Resource
| Id | ATAC-seq/ENCSR999NKW |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR999NKW [biosample_summary="Homo sapiens prostate gland tissue male adult (54 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (54 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN518UZV|/analyses/ENCAN518UZV/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_internal_action: Released analysis {ENCAN518UZV|/analyses/ENCAN518UZV/} has in progress subobject document {7e497c52-6f63-4231-bc89-c15a5f751eb4|/documents/7e497c52-6f63-4231-bc89-c15a5f751eb4/} 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. {ENCFF030AIT|/files/ENCFF030AIT/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a FRiP score of 0.06. audit_not_compliant: According to ENCODE4 standards, ATAC-seq assays processed by the uniform processing pipeline should have either >150k reproducible peaks in an overlap peaks file, or >70k in an IDR thresholded peaks file. 100-150k or 50-70k peaks respectively is acceptable, and <100k or <50k respectively is not compliant. File(s) {ENCFF030AIT|/files/ENCFF030AIT/} (overlap peaks) and {ENCFF963ISM|/files/ENCFF963ISM/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have 65658 and 20844 peaks. audit_warning: Alignment file {ENCFF678CZL|/files/ENCFF678CZL/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has 21947987 usable fragments. According to ENCODE4 standards, ATAC-seq assays processed by the uniform processing pipeline should have > 25 million usable fragments. 20-25 million is acceptable and < 15 million is not compliant. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR999NKW | float |
ATAC-seq_ENCSR999NKW |
ATAC-seq ENCSR999NKW [biosample_summary="Homo sapiens prostate gland tissue male adult (54 years)"]
|
 |
[1.73, 24.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 20545100 | 0.64% | 51636 |
| chr1 | 1910391 | 0.77% | 4739 |
| chr2 | 1636779 | 0.68% | 4150 |
| chr3 | 1345215 | 0.68% | 3383 |
| chr4 | 1122467 | 0.59% | 2907 |
| chr5 | 1132620 | 0.62% | 2915 |
| chr6 | 1190484 | 0.70% | 2985 |
| chr7 | 1131636 | 0.71% | 2807 |
| chr8 | 956716 | 0.66% | 2471 |
| chr9 | 830905 | 0.60% | 2086 |
| chr10 | 976891 | 0.73% | 2548 |
| chr11 | 1101246 | 0.82% | 2779 |
| chr12 | 1078628 | 0.81% | 2683 |
| chr13 | 614797 | 0.54% | 1697 |
| chr14 | 653898 | 0.61% | 1599 |
| chr15 | 574153 | 0.56% | 1415 |
| chr16 | 686021 | 0.76% | 1717 |
| chr17 | 779751 | 0.94% | 1884 |
| chr18 | 492950 | 0.61% | 1304 |
| chr19 | 837820 | 1.43% | 1867 |
| chr20 | 499322 | 0.77% | 1260 |
| chr21 | 267109 | 0.57% | 706 |
| chr22 | 333833 | 0.66% | 830 |
| chrX | 365753 | 0.23% | 842 |
| chrY | 25715 | 0.04% | 62 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 51636 | 150 | 2316 | 397.88 | 324 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF030AIT.bed.gz | 1.49 MB | 891e6c4cb3c072fea3d81e1b33742c54 |
| ENCFF030AIT.tabix.bed.gz | 553.36 KB | 7d657672861e45b7aeee911a929dd620 |
| ENCFF030AIT.tabix.bed.gz.tbi | 328.28 KB | 5e3df81f62eaa6dbc6e66835db392c45 |
| genomic_resource.yaml | 2.95 KB | a4e26c6b5fcc9ed323ac9ce3cd32102b |
| statistics/ |