Cell Ranger · hgmm · 1:1 mixture of fresh frozen human (HEK293T) and mouse (NIH3T3) cells
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SUMMARY      ANALYSIS
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Number of Cells

1,380

Mean Reads per Cell

80,948
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 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.
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.
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 94.7%
hg19 Reads Mapped Confidently to Transcriptome 35.0%
mm10 Reads Mapped Confidently to Transcriptome 30.7%
hg19 Reads Mapped Confidently to Intergenic Regions 2.5%
mm10 Reads Mapped Confidently to Intergenic Regions 1.6%
hg19 Reads Mapped Confidently to Intronic Regions 5.3%
mm10 Reads Mapped Confidently to Intronic Regions 2.7%
cDNA PCR Duplication 51.9%
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 1,380
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 1,380
hg19 Number of Cell Partitions 704
mm10 Number of Cell Partitions 686
hg19 Fraction Reads in Cells 91.8%
mm10 Fraction Reads in Cells 92.5%
Mean Reads per Cell 80,948
hg19 Median Genes per Cell 4,531
mm10 Median Genes per Cell 3,831
hg19 Median UMI Counts per Cell 22,156
mm10 Median UMI Counts per Cell 20,582

Sample

Name hgmm
Description 1:1 mixture of fresh frozen human (HEK293T) and mouse (NIH3T3) cells
Transcriptome hg19, mm10
Cell Ranger Version 1.0.0

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