Estimated Number of Cells

12,831

Mean Reads per Cell

30,385

Sequencing

Number of Reads 389,876,649
Valid Barcodes 98.5%
hg19 Reads Mapped Confidently to Transcriptome 47.3%
mm10 Reads Mapped Confidently to Transcriptome 26.9%
hg19 Reads Mapped Confidently to Exonic Regions 50.2%
mm10 Reads Mapped Confidently to Exonic Regions 28.0%
hg19 Reads Mapped Confidently to Intronic Regions 7.3%
mm10 Reads Mapped Confidently to Intronic Regions 3.4%
hg19 Reads Mapped Confidently to Intergenic Regions 1.7%
mm10 Reads Mapped Confidently to Intergenic Regions 1.1%
Sequencing Saturation 20.3%
Q30 Bases in Barcode 97.9%
Q30 Bases in RNA Read 81.9%
Q30 Bases in Sample Index 96.2%
Q30 Bases in UMI 98.0%

GEM Partitions

GEMs with >0 Cells 12,831
GEMs with >1 Cell 1,478
Fraction GEMs with >1 Cell 11.5%
Mean UMI Count Purity 97.8%
 

Cells

Cells
CellsBackground
Estimated Number of Cells 12,831
hg19 Estimated Number of Cell Partitions 6,894
mm10 Estimated Number of Cell Partitions 6,668
hg19 Fraction Reads in Cells 88.1%
mm10 Fraction Reads in Cells 89.2%
Mean Reads per Cell 30,385
hg19 Median Genes per Cell 3,943
mm10 Median Genes per Cell 2,629
hg19 Total Genes Detected 21,254
mm10 Total Genes Detected 16,477
hg19 Median UMI Counts per Cell 17,724
mm10 Median UMI Counts per Cell 10,449

Sample

Name hgmm_12k
Description 1:1 mixture of fresh frozen human (HEK293T) and mouse (NIH3T3) cells
Transcriptome hg19, mm10
Chemistry Single Cell 3' v2
Cell Ranger Version 1.3.0
Each point represents a cell-barcode. The axes measure the total UMI counts in each cell-barcode that mapped to each transcriptome reference. The points are colored by the number of inferred cells in the GEM associated with each barcode. A multiplet represents either a GEM inferred to have encapsulated >1 cell or a barcode sequence that was shared by multiple single-cell GEMs.

Cell UMI Counts

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hg19 UMI countsmm10 UMI countshg19mm10Multiplet
 
This plot shows the Sequencing Saturation metric as a function of downsampled sequencing depth in mean reads per cell, up to the observed sequencing depth. Sequencing Saturation is a measure of the observed library complexity, and approaches 1.0 (100%) when all converted mRNA transcripts have been sequenced. The slope of the curve near the endpoint can be interpreted as an upper bound to the benefit to be gained from increasing the sequencing depth beyond this point. The dotted line is drawn at a value reasonably approximating the saturation point.

Sequencing Saturation

05k10k15k20k25k00.20.40.60.81
Mean Reads per CellSequencing Saturation
 
This plot shows the Median Genes per Cell as a function of downsampled sequencing depth in mean reads per cell, up to the observed sequencing depth. The slope of the curve near the endpoint can be interpreted as an upper bound to the benefit to be gained from increasing the sequencing depth beyond this point.

Median Genes per Cell

05k10k15k20k25k0500100015002000250030003500
Mean Reads per CellMedian Genes per Cellhg19mm10