Alert	Value	Detail
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Number of Cells

3,592

Mean Reads per Cell

16,593

662

Number of Reads: Total number of single-end reads that were sequenced.
Valid Barcodes: Fraction of reads with barcodes that match the whitelist.
Reads Mapped Confidently to Transcriptome: Fraction of reads that mapped to a unique gene in the transcriptome with a high mapping quality score as reported by the aligner.
Reads Mapped Confidently to Exonic Regions: Fraction of reads that mapped to the exonic regions of the genome with a high mapping quality score as reported by the aligner.
Reads Mapped Confidently to Intronic Regions: Fraction of reads that mapped to the intronic regions of the genome with a high mapping quality score as reported by the aligner.
Reads Mapped Confidently to Intergenic Regions: Fraction of reads that mapped to the intergenic regions of the genome with a high mapping quality score as reported by the aligner.
cDNA PCR Duplication: The fraction of duplicated reads that can be attributed to the cDNA amplification process; this is the number of non-unique reads divided by the number of reads.
Q30 Bases in Barcode: Fraction of bases with Q-score at least 30 in the cell barcode sequences.
Q30 Bases in Read 1: Fraction of bases with Q-score at least 30 in the read 1 sequences.
Q30 Bases in Sample Index: Fraction of bases with Q-score at least 30 in the sample index sequences.
Q30 Bases in UMI: Fraction of bases with Q-score at least 30 in the UMI sequences.

Number of Reads	59,605,204
Valid Barcodes	92.8%
Reads Mapped Confidently to Transcriptome	69.3%
Reads Mapped Confidently to Exonic Regions	71.7%
Reads Mapped Confidently to Intronic Regions	8.5%
Reads Mapped Confidently to Intergenic Regions	1.9%
cDNA PCR Duplication	35.0%
Q30 Bases in Barcode	76.0%
Q30 Bases in Read 1	81.8%
Q30 Bases in Sample Index	90.1%
Q30 Bases in UMI	79.8%

Number of Cells: The total number of barcodes associated with cell-containing partitions, based on the barcode count distribution.
Fraction Reads in Cells: The fraction of barcoded, confidently mapped reads with cell-associated barcodes.
Mean Reads per Cell: The total number of sequenced 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.