Cell Ranger · pbmc3k · Peripheral blood mononuclear cells (PBMCs) from a healthy donor
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SUMMARY      ANALYSIS
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Number of Cells

2,700

Mean Reads per Cell

68,881

Median Genes per Cell

817
Number of Reads
Total number of single-end reads that were sequenced.
Valid Barcodes
Fraction of reads with barcodes that match the whitelist.
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.
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.
cDNA PCR Duplication
The fraction of duplicated reads that can be attributed to the cDNA amplification process; this is the number of non-unique reads divided by the number of reads.
Q30 Bases in Barcode
Fraction of bases with Q-score at least 30 in the cell barcode sequences.
Q30 Bases in Read 1
Fraction of bases with Q-score at least 30 in the read 1 sequences.
Q30 Bases in Sample Index
Fraction of bases with Q-score at least 30 in the sample index sequences.
Q30 Bases in UMI
Fraction of bases with Q-score at least 30 in the UMI sequences.

Sequencing

Number of Reads 185,980,783
Valid Barcodes 96.3%
Reads Mapped Confidently to Transcriptome 66.0%
Reads Mapped Confidently to Exonic Regions 69.4%
Reads Mapped Confidently to Intronic Regions 15.9%
Reads Mapped Confidently to Intergenic Regions 3.5%
cDNA PCR Duplication 94.0%
Q30 Bases in Barcode 70.9%
Q30 Bases in Read 1 93.0%
Q30 Bases in Sample Index 97.2%
Q30 Bases in UMI 96.0%
 
Number of Cells
The total number of barcodes associated with cell-containing partitions, based on the barcode count distribution.
Fraction Reads in Cells
The fraction of barcoded, confidently mapped 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.
Median UMI Counts per Cell
The median number of UMI counts per cell-associated barcode.

Cells

Number of Cells 2,700
Fraction Reads in Cells 96.8%
Mean Reads per Cell 68,881
Median Genes per Cell 817
Median UMI Counts per Cell 2,197

Sample

Name pbmc3k
Description Peripheral blood mononuclear cells (PBMCs) from a healthy donor
Transcriptome hg19
Cell Ranger Version 1.1.0

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