Cell Ranger · cd4_t_helper · CD4+ T Helper 2 Cells
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SUMMARY      ANALYSIS
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Number of Cells

11,213

Mean Reads per Cell

21,329

Median Genes per Cell

546
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 239,163,470
Valid Barcodes 96.6%
Reads Mapped Confidently to Transcriptome 76.1%
Reads Mapped Confidently to Exonic Regions 79.4%
Reads Mapped Confidently to Intronic Regions 5.5%
Reads Mapped Confidently to Intergenic Regions 2.2%
cDNA PCR Duplication 90.4%
Q30 Bases in Barcode 90.7%
Q30 Bases in Read 1 87.1%
Q30 Bases in Sample Index 94.8%
Q30 Bases in UMI 92.6%
 
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 11,213
Fraction Reads in Cells 95.2%
Mean Reads per Cell 21,329
Median Genes per Cell 546
Median UMI Counts per Cell 1,326

Sample

Name cd4_t_helper
Description CD4+ T Helper 2 Cells
Transcriptome hg19
Cell Ranger Version 1.1.0

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