Resource
| Id | ATAC-seq/ENCSR979TCG |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR979TCG [biosample_summary="Homo sapiens spleen tissue female adult (47 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (47 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN653JWH|/analyses/ENCAN653JWH/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_not_compliant: According to ENCODE4 standards, overlap peaks files in ATAC-seq assays processed by the uniform processing pipeline should have FRiP (fraction of reads in called peak regions) scores > 0.3. FRiP scores 0.2-0.3 are acceptable, and < 0.2 are not compliant. {ENCFF468VMN|/files/ENCFF468VMN/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a FRiP score of 0.19. audit_warning: NRF (Non Redundant Fraction) is equal to the result of the division of the number of reads after duplicates removal by the total number of reads. An NRF value < 0.7 is poor complexity, between 0.7 and 0.9 is moderate complexity, and >= 0.9 high complexity. NRF value > 0.9 is recommended, but > 0.7 is acceptable. ENCODE processed file {ENCFF503TXC|/files/ENCFF503TXC/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.864606. audit_warning: PBC1 (PCR Bottlenecking Coefficient 1, M1/M_distinct) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where some reads map (M_distinct). A PBC1 value in the range 0 - 0.5 is severe bottlenecking, 0.5 - 0.8 is moderate bottlenecking, 0.8 - 0.9 is mild bottlenecking, and > 0.9 is no bottlenecking. PBC1 value > 0.9 is recommended, but > 0.7 is acceptable. ENCODE processed file {ENCFF503TXC|/files/ENCFF503TXC/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.87. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR979TCG | float |
ATAC-seq_ENCSR979TCG |
ATAC-seq ENCSR979TCG [biosample_summary="Homo sapiens spleen tissue female adult (47 years)"]
|
 |
[1.75, 43.7] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 109740725 | 3.41% | 171629 |
| chr1 | 8087807 | 3.25% | 13083 |
| chr2 | 10044343 | 4.15% | 15713 |
| chr3 | 7470755 | 3.77% | 11873 |
| chr4 | 6656641 | 3.50% | 10274 |
| chr5 | 7131621 | 3.93% | 11087 |
| chr6 | 6636070 | 3.89% | 10760 |
| chr7 | 6505962 | 4.08% | 10080 |
| chr8 | 5997366 | 4.13% | 9446 |
| chr9 | 4474241 | 3.23% | 6994 |
| chr10 | 5959736 | 4.45% | 9086 |
| chr11 | 5234567 | 3.87% | 8082 |
| chr12 | 4665411 | 3.50% | 7598 |
| chr13 | 3749532 | 3.28% | 5737 |
| chr14 | 3027254 | 2.83% | 4830 |
| chr15 | 3159231 | 3.10% | 4945 |
| chr16 | 2702564 | 2.99% | 4329 |
| chr17 | 2645450 | 3.18% | 4377 |
| chr18 | 3410545 | 4.24% | 5281 |
| chr19 | 1936126 | 3.30% | 3146 |
| chr20 | 2564037 | 3.98% | 4061 |
| chr21 | 1262336 | 2.70% | 1943 |
| chr22 | 1288929 | 2.54% | 2019 |
| chrX | 5126718 | 3.29% | 6872 |
| chrY | 3483 | 0.01% | 13 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 171629 | 150 | 4418 | 639.41 | 549 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF468VMN.bed.gz | 5.6 MB | b5af80fcb3a9bb068c4ca68ae49ef083 |
| ENCFF468VMN.tabix.bed.gz | 1.85 MB | 209bf7f918b143c7eda5676db47c30c1 |
| ENCFF468VMN.tabix.bed.gz.tbi | 656.14 KB | c3ba0f3ff2add50a7caa987ec2d554a7 |
| genomic_resource.yaml | 3.32 KB | fc2ee2f4ea5be469f7f4f706fd8e97b8 |
| statistics/ |