10x Genomics Support/Cell Ranger 7.2/Analysis/

Metrics Output from the Cell Ranger count Pipeline

The metrics_summary.csv is organized with each column specifying one metric name. The metric values are specified in a single row. Column names are described in the table below:

Column NameDescription
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 CellMedian number of read pairs sequenced from the cells assigned to this sample. In case of multiplexing, only cell-associated barcodes assigned exactly one CMO can be assigned to a sample.
Number of ReadsTotal number of sequenced reads.
Valid BarcodesFraction of reads with cell-barcodes that match the whitelist.
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 RNAFraction 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 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.
Reads Mapped to GenomeFraction of reads that mapped to the genome.
Reads Mapped Confidently to GenomeFraction of reads that mapped uniquely to the genome. If a read mapped to exonic loci from a single gene and also to non-exonic loci, it is considered uniquely mapped to one of the exonic loci.
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.
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 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 TranscriptomeFraction of reads that mapped to a unique gene in the transcriptome with a high mapping quality score as reported by the aligner. The read must be consistent with annotated splice junctions when include-introns=false. These reads are considered for UMI counting.
Reads Confidently Mapped AntisenseFraction of reads confidently mapped to the transcriptome, but on the opposite strand of their annotated gene. A read is counted as antisense if it has any alignments that are consistent with an exon of a transcript but antisense to it, and has no sense alignments.
Total Genes Detected Median UMI Counts per CellThe number of genes with at least one UMI count in any cell.