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SUMMARY      ANALYSIS
The analysis detected some serious issues.   Details »

Estimated Number of Cells

19,128

Post-Normalization Mean Reads per Cell

44,228

Median Genes per Cell

1,521
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 1,128,216,944
Post-Normalization Number of Reads 846,003,211
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 2 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 3 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 2 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 3 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 2 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.
library 3 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 2 Fraction of Reads Kept 69.1%
library 1 Fraction of Reads Kept 100.0%
library 3 Fraction of Reads Kept 32.3%
library 0 Pre-Normalization Total Reads per Cell 47,357
library 2 Pre-Normalization Total Reads per Cell 61,349
library 1 Pre-Normalization Total Reads per Cell 43,487
library 3 Pre-Normalization Total Reads per Cell 130,052
library 0 Pre-Normalization Confidently Mapped Barcoded Reads per Cell 27,737
library 2 Pre-Normalization Confidently Mapped Barcoded Reads per Cell 40,127
library 1 Pre-Normalization Confidently Mapped Barcoded Reads per Cell 27,739
library 3 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 19,128
Fraction Reads in Cells 95.5%
Pre-Normalization Mean Reads per Cell 58,982
Post-Normalization Mean Reads per Cell 44,228
Median Genes per Cell 1,521
Median UMI Counts per Cell 3,940

Sample

Name JP34353637
Description
Transcriptome mm10
Chemistry Single Cell 3' v2
Cell Ranger Version 2.2.0

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