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SUMMARY      ANALYSIS
The analysis detected some serious issues.   Details »

Estimated Number of Cells

9,128

Mean Reads per Cell

41,998

Median Genes per Cell

2,508
Number of Reads
Total number of single-end reads that were assigned to this library in demultiplexing.
Valid Barcodes
Fraction of reads with barcodes that match the whitelist after barcode correction.
Reads Mapped Confidently to Transcriptome
Fraction of reads that mapped to a unique gene in the transcriptome with a high mapping quality score as reported by the aligner. At least 50% of the read must overlap with an exon and the read must be consistent with annotated splice junctions.
Reads Mapped Confidently to Exonic Regions
Fraction of reads that mapped to the exonic regions of the genome with a high mapping quality score as reported by the aligner.
Reads Mapped Confidently to Intronic Regions
Fraction of reads that mapped to the intronic regions of the genome with a high mapping quality score as reported by the aligner.
Reads Mapped Confidently to Intergenic Regions
Fraction of reads that mapped to the intergenic regions of the genome with a high mapping quality score as reported by the aligner.
Reads Mapped Antisense to Gene
Fraction of reads confidently mapped to the transcriptome, but on the opposite strand of their annotated gene.
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 383,366,284
Valid Barcodes 98.3%
Reads Mapped Confidently to Transcriptome 62.4%
Reads Mapped Confidently to Exonic Regions 65.8%
Reads Mapped Confidently to Intronic Regions 22.1%
Reads Mapped Confidently to Intergenic Regions 3.5%
Reads Mapped Antisense to Gene 4.1%
Sequencing Saturation 65.2%
Q30 Bases in Barcode 98.3%
Q30 Bases in RNA Read 81.6%
Q30 Bases in Sample Index 95.8%
Q30 Bases in UMI 98.2%
 
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 9,128
Fraction Reads in Cells 83.2%
Mean Reads per Cell 41,998
Median Genes per Cell 2,508
Total Genes Detected 19,205
Median UMI Counts per Cell 6,360

Sample

Name neuron_9k
Description Cells from cortex, hippocampus and subventricular zone of an E18 mouse
Transcriptome mm10
Chemistry Single Cell 3' v2
Cell Ranger Version 2.0.1

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