The number of reads that mapped to a unique gene in the transcriptome divided by the number of barcodes associated with cell-containing partitions.
Median UMI Counts per Cell
The median number of UMI counts per % cell-associated barcode.
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.
Risk evaluation: Low risk
Sequence depth: 54 G bases (Medium)
8,420
Estimated Number of Cells
1,332
Mean reads per Cell
360
Median UMI Counts per Cell
99
Median Genes per Cell
Cells
Estimated Number of Cells
The number of barcodes associated with at least one cell.
Fraction Reads in cells
.
Mean Reads per Cell
The number of reads that mapped to a unique gene in the transcriptome divided by the number of barcodes associated with cell-containing partitions.
Median UMI Counts per Cell
The median number of UMI counts per %s cell-associated barcode.
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.
Total Genes Detected
The number of genes with at least one UMI count in any cell.
Barcode Rank Plot
The plot shows the count of filtered UMIs mapped to each barcode.
Sample Name
humangut
Type
NA
Estimated Number of Cells
8,420
Fraction Reads in cells
34.0%
Mean Reads per Cell
1,332
Median UMI Counts per Cell
360
Median genes per cell
99
Total genes detected
46,240
Sequencing & Mapping
Number of Reads
Total number of read pairs that were assigned to this library in demultiplexing.
Valid Barcodes
Fraction of reads with barcodes that match the whitelist after barcode correction.
Reads to Align
Fraction of reads used for aligning to genome after quality control and filtering.
Sequencing Saturation
The fraction of reads originating from an already-observed UMI. This is a function of library complexity and sequencing depth. More specifically, this is the fraction of confidently mapped, valid cell-barcode, valid UMI reads that had a non-unique (cell-barcode, UMI, gene).
Q30 Bases in RNA Read
Fraction of RNA read bases with Q-score ≥ 30.
Reads Mapped to Genome
Fraction of reads that mapped to the genome.
Reads Mapped Confidently to Genome
Fraction of reads that mapped uniquely to the genome.
Reads Mapped Confidently to Transcriptome
Fraction of reads that mapped to a unique gene in the transcriptome. These reads are considered for UMI counting.
Sequencing
Number of Reads
180,654,876
Valid Barcodes
86.88%
Reads to Align
85.34%
Sequencing Saturation
56.71%
Q30 Bases in RNA Read
95.24%
Mapping
Reads Mapped to Genome
74.74%
Reads Mapped Confidently to Genome
28.36%
Reads Mapped Confidently to Transcriptome
21.51%
Species Classification
Species Classification
This plot illustrates the species classification and the respective abundance. Individual reads are classified by Kraken and the estimation of abundance at the species level is performed by Bracken. Reads from the same barcode are organized, and each barcode is then assigned with the name of the most abundant species. Species names are presented in the descending order in the legend, and top 30 species are colored.
Cluster
Left
The figure presents the automated clustering results by UMAP algorithm. The cells clustered into the same group have similar expression profiles. Each dot represents a cell, and is colored according to different cluster.
Right
The figure presents the automated clustering results by UMAP algorithm. Each dot represents a cell, and is colored according to its species label.