cra_BAAJ-Young_Spleen-AS010-1

8,562
Estimated number of cells
3,108
Median fragments per cell
76.0%
Fraction of fragments overlapping any targeted region
58.1%
Fraction of transposition events in peaks in cell barcodes

Sample

Sample IDcra_BAAJ-Young_Spleen-AS010-1
Sample description
FASTQ path
‎/scratch/oshpynov/2019_gxfer1_DT1634_Denis‎
Pipeline version1.1.0
Reference path
‎/scratch/oshpynov/refdata-cellranger-atac-mm10-1.1.0‎
OrganismMus_musculus
Assemblymm10
Annotationgencode.vM17.basic

Sequencing

Total number of read pairs
Total number of read pairs that were assigned to this library in demultiplexing.
Fraction of read pairs with a valid barcode
Fraction of read pairs with barcodes that match the whitelist after barcode correction.
Q30 bases in Read 1
Fraction of read 1 bases with Q-score >= 30.
Q30 bases in Read 2
Fraction of read 2 bases with Q-score >= 30.
Q30 bases in Barcode
Fraction of cell barcode bases with Q-score >= 30.
Q30 bases in Sample Index
Fraction of sample index bases with Q-score >= 30.
Total number of read pairs198,633,644
Fraction of read pairs with a valid barcode96.0%
Q30 bases in Read 188.2%
Q30 bases in Read 287.6%
Q30 bases in Barcode81.9%
Q30 bases in Sample IndexNone

Cells

Estimated number of cells
The total number of barcodes identified as cells.
Lower threshold on the number of fragments overlapping peaks per barcode to annotate barcode as cell
If the number of fragments (that passed all filters and overlap peaks) associated with a barcode is greater than this threshold (as determined by the cell calling algorithm), the barcode is annotated as cell.
Median fragments per cell
Among barcodes identified as cells, the median number of fragments per barcode.
Median fragments per non-cell barcode
Among barcodes not identified as cells, the median number of fragments per barcode.
Plots
(left) Knee plot of number of fragments overlapping peaks for all the barcodes in the library. This number is used to call cells.
(right) Histograms of number of fragments per cell barcode for non-cells and cells.
Estimated number of cells8,562
Lower threshold on the number of fragments overlapping peaks per barcode to annotate barcode as cell109.00
Median fragments per cell3,108
Median fragments per non-cell barcode0
110010k12510251002510002510k25100k
Non-cells CellsCells​Sample cra_BAAJ-Young_Spleen-AS010-1 - ​BarcodesFragments Overlapping Peaks
110010k512510251002510002510k25100k25
Non-cells CellsFragment Distribution​Sample cra_BAAJ-Young_Spleen-AS010-1 - ​Fragments Per BarcodeBarcodes

Cell Clustering

Plots
(left) Scatter plot of barcodes annotated as cells, colored by automatically computed clusters via graph clustering.
(right) Scatter plot of barcodes annotated as cells, colored by number of fragments in the barcode.
−500−40−30−20−100102030
Cluster 1 (1808)Cluster 2 (1385)Cluster 3 (1055)Cluster 4 (827)Cluster 5 (674)Cluster 6 (612)Cluster 7 (522)Cluster 8 (517)Cluster 9 (496)Cluster 10 (384)Cluster 11 (282)Cell Clustering (By Cluster)​Sample cra_BAAJ-Young_Spleen-AS010-1 - ​tSNE axis 1tSNE axis 2
−500−40−30−20−100102030
2.533.544.55log10 FragmentsCell Clustering (By Depth)​Sample cra_BAAJ-Young_Spleen-AS010-1 - ​tSNE axis 1tSNE axis 2

Insert Sizes

Fragments in nucleosome-free regions
Fraction of fragments (that passed all filters) of size smaller than 147 basepairs.
Fragments flanking a single nucleosome
Fraction of fragments (that passed all filters) of size between 147 and 294 basepairs.
Plots
Insert size distribution in linear scale.
Fragments in nucleosome-free regions51.6%
Fragments flanking a single nucleosome34.7%
2004006000100k200k300k400k500k
Insert Size Distribution​Sample cra_BAAJ-Young_Spleen-AS010-1 - ​Insert SizeFragment Count (linear scale)

Targeting

Enrichment score of transcription start sites
The TSS profile is the summed accessibility signal (defined as number of cut sites per base) in a window of 2,000 bases around all the annotated TSSs, normalized by the minimum signal in the window. This metric reports the maximum value in the profile.
Fraction of fragments overlapping TSS
The fraction of fragments (that passed all filters) overlapping transcription start sites, as defined by the GENCODE basic annotation.
Fraction of fragments overlapping called peaks
The fraction of fragments (that passed all filters) overlapping the set of peaks called for the library.
Fraction of fragments overlapping any targeted region
The fraction of fragments (that passed all filters) overlapping targeted regions (transcription start sites, DNase hypersensitive regions, enhancer or promoter regions, as present in the reference).
Fraction of total read pairs mapped confidently to genome (>30 mapq)
Fraction of all the sequenced read pairs that mapped to the genome with high mapping quality. Includes unique and duplicate read pairs from any barcode.
Fraction of total read pairs that are unmapped and in cell barcodes
Fraction of all the sequenced read pairs that come from cell barcodes and could not be mapped to the genome with confidence.
Fraction of total read pairs in mitochondria and in cell barcodes
Fraction of all the sequenced read pairs that come from cell barcodes and map to the mitochondrial genome.
Plots
(left) TSS profile, as described above.
(right) Targeting scatter plot. Each dot represents a barcode. Horizontal axis is the barcode's number of fragments, vertical axis is the percentage of those fragments that overlap peaks. Non-cell and cell groups are represented with different colors.
Enrichment score of transcription start sites13.39
Fraction of fragments overlapping TSS42.8%
Fraction of fragments overlapping called peaks60.3%
Fraction of fragments overlapping any targeted region76.0%
Fraction of total read pairs mapped confidently to genome (>30 mapq)82.4%
Fraction of total read pairs that are unmapped and in cell barcodes2.2%
Fraction of total read pairs in mitochondria and in cell barcodes0.2%
−1000−500050010002468101214
Enrichment around TSS (normalized)​Sample cra_BAAJ-Young_Spleen-AS010-1 - ​Relative Position (bp from TSS)Relative Enrichment
110010k1M00.20.40.60.81
Non-cellsCellsSinglecell Targeting (Peaks)​Sample cra_BAAJ-Young_Spleen-AS010-1 - ​Fragments per BarcodeFraction Fragments Overlapping Peaks

Library Complexity

Percent duplicates
Fraction of all the sequenced read pairs that come from cell barcodes and are deemed to be PCR duplicates due to alignment to the same genomic position as another read pair in the library.
Sequencing saturation
Estimated sequencing saturation of high-quality fragment pool. Computed as the ratio of observed unique read pairs to estimated library complexity.
Estimated bulk library complexity
Estimated complexity of the library given the observed unique read pairs when sequenced to current depth.
Plots
Observed per cell complexity as a function of downsampling rate in mean reads per cell.
Percent duplicates52.2%
Sequencing saturation82.5%
Estimated bulk library complexity65,358,564
010k20k30k40k050010001500200025003000
Per-Cell Library Complexity At Read Depth​Sample cra_BAAJ-Young_Spleen-AS010-1 - ​Mean Reads Per CellMedian Unique Fragments Per Cell