Alert	Value	Detail
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Number of Cells

1,387

Mean Reads per Cell

80,540

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.
cDNA PCR Duplication: The fraction of duplicated reads that can be attributed to the cDNA amplification process; this is the number of non-unique reads divided by the number of reads.
Q30 Bases in Barcode: Fraction of bases with Q-score at least 30 in the cell barcode sequences.
Q30 Bases in Read 1: Fraction of bases with Q-score at least 30 in the read 1 sequences.
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	111,709,061
Valid Barcodes	96.4%
hg19 Reads Mapped Confidently to Transcriptome	36.1%
mm10 Reads Mapped Confidently to Transcriptome	30.9%
hg19 Reads Mapped Confidently to Exonic Regions	38.1%
mm10 Reads Mapped Confidently to Exonic Regions	32.1%
hg19 Reads Mapped Confidently to Intronic Regions	5.3%
mm10 Reads Mapped Confidently to Intronic Regions	2.7%
hg19 Reads Mapped Confidently to Intergenic Regions	1.4%
mm10 Reads Mapped Confidently to Intergenic Regions	1.4%
cDNA PCR Duplication	52.3%
Q30 Bases in Barcode	71.0%
Q30 Bases in Read 1	93.2%
Q30 Bases in Sample Index	96.8%
Q30 Bases in UMI	95.4%

GEMs with >0 Cells: The number of barcodes associated with at least one cell.
GEMs with >1 Cell: The estimated number of barcodes that are associated with multiple cells.
Fraction GEMs with >1 Cell: The fraction of cell-associated barcodes estimated to be associated with more than one cell.
Mean UMI Count Purity: Among single-cell barcodes, the mean fraction of UMI counts coming from the non-cell transcriptome.

GEM Partitions

GEMs with >0 Cells	1,387
GEMs with >1 Cell	20
Fraction GEMs with >1 Cell	1.5%
Mean UMI Count Purity	99.1%

Number of Cells: The total number of barcodes associated with cell-containing partitions, based on the barcode count distribution.
hg19 Number of Cell Partitions: The number of barcodes associated with hg19 cell-containing partitions, based on the barcode count distribution.
mm10 Number of Cell Partitions: The number of barcodes associated with mm10 cell-containing partitions, based on 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 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

Number of Cells	1,387
hg19 Number of Cell Partitions	707
mm10 Number of Cell Partitions	690
hg19 Fraction Reads in Cells	91.5%
mm10 Fraction Reads in Cells	92.5%
Mean Reads per Cell	80,540
hg19 Median Genes per Cell	4,557
mm10 Median Genes per Cell	3,856
hg19 Median UMI Counts per Cell	23,020
mm10 Median UMI Counts per Cell	20,736

Sample

Name	hgmm
Description	1:1 mixture of fresh frozen human (HEK293T) and mouse (NIH3T3) cells
Transcriptome	hg19, mm10
Cell Ranger Version	1.1.0

Number of Cells

Mean Reads per Cell

Sequencing

GEM Partitions

Cells

Sample

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