Alert	Value	Detail
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Estimated Number of Cells

3,477

Mean Reads per Cell

85,248

2,536

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.

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	92.7%
Reads Mapped Confidently to Genome	86.7%
Reads Mapped Confidently to Intergenic Regions	5.5%
Reads Mapped Confidently to Intronic Regions	18.9%
Reads Mapped Confidently to Exonic Regions	62.4%
Reads Mapped Confidently to Transcriptome	59.1%
Reads Mapped Antisense to Gene	1.5%

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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.

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