Resource
| Id | ATAC-seq/ENCSR939EVW |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR939EVW [biosample_summary="Homo sapiens GM21528"] |
| Description |
status: released biological_replicates: Rep 1 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN429VFC|/analyses/ENCAN429VFC/} 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. {ENCFF249WBT|/files/ENCFF249WBT/} 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 {ENCFF088VJQ|/files/ENCFF088VJQ/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.795735. 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 {ENCFF088VJQ|/files/ENCFF088VJQ/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.82. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR939EVW | float |
ATAC-seq_ENCSR939EVW |
ATAC-seq ENCSR939EVW [biosample_summary="Homo sapiens GM21528"]
|
 |
[1.52, 23.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 49030159 | 1.52% | 84402 |
| chr1 | 4499489 | 1.81% | 7595 |
| chr2 | 4244630 | 1.75% | 7544 |
| chr3 | 3407792 | 1.72% | 6094 |
| chr4 | 2818984 | 1.48% | 5193 |
| chr5 | 2970499 | 1.64% | 5298 |
| chr6 | 3309198 | 1.94% | 5742 |
| chr7 | 2695918 | 1.69% | 4740 |
| chr8 | 2409855 | 1.66% | 4330 |
| chr9 | 1945292 | 1.41% | 3378 |
| chr10 | 2321375 | 1.73% | 4034 |
| chr11 | 2359294 | 1.75% | 4005 |
| chr12 | 2464829 | 1.85% | 4208 |
| chr13 | 1330300 | 1.16% | 2355 |
| chr14 | 1523592 | 1.42% | 2569 |
| chr15 | 1411856 | 1.38% | 2356 |
| chr16 | 1425518 | 1.58% | 2219 |
| chr17 | 1696054 | 2.04% | 2618 |
| chr18 | 1136229 | 1.41% | 2067 |
| chr19 | 1430008 | 2.44% | 1991 |
| chr20 | 1034104 | 1.60% | 1777 |
| chr21 | 467993 | 1.00% | 759 |
| chr22 | 646164 | 1.27% | 975 |
| chrX | 1388793 | 0.89% | 2377 |
| chrY | 92393 | 0.16% | 178 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 84402 | 150 | 3411 | 580.91 | 470 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF249WBT.bed.gz | 3.58 MB | b4235b51ee93731182382b196b7e7f15 |
| ENCFF249WBT.tabix.bed.gz | 953.56 KB | 09c3fd430aa1dcd24bc3b95f15decf6c |
| ENCFF249WBT.tabix.bed.gz.tbi | 398.82 KB | 1316c79f17a784e5d13d1bb6d14d1b97 |
| genomic_resource.yaml | 2.91 KB | 3c721cfdcca2dff2d92d240072d645b3 |
| statistics/ |