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Estimated Number of Cells

8,394

Mean Reads per Cell

40,193

Median Genes per Cell

3,170
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 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 337,383,459
Valid Barcodes 98.1%
Sequencing Saturation 41.2%
Q30 Bases in Barcode 98.3%
Q30 Bases in RNA Read 90.7%
Q30 Bases in UMI 98.5%
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 97.8%
Reads Mapped Confidently to Genome 94.7%
Reads Mapped Confidently to Intergenic Regions 3.9%
Reads Mapped Confidently to Intronic Regions 13.8%
Reads Mapped Confidently to Exonic Regions 77.0%
Reads Mapped Confidently to Transcriptome 72.8%
Reads Mapped Antisense to Gene 1.4%
 
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 8,394
Fraction Reads in Cells 87.3%
Mean Reads per Cell 40,193
Median Genes per Cell 3,170
Total Genes Detected 22,996
Median UMI Counts per Cell 14,307

Sample

Name H9_prime_ES
Description
Transcriptome hg19
Chemistry Single Cell 3' v2
Cell Ranger Version 2.1.1

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