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SUMMARY      ANALYSIS
The analysis detected some serious issues.   Details »

Estimated Number of Cells

8,291

Post-Normalization Mean Reads per Cell

91,772

Median Genes per Cell

2,529
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 760,888,734
Post-Normalization Number of Reads 760,888,734
Org1 Fraction of Reads Kept
The fraction of reads kept for this input sample, after normalizing depth across samples to reduce batch effects.
Org2 Fraction of Reads Kept
The fraction of reads kept for this input sample, after normalizing depth across samples to reduce batch effects.
Org3 Fraction of Reads Kept
The fraction of reads kept for this input sample, after normalizing depth across samples to reduce batch effects.
Org1 Pre-Normalization Total Reads per Cell
The mean number of total sequencing reads per cell in this input sample, prior to depth normalization.
Org2 Pre-Normalization Total Reads per Cell
The mean number of total sequencing reads per cell in this input sample, prior to depth normalization.
Org3 Pre-Normalization Total Reads per Cell
The mean number of total sequencing reads per cell in this input sample, prior to depth normalization.
Org1 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.
Org2 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.
Org3 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

Org1 Fraction of Reads Kept 100.0%
Org2 Fraction of Reads Kept 100.0%
Org3 Fraction of Reads Kept 100.0%
Org1 Pre-Normalization Total Reads per Cell 90,140
Org2 Pre-Normalization Total Reads per Cell 96,378
Org3 Pre-Normalization Total Reads per Cell 89,063
Org1 Pre-Normalization Confidently Mapped Barcoded Reads per Cell 43,664
Org2 Pre-Normalization Confidently Mapped Barcoded Reads per Cell 46,309
Org3 Pre-Normalization Confidently Mapped Barcoded Reads per Cell 42,308
 
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 8,291
Fraction Reads in Cells 88.1%
Pre-Normalization Mean Reads per Cell 91,772
Post-Normalization Mean Reads per Cell 91,772
Median Genes per Cell 2,529
Median UMI Counts per Cell 7,938

Sample

Name Orgs123
Description
Transcriptome GRCh38
Chemistry Single Cell 3' v2
Cell Ranger Version 3.0.1

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