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SUMMARY      ANALYSIS
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Estimated Number of Cells

8,412

Mean Reads per Cell

32,721

Median Genes per Cell

1,073
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 275,250,656
Valid Barcodes 97.5%
Sequencing Saturation 69.0%
Q30 Bases in Barcode 93.2%
Q30 Bases in RNA Read 89.0%
Q30 Bases in Sample Index 89.8%
Q30 Bases in UMI 90.3%
Reads Mapped to Genome
Fraction of reads that mapped to the 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.
Reads Mapped Confidently to Intergenic Regions
Fraction of reads that mapped uniquely to an intergenic region of the genome.
Reads Mapped Confidently to Intronic Regions
Fraction of reads that mapped uniquely to an intronic region of the genome.
Reads Mapped Confidently to Exonic Regions
Fraction of reads that mapped uniquely to an exonic region of the 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.
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 95.2%
Reads Mapped Confidently to Genome 92.4%
Reads Mapped Confidently to Intergenic Regions 4.8%
Reads Mapped Confidently to Intronic Regions 36.4%
Reads Mapped Confidently to Exonic Regions 51.2%
Reads Mapped Confidently to Transcriptome 47.8%
Reads Mapped Antisense to Gene 1.5%
Antibody: Number of Reads
Total number of Antibody library reads
Antibody: Mean Reads per Cell
The total number of sequenced Antibody library reads divided by the number of barcodes associated with cell-containing partitions.
Antibody: Valid Barcodes
Fraction of Antibody library reads with a barcode found in or corrected to one that is found in the whitelist
Antibody: Sequencing Saturation
The fraction of Antibody library 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, antibody feature barcode).
Antibody: Q30 Bases in Barcode
Fraction of Antibody library cell barcode bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.
Antibody: Q30 Bases in Antibody Read
Fraction of Antibody library read bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator. This is Read 2 for the Single Cell 3' v3 and Single Cell 5' chemistries.
Antibody: Q30 Bases in Sample Index
Fraction of Antibody library sample index bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.
Antibody: Q30 Bases in UMI
Fraction of Antibody library UMI bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.

Antibody Sequencing

Antibody: Number of Reads 120,294,764
Antibody: Mean Reads per Cell 14,300
Antibody: Valid Barcodes 98.9%
Antibody: Sequencing Saturation 47.2%
Antibody: Q30 Bases in Barcode 94.7%
Antibody: Q30 Bases in Antibody Read 92.7%
Antibody: Q30 Bases in Sample Index 91.1%
Antibody: Q30 Bases in UMI 93.8%
 
Barcode Rank Plot
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Estimated Number of Cells
The total number of barcodes associated with cell-containing partitions, estimated from the barcode count distribution.
Fraction Reads in Cells
The fraction of valid-barcode, confidently-mapped-to-transcriptome reads with cell-associated barcodes.
Mean Reads per Cell
The total number of sequenced reads divided by the number of barcodes associated with cell-containing partitions.
Median Genes per Cell
The median number of genes detected per cell-associated barcode. Detection is defined as the presence of at least 1 UMI count.
Total Genes Detected
The number of genes with at least one UMI count in any cell.
Median UMI Counts per Cell
The median number of UMI counts per cell-associated barcode.

Cells

Estimated Number of Cells 8,412
Fraction Reads in Cells 93.2%
Mean Reads per Cell 32,721
Median Genes per Cell 1,073
Total Genes Detected 22,042
Median UMI Counts per Cell 3,238
Antibody: Fraction Antibody Reads
Fraction of Antibody library reads that contain a recognized antibody barcode
Antibody: Fraction Antibody Reads Usable
Fraction of Antibody library reads that contain a recognized antibody barcode, a valid UMI, and a cell-associated barcode
Antibody: Antibody Reads Usable per Cell
Number of Antibody library reads usable divided by the number of cell-associated barcodes
Antibody: Fraction Reads in Barcodes with High UMI Counts
Fraction of Antibody library reads that was lost after removing barcodes with unusually high UMI counts (possibly aggregates).
Antibody: Fraction Unrecognized Antibody
Among all Antibody library reads, the fraction with an unrecognizable antibody barcode
Antibody: Antibody Reads in Cells
Among Antibody library reads with a recognized antibody barcode, a valid UMI, and a valid barcode, the fraction associated with cell-containing partitions
Antibody: Median UMIs per Cell (summed over all recognized antibody barcodes)
Median UMIs per Cell (summed over all recognized antibody barcodes)

Antibody Application

Antibody: Fraction Antibody Reads 94.5%
Antibody: Fraction Antibody Reads Usable 63.7%
Antibody: Antibody Reads Usable per Cell 9,102
Antibody: Fraction Reads in Barcodes with High UMI Counts 0.0%
Antibody: Fraction Unrecognized Antibody 5.5%
Antibody: Antibody Reads in Cells 67.9%
Antibody: Median UMIs per Cell (summed over all recognized antibody barcodes) 2,370

Sample

Name malt_10k_protein_v3
Description Cells from a dissociated Extranodal Marginal Zone B-Cell Tumor (MALT)
Transcriptome GRCh38
Chemistry Single Cell 3' v3
Cell Ranger Version 3.0.0

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