Estimated Number of Cells

1,015

Mean Reads per Cell

60,793

Number of Reads: Total number of single-end reads that were sequenced.
Valid Barcodes: Fraction of reads with barcodes that match the whitelist.
hg19 Reads Mapped Confidently to Transcriptome: Fraction of reads that mapped to a unique gene in the hg19 transcriptome with a high mapping quality score as reported by the aligner.
mm10 Reads Mapped Confidently to Transcriptome: Fraction of reads that mapped to a unique gene in the mm10 transcriptome with a high mapping quality score as reported by the aligner.
hg19 Reads Mapped Confidently to Exonic Regions: Fraction of reads that mapped to the exonic regions of the genome with a high mapping quality score as reported by the aligner.
mm10 Reads Mapped Confidently to Exonic Regions: Fraction of reads that mapped to the exonic regions of the genome with a high mapping quality score as reported by the aligner.
hg19 Reads Mapped Confidently to Intronic Regions: Fraction of reads that mapped to the intronic regions of the hg19 genome with a high mapping quality score as reported by the aligner.
mm10 Reads Mapped Confidently to Intronic Regions: Fraction of reads that mapped to the intronic regions of the mm10 genome with a high mapping quality score as reported by the aligner.
hg19 Reads Mapped Confidently to Intergenic Regions: Fraction of reads that mapped to the intergenic regions of the hg19 genome with a high mapping quality score as reported by the aligner.
mm10 Reads Mapped Confidently to Intergenic Regions: Fraction of reads that mapped to the intergenic regions of the mm10 genome with a high mapping quality score as reported by the aligner.
Sequencing Saturation: The fraction of reads originating from an already-observed UMI. This is a function of library complexity and sequencing depth. More specifically, this is the fraction of confidently mapped, valid cell-barcode, valid UMI reads that had a non-unique (cell-barcode, UMI, gene). This metric was called "cDNA PCR Duplication" in versions of Cell Ranger prior to 1.2.
Q30 Bases in Barcode: Fraction of bases with Q-score at least 30 in the cell barcode sequences.
Q30 Bases in RNA Read: Fraction 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 Index: Fraction of bases with Q-score at least 30 in the sample index sequences.
Q30 Bases in UMI: Fraction of bases with Q-score at least 30 in the UMI sequences.

Sequencing

Number of Reads	61,705,744
Valid Barcodes	98.3%
hg19 Reads Mapped Confidently to Transcriptome	42.4%
mm10 Reads Mapped Confidently to Transcriptome	23.7%
hg19 Reads Mapped Confidently to Exonic Regions	45.2%
mm10 Reads Mapped Confidently to Exonic Regions	24.9%
hg19 Reads Mapped Confidently to Intronic Regions	6.5%
mm10 Reads Mapped Confidently to Intronic Regions	3.5%
hg19 Reads Mapped Confidently to Intergenic Regions	1.6%
mm10 Reads Mapped Confidently to Intergenic Regions	1.1%
Sequencing Saturation	24.4%
Q30 Bases in Barcode	97.9%
Q30 Bases in RNA Read	82.3%
Q30 Bases in Sample Index	96.9%
Q30 Bases in UMI	98.0%

GEM Partitions

GEMs with >0 Cells	1,015
GEMs with >1 Cell	6
Fraction GEMs with >1 Cell	0.6%
Mean UMI Count Purity	99.1%

Estimated Number of Cells: The total number of barcodes associated with cell-containing partitions, estimated from the barcode count distribution.
hg19 Estimated Number of Cell Partitions: The number of barcodes associated with hg19 cell-containing partitions, estimated from the barcode count distribution.
mm10 Estimated Number of Cell Partitions: The number of barcodes associated with mm10 cell-containing partitions, estimated from the barcode count distribution.
hg19 Fraction Reads in Cells: The fraction of barcoded, confidently mapped reads with hg19 cell-associated barcodes.
mm10 Fraction Reads in Cells: The fraction of barcoded, confidently mapped reads with mm10 cell-associated barcodes.
Mean Reads per Cell: The total number of sequenced reads divided by the number of barcodes associated with cell-containing partitions.
hg19 Median Genes per Cell: The median number of genes detected per hg19 cell-associated barcode. Detection is defined as the presence of at least 1 UMI count.
mm10 Median Genes per Cell: The median number of genes detected per mm10 cell-associated barcode. Detection is defined as the presence of at least 1 UMI count.
hg19 Total Genes Detected: The number of hg19 genes with at least one count in any cell.
mm10 Total Genes Detected: The number of mm10 genes with at least one count in any cell.
hg19 Median UMI Counts per Cell: The median number of UMI counts per hg19 cell-associated barcode.
mm10 Median UMI Counts per Cell: The median number of UMI counts per mm10 cell-associated barcode.

Cells

Estimated Number of Cells	1,015
hg19 Estimated Number of Cell Partitions	504
mm10 Estimated Number of Cell Partitions	514
hg19 Fraction Reads in Cells	85.1%
mm10 Fraction Reads in Cells	88.6%
Mean Reads per Cell	60,793
hg19 Median Genes per Cell	5,443
mm10 Median Genes per Cell	3,901
hg19 Total Genes Detected	17,517
mm10 Total Genes Detected	14,031
hg19 Median UMI Counts per Cell	33,185
mm10 Median UMI Counts per Cell	18,716

Sample

Name	hgmm_1k
Description	1:1 mixture of fresh frozen human (HEK293T) and mouse (NIH3T3) cells
Transcriptome	hg19, mm10
Chemistry	Single Cell 3' v2
Cell Ranger Version	1.2.0

Estimated Number of Cells

Mean Reads per Cell

Sequencing

GEM Partitions

Cells

Sample

Cell UMI Counts

Sequencing Saturation

Median Genes per Cell