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# Gene Expression Metrics

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

## "cellranger count" Metrics Definitions

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

MetricDescription
Estimated Number of CellsThe number of barcodes associated with cell-containing partitions, estimated from the barcode UMI count distribution.
Mean Reads per CellThe total number of reads divided by the estimated number of cells.
Median Genes per CellThe median number of genes detected (with nonzero UMI counts) across all cell-associated barcodes.
Number of ReadsTotal number of sequenced reads.
Valid BarcodesFraction of reads with cell-barcodes that match the whitelist.
Reads Mapped Confidently to TranscriptomeFraction of reads that mapped to a unique gene in the transcriptome with a high mapping quality score as reported by the aligner.
Reads Mapped Confidently to Exonic RegionsFraction of reads that mapped to the exonic regions of the genome with a high mapping quality score as reported by the aligner.
Reads Mapped Confidently to Intronic RegionsFraction of reads that mapped to the intronic regions of the genome with a high mapping quality score as reported by the aligner.
Reads Mapped Confidently to Intergenic RegionsFraction of reads that mapped to the intergenic regions of the genome with a high mapping quality score as reported by the aligner.
Sequencing SaturationFraction of 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 confidently-mapped reads with a 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, gene). This metric was called "cDNA PCR Duplication" in versions of Cell Ranger prior to 1.2.
Q30 Bases in BarcodeFraction of bases with Q-score at least 30 in the cell barcode sequences. This is the i7 index (I1) read for the Single Cell 3' v1 chemistry and the R1 read for the Single Cell 3' v2 chemistry.
Q30 Bases in RNA ReadFraction of bases with Q-score at least 30 in the RNA read sequences. This is Illumina R1 for the Single Cell 3' v1 chemistry and Illumina R2 for the Single Cell 3' v2 chemistry.
Q30 Bases in Sample IndexFraction of bases with Q-score at least 30 in the sample index sequences. This is the i5 index (I2) read for the Single Cell 3' v1 chemistry and the i7 index (I1) read for the Single Cell 3' v2 chemistry.
Q30 Bases in UMIFraction of bases with Q-score at least 30 in the UMI sequences. This is the R2 read for the Single Cell 3' v1 chemistry and the R1 read for the Single Cell 3' v2 chemistry.
Fraction Reads in CellsThe fraction of cell-barcoded, confidently mapped reads with cell-associated barcodes.
Total Genes DetectedThe number of genes with at least one UMI count in any cell.
Median UMI Counts per CellThe median number of total UMI counts across all cell-associated barcodes.

If the sample was a Targeted Gene Expression sample, these additional metrics will also appear:

MetricDescription
Mean Targeted Reads per CellThe total number of targeted reads in cells divided by the number of barcodes associated with cell-containing partitions.
Number of Targeted GenesNumber of targeted genes as specified in the input target panel file.
Median Targeted Genes per CellThe median number of targeted genes detected per cell-associated barcode. Detection is defined as the presence of at least 1 UMI count. This metric will appear instead of the metric Median Genes per Cell above.
Median Targeted UMI Counts per CellThe median number of Targeted UMI counts per cell-associated barcode. This metric will appear instead of the metric Median UMI Counts per Cell above.
Targeted Sequencing SaturationThe fraction of targeted reads originating from an already-observed targeted UMI. This is a function of library complexity and sequencing depth. More specifically, this is the fraction of confidently mapped, valid cell-barcode, valid targeted UMI reads that had a non-unique (cell-barcode, UMI, gene). This metric will appear instead of the metric Sequencing Saturation above.
Total Targeted Genes DetectedThe number of targeted genes with at least one UMI count in any cell. This metric will appear instead of the metric Total Genes Detected above.
Number of Targeted GenesNumber of targeted genes as specified in the input target panel file.
Number of Non-Targeted GenesNumber of genes in the reference genome that are not targeted.
Number of Targeted Genes >= 10 UMIsNumber of targeted genes with at least 10 UMIs in cell-associated barcodes. These genes are then considered in the calculation of per-gene enrichments.
Number of Non-Targeted Genes >= 10 UMIsNumber of non-targeted genes with at least 10 UMIs in cell-associated barcodes. These genes are then considered in the calculation of per-gene enrichments.
Number of Enriched Targeted GenesNumber of targeted genes that are classified as enriched as a result of having high mean reads per UMI. Only genes with at least 10 cell-associated UMIs can be enriched. See Targeted Gene Expression Algorithms.
Number of Enriched Non-Targeted GenesNumber of non-targeted genes that are classified as enriched as a result of having high mean reads per UMI. Only genes with at least 10 cell-associated UMIs can be enriched. See Targeted Gene Expression Algorithms..
Mean Reads per UMI per Targeted GeneMean number of reads per UMI per targeted gene, averaged across all targeted genes with at least 10 cell-associated UMIs.
Mean Reads per UMI per Non-Targeted GeneMean number of reads per UMI per non-targeted gene, averaged across all targeted genes with at least 10 cell-associated UMIs.
Fraction of Reads Removed by UMI FilteringFraction of reads confidently mapped to the targeted transcriptome and removed by targeted UMI filtering.
Reads per UMI threshold for UMI filteringReads per UMI threshold for UMI filtering. UMIs in targeted genes where the read support is (strictly) lower than this threshold are filtered out.

## "cellranger aggr" Metrics Definitions

The cellranger aggr pipeline outputs summary.json which contains metrics relating to the aggregated datasets. Note: square brackets denote a variable that depends on the pipeline input, e.g. [library_id]_frac_reads_kept means that if your aggregation contains two libraries with IDs sample123 and sample456, there will be two output metrics sample123_frac_reads_kept and sample456_frac_reads_kept.

MetricDescription
filtered_bcs_transcriptome_unionThe estimated number of barcodes associated with cell-containing partitions, summed across all input libraries.
total_readsTotal number of sequenced reads, summed across all input libraries.
multi_transcriptome_total_raw_reads_per_filtered_bctotal_reads divided by filtered_bcs_transcriptome_union.
[library_id]_pre_normalization_raw_reads_per_filtered_bcThe mean total reads per cell prior to depth normalization, for the library denoted by library_id.
[library_id]_pre_normalization_cmb_reads_per_filtered_bcThe mean confidently mapped and barcoded (CMB) reads per cell prior to depth normalization, for the library denoted by library_id.
[library_id]_frac_reads_keptThe fraction of reads that were retained after depth normalization for the library denoted by library_id.
lowest_frac_reads_keptThe lowest fraction of reads retained, corresponding to the library which lost the most reads during normalization. A low value may indicate a large disparity in the initial depth of the input libraries.

If one or more of the aggregated samples was a Targeted Gene Expression sample, these additional metrics will also appear:

MetricDescription
[library_id]_pre_normalization_targeted_reads_per_filtered_bcThe mean targeted reads per cell prior to depth normalization, for the library denoted by library_id.
[library_id]_frac_targeted_reads_keptThe fraction of reads mapped uniquely and confidently to targeted genes that were retained after depth normalization for the library denoted by library_id. This field will be shown instead of the metric [library_id]_frac_reads_kept above.