in the expected part of the V sequence, has an in-frame CDR3, and has no stop codons in the V-J region.
float Cells With Productive TRB Contig Fraction of cell-associated barcodes with at least one contig that spans the 5′ end of the V region and the 3′ end of the J region for TRB, has a start codon in the expected part of the V sequence, has an in-frame CDR3, and has no stop codons in the V-J region.
float Cells With Productive V-J Spanning (TRA, TRB) Pair Fraction of cell-associated barcodes with at least one contig for each chain of the receptor pair satisfying the following: the contig annotations span the 5′ end of the V region and the 3′ end of the J region of the chain, a start codon was found in the expected part of the V sequence, an in-frame CDR3 amino acid motif was found, and no stop codons were found in the V-J region.
float Contigs Unannotated Fraction of assembled contigs not annotated with any V(D)J gene.
float Cell Count Confidence Fraction of cell barcodes that have been very confidently called as cells. This indicates the quality of the separation between background and cell-associated barcodes.