atac_hgmm_1k_v1 - 1:1 mixture of fresh frozen human (GM12878) and mouse (A20) cells

Alerts

The analysis detected 2 warnings.
AlertValueDetail
Estimated number of cells is low (hg19)426Number of cells detected is expected to be higher than 500. This usually indicates poor cell, library, or sequencing quality.
Estimated number of cells is low (mm10)431Number of cells detected is expected to be higher than 500. This usually indicates poor cell, library, or sequencing quality.
For guidance, please consult "Interpreting Cell Ranger ATAC Web Summary Files" or contact 10x Genomics Support (support@10xgenomics.com)
426
Estimated number of cells (hg19)
431
Estimated number of cells (mm10)
20,114
Median fragments per cell (hg19)
19,393
Median fragments per cell (mm10)
82.9%
Fraction of fragments overlapping any targeted region (hg19)
67.7%
Fraction of fragments overlapping any targeted region (mm10)
60.9%
Fraction of transposition events in peaks in cell barcodes

Sample

Sample IDatac_hgmm_1k_v1
Sample description1:1 mixture of fresh frozen human (GM12878) and mouse (A20) cells
FASTQ path
‎/mnt/scratch2/cellranger-atac/fastqs/atac_hgmm_1k_v1_fastqs‎
Pipeline version1.2.0
Reference path
‎/mnt/scratch2/cellranger-atac/references/refdata-cellranger-atac-hg19-and-mm10-1.2.0‎
OrganismHomo_sapiens_and_Mus_musculus
Assemblyhg19_and_mm10
Annotationbarnyard

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 pairs31,836,548
Fraction of read pairs with a valid barcode98.2%
Q30 bases in Read 194.7%
Q30 bases in Read 294.4%
Q30 bases in Barcode90.5%
Q30 bases in Sample Index94.0%

Barnyard

Observed multiplet rate
The observed fraction of cell barcodes that appear to have cells from both species present.
Inferred multiplet rate
The estimated fraction of cell barcodes containing more than one cell.
Median barcode purity
The median, across all cell barcodes, of the fraction of fragments in the barcode that align uniquely to the species assigned to the barcode.
Plots
(left) Barnyard scatter plot, where each dot represents a barcode and its coordinates indicate number of fragments, from each species, assigned to the barcode. Groups are estimated computationally.
(right) Histograms of per barcode purities estimated for barcodes in each species.
Observed multiplet rate0.9%
Inferred multiplet rate1.9%
Median barcode purity (hg19)100.0%
Median barcode purity (mm10)99.9%
110010k512510251002510002510k25100k
Non-cellsMultipletshg19 Cellsmm10 CellsBarnyard​Sample atac_hgmm_1k_v1 - 1:1 mixture of fresh frozen human (GM12878) and mouse (A20) cells​hg19 Fragments Per Cellmm10 Fragments Per Cell
0.60.70.80.9050100150200250300350400
hg19 Cellsmm10 CellsPurity (Cell Barcodes)​Sample atac_hgmm_1k_v1 - 1:1 mixture of fresh frozen human (GM12878) and mouse (A20) cells​Fraction of Fragments in Primary Species# of Cell Barcodes

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 cells (hg19)426
Estimated number of cells (mm10)431
Lower threshold on the number of fragments overlapping peaks per barcode to annotate barcode as cell (hg19)398.00
Lower threshold on the number of fragments overlapping peaks per barcode to annotate barcode as cell (mm10)132.00
Median fragments per cell (hg19)20,114
Median fragments per cell (mm10)19,393
Median fragments per non-cell barcode1
110010k12510251002510002510k25
Non-cellshg19 Cellshg19 Cells​Sample atac_hgmm_1k_v1 - 1:1 mixture of fresh frozen human (GM12878) and mouse (A20) cells​Barcodeshg19 Fragments Overlapping Peaks
110100100010k12510251002510002510k25100k2
Non-cellshg19 Cellshg19 Fragment Distribution​Sample atac_hgmm_1k_v1 - 1:1 mixture of fresh frozen human (GM12878) and mouse (A20) cells​hg19 Fragments Per BarcodeBarcodes
110010k12510251002510002510k25
Non-cellsmm10 Cellsmm10 Cells​Sample atac_hgmm_1k_v1 - 1:1 mixture of fresh frozen human (GM12878) and mouse (A20) cells​Barcodesmm10 Fragments Overlapping Peaks
110100100010k12510251002510002510k25100k2
Non-cellsmm10 Cellsmm10 Fragment Distribution​Sample atac_hgmm_1k_v1 - 1:1 mixture of fresh frozen human (GM12878) and mouse (A20) cells​mm10 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.
(bottom) Scatter plot of barcodes annotated as cells, colored by species.
−20020−20−100102030
Cluster 1 (173)Cluster 2 (167)Cluster 3 (152)Cluster 4 (151)Cluster 5 (118)Cluster 6 (88)Cell Clustering (By Cluster)​Sample atac_hgmm_1k_v1 - 1:1 mixture of fresh frozen human (GM12878) and mouse (A20) cells​tSNE axis 1tSNE axis 2
−20020−20−100102030
2.533.544.55log10 FragmentsCell Clustering (By Depth)​Sample atac_hgmm_1k_v1 - 1:1 mixture of fresh frozen human (GM12878) and mouse (A20) cells​tSNE axis 1tSNE axis 2
−20020−20−100102030
hg19 (418)mm10 (423)Doublet (8)Cell Clustering (By Species)​Sample atac_hgmm_1k_v1 - 1:1 mixture of fresh frozen human (GM12878) and mouse (A20) cells​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 regions33.2%
Fragments flanking a single nucleosome47.4%
200400600020k40k60k80k100k120k
Insert Size Distribution​Sample atac_hgmm_1k_v1 - 1:1 mixture of fresh frozen human (GM12878) and mouse (A20) cells​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 transposition events in peaks in cell barcodes
Transposition events are located at both ends of fragments that pass all filters. This metric measures the percentage of such events that fall in called peaks.
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 sites7.32
Fraction of fragments overlapping TSS (hg19)33.0%
Fraction of fragments overlapping TSS (mm10)33.2%
Fraction of fragments overlapping called peaks (hg19)64.9%
Fraction of fragments overlapping called peaks (mm10)65.1%
Fraction of transposition events in peaks in cell barcodes60.9%
Fraction of fragments overlapping any targeted region (hg19)82.9%
Fraction of fragments overlapping any targeted region (mm10)67.7%
Fraction of total read pairs mapped confidently to genome (>30 mapq)87.3%
Fraction of total read pairs that are unmapped and in cell barcodes0.9%
Fraction of total read pairs in mitochondria and in cell barcodes0.2%
−1000−500050010001234567
Enrichment around TSS (normalized)​Sample atac_hgmm_1k_v1 - 1:1 mixture of fresh frozen human (GM12878) and mouse (A20) cells​Relative Position (bp from TSS)Relative Enrichment
110010k00.20.40.60.81
Non-cellshg19mm10Singlecell Targeting (Peaks)​Sample atac_hgmm_1k_v1 - 1:1 mixture of fresh frozen human (GM12878) and mouse (A20) cells​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 duplicates25.3%
Sequencing saturation32.3%
Estimated bulk library complexity59,558,993
020k40k60k05k10k15k20k
Per-Cell Library Complexity At Read Depth​Sample atac_hgmm_1k_v1 - 1:1 mixture of fresh frozen human (GM12878) and mouse (A20) cells​Mean Reads Per CellMedian Unique Fragments Per Cell