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SUMMARY      ANALYSIS
The analysis detected some serious issues.   Details »

Estimated Number of Cells

8,083

Post-Normalization Mean Reads per Cell

74,624

Median Genes per Cell

1,077
Pre-Normalization Number of Reads
Total number of single-end reads that were sequenced.
Post-Normalization Number of Reads
Number of single-end reads after normalizing for depth among multiple libraries.

Sequencing

Pre-Normalization Number of Reads 696,377,874
Post-Normalization Number of Reads 603,189,074
t 3k Fraction of Reads Kept
The fraction of reads kept for this input sample, after normalizing depth across samples to reduce batch effects.
t 4k Fraction of Reads Kept
The fraction of reads kept for this input sample, after normalizing depth across samples to reduce batch effects.
t 3k Pre-Normalization Total Reads per Cell
The mean number of total sequencing reads per cell in this input sample, prior to depth normalization.
t 4k Pre-Normalization Total Reads per Cell
The mean number of total sequencing reads per cell in this input sample, prior to depth normalization.
t 3k Pre-Normalization Confidently Mapped Barcoded Reads per Cell
The mean number of confidently mapped, barcoded reads per cell in this input sample, prior to depth normalization.
t 4k Pre-Normalization Confidently Mapped Barcoded Reads per Cell
The mean number of confidently mapped, barcoded reads per cell in this input sample, prior to depth normalization.

Aggregation

t 3k Fraction of Reads Kept 74.2%
t 4k Fraction of Reads Kept 100.0%
t 3k Pre-Normalization Total Reads per Cell 101,712
t 4k Pre-Normalization Total Reads per Cell 73,962
t 3k Pre-Normalization Confidently Mapped Barcoded Reads per Cell 54,144
t 4k Pre-Normalization Confidently Mapped Barcoded Reads per Cell 40,174
 
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 barcoded, confidently mapped 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 8,083
Fraction Reads in Cells 88.4%
Pre-Normalization Mean Reads per Cell 86,153
Post-Normalization Mean Reads per Cell 74,624
Median Genes per Cell 1,077
Median UMI Counts per Cell 3,749

Sample

Name t_3k_4k_aggregate
Description Aggregate of t_3k and t_4k
Transcriptome GRCh38
Chemistry Single Cell 3' v2
Cell Ranger Version 1.3.0

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