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SUMMARY      ANALYSIS
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Estimated Number of Cells

6,163

Mean Reads per Cell

72,279
Number of Reads
Total number of read pairs that were assigned to this library in demultiplexing.
Valid Barcodes
Fraction of reads with barcodes that match the whitelist after barcode correction.
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 cell barcode bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.
Q30 Bases in RNA Read
Fraction of RNA read bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator. This is Read 1 for the Single Cell 3' v1 chemistry and Read 2 for the Single Cell 3' v2 chemistry.
Q30 Bases in Sample Index
Fraction of sample index bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.
Q30 Bases in UMI
Fraction of UMI bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.

Sequencing

Number of Reads 445,459,017
Valid Barcodes 97.5%
Sequencing Saturation 23.4%
Q30 Bases in Barcode 96.7%
Q30 Bases in RNA Read 95.5%
Q30 Bases in Sample Index 95.2%
Q30 Bases in UMI 96.7%
Reads Mapped to Genome
Fraction of reads that mapped to the genome.
hg19 Reads Mapped to Genome
Fraction of reads that mapped to the hg19 genome.
mm10 Reads Mapped to Genome
Fraction of reads that mapped to the mm10 genome.
Reads Mapped Confidently to Genome
Fraction of reads that mapped uniquely to the genome. If a gene 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.
hg19 Reads Mapped Confidently to Genome
Fraction of reads that mapped uniquely to the hg19 genome. If a gene 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.
mm10 Reads Mapped Confidently to Genome
Fraction of reads that mapped uniquely to the mm10 genome. If a gene 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 Regions
Fraction of reads that mapped uniquely to an intergenic region of the genome.
hg19 Reads Mapped Confidently to Intergenic Regions
Fraction of reads that mapped uniquely to an intergenic region of the hg19 genome.
mm10 Reads Mapped Confidently to Intergenic Regions
Fraction of reads that mapped uniquely to an intergenic region of the mm10 genome.
Reads Mapped Confidently to Intronic Regions
Fraction of reads that mapped uniquely to an intronic region of the genome.
hg19 Reads Mapped Confidently to Intronic Regions
Fraction of reads that mapped uniquely to an intronic region of the hg19 genome.
mm10 Reads Mapped Confidently to Intronic Regions
Fraction of reads that mapped uniquely to an intronic region of the mm10 genome.
Reads Mapped Confidently to Exonic Regions
Fraction of reads that mapped uniquely to an exonic region of the genome.
hg19 Reads Mapped Confidently to Exonic Regions
Fraction of reads that mapped uniquely to an exonic region of the hg19 genome.
mm10 Reads Mapped Confidently to Exonic Regions
Fraction of reads that mapped uniquely to an exonic region of the mm10 genome.
Reads Mapped Confidently to Transcriptome
Fraction of reads that mapped to a unique gene in the transcriptome. The read must be consistent with annotated splice junctions. These reads are considered for UMI counting.
hg19 Reads Mapped Confidently to Transcriptome
Fraction of reads that mapped to a unique gene in the hg19 transcriptome. The read must be consistent with annotated splice junctions. These reads are considered for UMI counting.
mm10 Reads Mapped Confidently to Transcriptome
Fraction of reads that mapped to a unique gene in the mm10 transcriptome. The read must be consistent with annotated splice junctions. These reads are considered for UMI counting.
Reads Mapped Antisense to Gene
Fraction 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.

Mapping

Reads Mapped to Genome 96.9%
hg19 Reads Mapped to Genome 59.6%
mm10 Reads Mapped to Genome 37.7%
Reads Mapped Confidently to Genome 87.8%
hg19 Reads Mapped Confidently to Genome 55.6%
mm10 Reads Mapped Confidently to Genome 32.1%
Reads Mapped Confidently to Intergenic Regions 3.2%
hg19 Reads Mapped Confidently to Intergenic Regions 2.1%
mm10 Reads Mapped Confidently to Intergenic Regions 1.2%
Reads Mapped Confidently to Intronic Regions 23.8%
hg19 Reads Mapped Confidently to Intronic Regions 16.0%
mm10 Reads Mapped Confidently to Intronic Regions 7.8%
Reads Mapped Confidently to Exonic Regions 60.7%
hg19 Reads Mapped Confidently to Exonic Regions 37.6%
mm10 Reads Mapped Confidently to Exonic Regions 23.1%
Reads Mapped Confidently to Transcriptome 56.9%
hg19 Reads Mapped Confidently to Transcriptome 35.2%
mm10 Reads Mapped Confidently to Transcriptome 21.7%
Reads Mapped Antisense to Gene 1.3%
GEMs with >0 Cells
The number of barcodes associated with at least one cell.
GEMs with >1 Cell
The inferred number of barcodes that are associated with multiple cells.
Fraction GEMs with >1 Cell
The mean fraction of cell-associated barcodes estimated to be associated with more than one cell, calculated via bootstrap sampling and adjusting for the ratio of the two cell types.
Fraction GEMs with >1 Cell (Lower Bound)
The lower bound of the 95% confidence interval of the fraction of cell-associated barcodes estimated to be associated with more than one cell, calculated via bootstrap sampling and adjusting for the ratio of the two cell types.
Fraction GEMs with >1 Cell (Upper Bound)
The upper bound of the 95% confidence interval of the fraction of cell-associated barcodes estimated to be associated with more than one cell, calculated via bootstrap sampling and adjusting for the ratio of the two cell types.
Mean UMI Count Purity
Among single-cell GEM barcodes, the total fraction of UMI counts coming from the transcriptome of the cell inferred to be in the GEM, as opposed to a transcriptome that should not be present in the cell.

GEM Partitions

GEMs with >0 Cells 6,163
GEMs with >1 Cell 246
Fraction GEMs with >1 Cell 4.0%
Fraction GEMs with >1 Cell (Lower Bound) 3.3%
Fraction GEMs with >1 Cell (Upper Bound) 4.7%
Mean UMI Count Purity 98.7%
 
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 UMI count distribution.
mm10 Estimated Number of Cell Partitions
The number of barcodes associated with mm10 cell-containing partitions, estimated from the barcode UMI count distribution.
Fraction Reads in Cells
The fraction of valid-barcode, confidently-mapped-to-transcriptome reads with cell-associated barcodes.
hg19 Fraction Reads in Cells
The fraction of valid-barcode, confidently-mapped-to-transcriptome reads with hg19 cell-associated barcodes.
mm10 Fraction Reads in Cells
The fraction of valid-barcode, confidently-mapped-to-transcriptome 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 UMI count in any cell.
mm10 Total Genes Detected
The number of mm10 genes with at least one UMI 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 6,163
hg19 Estimated Number of Cell Partitions 2,897
mm10 Estimated Number of Cell Partitions 3,366
Fraction Reads in Cells 87.4%
hg19 Fraction Reads in Cells 83.8%
mm10 Fraction Reads in Cells 89.2%
Mean Reads per Cell 72,279
hg19 Median Genes per Cell 6,520
mm10 Median Genes per Cell 4,547
hg19 Total Genes Detected 29,183
mm10 Total Genes Detected 24,480
hg19 Median UMI Counts per Cell 36,036
mm10 Median UMI Counts per Cell 19,115

Sample

Name 5k_hgmm_v3_nextgem
Description 1:1 mixture of fresh frozen human (HEK293T) and mouse (NIH3T3) cells
Transcriptome hg19_and_mm10
Chemistry Single Cell 3' v3
Cell Ranger Version 3.0.2

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