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SUMMARY      ANALYSIS
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Estimated Number of Cells

6,643

Post-Normalization Mean Reads per Cell

61,141

Median Genes per Cell

1,705
Pre-Normalization Number of Reads
Total number of read pairs that were assigned to these libraries in demultiplexing.
Post-Normalization Number of Reads
Number of read pairs after normalizing for depth among multiple libraries.

Sequencing

Pre-Normalization Number of Reads 562,950,241
Post-Normalization Number of Reads 406,165,413
library 0 Fraction of Reads Kept
The fraction of reads kept for this input sample, after normalizing depth across samples to reduce batch effects.
library 1 Fraction of Reads Kept
The fraction of reads kept for this input sample, after normalizing depth across samples to reduce batch effects.
library 0 Pre-Normalization Total Reads per Cell
The mean number of total sequencing reads per cell in this input sample, prior to depth normalization.
library 1 Pre-Normalization Total Reads per Cell
The mean number of total sequencing reads per cell in this input sample, prior to depth normalization.
library 0 Pre-Normalization Confidently Mapped Barcoded Reads per Cell
The mean number of confidently-mapped-to-transcriptome, valid-barcode reads per cell in this input sample, prior to depth normalization.
library 1 Pre-Normalization Confidently Mapped Barcoded Reads per Cell
The mean number of confidently-mapped-to-transcriptome, valid-barcode reads per cell in this input sample, prior to depth normalization.

Aggregation

library 0 Fraction of Reads Kept 100.0%
library 1 Fraction of Reads Kept 46.7%
library 0 Pre-Normalization Total Reads per Cell 61,349
library 1 Pre-Normalization Total Reads per Cell 130,052
library 0 Pre-Normalization Confidently Mapped Barcoded Reads per Cell 40,127
library 1 Pre-Normalization Confidently Mapped Barcoded Reads per Cell 85,917
 
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.
Pre-Normalization Mean Reads per Cell
The total number of sequenced reads divided by the number of barcodes associated with cell-containing partitions.
Post-Normalization Mean Reads per Cell
The total number of (depth-normalized) 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

Estimated Number of Cells 6,643
Fraction Reads in Cells 95.7%
Pre-Normalization Mean Reads per Cell 84,743
Post-Normalization Mean Reads per Cell 61,141
Median Genes per Cell 1,705
Median UMI Counts per Cell 5,007

Sample

Name JP36_JP37
Description
Transcriptome mm10
Chemistry Single Cell 3' v2
Cell Ranger Version 2.2.0

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