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.
Valid UMIs
Fraction of reads with valid UMIs; i.e. UMI sequences that do not contain Ns and that are not homopolymers.
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 Single Cell 5' paired end, Read 2 for the Single Cell 3' v2/v3 chemistry and Single Cell 5' R2-only).
Q30 Bases in RNA Read 2
Fraction of RNA read 2 bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.
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.
Number of Reads
25,352,061
Valid Barcodes
93.5%
Valid UMIs
100.0%
Sequencing Saturation
2.3%
Q30 Bases in Barcode
97.0%
Q30 Bases in RNA Read
83.6%
Q30 Bases in Sample Index
97.0%
Q30 Bases in UMI
97.6%
Mapping
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.
Reads Mapped to Genome
93.5%
Reads Mapped Confidently to Genome
89.7%
Reads Mapped Confidently to Intergenic Regions
6.0%
Reads Mapped Confidently to Intronic Regions
7.7%
Reads Mapped Confidently to Exonic Regions
76.1%
Reads Mapped Confidently to Transcriptome
68.1%
Reads Mapped Antisense to Gene
3.3%
CRISPR Sequencing
Number of Reads
Total number of CRISPR library reads.
Valid Barcodes
Fraction of CRISPR library reads with a barcode found in or corrected to one that is found in the whitelist.
Valid UMIs
Fraction of CRISPR library reads with valid UMIs.
Sequencing Saturation
The fraction of CRISPR 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, CRISPR feature barcode).
Q30 Bases in Barcode
Fraction of CRISPR library cell barcode bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.
Q30 Bases in CRISPR Read
Fraction of CRISPR 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.
Q30 Bases in CRISPR Read 2
Fraction of CRISPR library read 2 bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.
Q30 Bases in Sample Index
Fraction of CRISPR library 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 CRISPR library UMI bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.
Number of Reads
8,865,829
Valid Barcodes
98.4%
Valid UMIs
100.0%
Sequencing Saturation
None
Q30 Bases in Barcode
97.2%
Q30 Bases in CRISPR Read
98.6%
Q30 Bases in Sample Index
96.2%
Q30 Bases in UMI
97.9%
Cells
Estimated Number of Cells
The number of barcodes associated with at least one cell.
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 %s cell-associated barcode.
Barcode Rank Plot
The plot shows the count of filtered UMIs mapped to each barcode. As barcodes are not determined to be cell-associated strictly based on their UMI count, but instead are determined by their expression profiles, some regions of the graph contain both cell-associated and background-associated barcodes. The color of the graph in these regions is based on the local density of barcodes that are cell-associated.
Fraction of feature barcoding library reads from which a putative protospacer sequence could be extracted.
Fraction Guide Reads
Fraction of CRISPR library reads with a recognized protospacer sequence.
Fraction Guide Reads Usable
Fraction of fCRISPR library reads with a recognized protospacer sequence, a valid UMI, and a cell-associated barcode.
Guide Reads Usable per Cell
Number of CRISPR library guide reads usable divided by the number of cell-associated barcodes.
Fraction Protospacer Not Recognized
Among all CRISPR library reads with a putative protospacer sequence, the fraction with a protospacer sequence that was not recognized.
Guide Reads in Cells
Among CRISPR library reads with a recognized protospacer sequence, a valid UMI, and a valid barcode, the fraction associated with cell-containing partitions.
Cells with 1 or more protospacers detected
Cells with 1 or more protospacers detected.
Cells with 2 or more protospacers detected
Cells with 2 or more protospacers detected.
Median UMIs per Cell
Median UMIs per Cell (summed over all recognized protospacers).