Cell Ranger · naive_t · CD4+/CD45RA+/CD25- Native T cells
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SUMMARY      ANALYSIS
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Number of Cells

10,479

Mean Reads per Cell

19,405

Median Genes per Cell

490
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 203,354,998
Valid Barcodes 96.7%
Reads Mapped Confidently to Transcriptome 75.8%
Reads Mapped Confidently to Exonic Regions 79.1%
Reads Mapped Confidently to Intronic Regions 5.7%
Reads Mapped Confidently to Intergenic Regions 2.2%
cDNA PCR Duplication 90.7%
Q30 Bases in Barcode 90.5%
Q30 Bases in Read 1 88.3%
Q30 Bases in Sample Index 94.3%
Q30 Bases in UMI 92.9%
 
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 10,479
Fraction Reads in Cells 95.9%
Mean Reads per Cell 19,405
Median Genes per Cell 490
Median UMI Counts per Cell 1,186

Sample

Name naive_t
Description CD4+/CD45RA+/CD25- Native T cells
Transcriptome hg19
Cell Ranger Version 1.1.0

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