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SUMMARY      ANALYSIS
The analysis detected some serious issues.   Details »

Estimated Number of Cells

15,846

Post-Normalization Mean Reads per Cell

57,565

Median Genes per Cell

2,033
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 1,050,692,816
Post-Normalization Number of Reads 912,177,644
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 2 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 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 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.
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.

Aggregation

library 0 Fraction of Reads Kept 91.6%
library 1 Fraction of Reads Kept 68.8%
library 2 Fraction of Reads Kept 100.0%
library 0 Pre-Normalization Total Reads per Cell 70,122
library 1 Pre-Normalization Total Reads per Cell 82,686
library 2 Pre-Normalization Total Reads per Cell 52,580
library 0 Pre-Normalization Confidently Mapped Barcoded Reads per Cell 34,672
library 1 Pre-Normalization Confidently Mapped Barcoded Reads per Cell 46,184
library 2 Pre-Normalization Confidently Mapped Barcoded Reads per Cell 31,755
 
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 15,846
Fraction Reads in Cells 96.6%
Pre-Normalization Mean Reads per Cell 66,306
Post-Normalization Mean Reads per Cell 57,565
Median Genes per Cell 2,033
Median UMI Counts per Cell 6,122

Sample

Name K72K73K74
Description
Transcriptome mm10
Chemistry Single Cell 3' v3
Cell Ranger Version 3.0.2

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