Resource
| Id | ATAC-seq/ENCSR159GFS |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR159GFS [biosample_summary="Homo sapiens CD4-positive, CD25-positive, alpha-beta regulatory T cell male adult (42 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (42 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN882BEC|/analyses/ENCAN882BEC/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_warning: Alignment file {ENCFF456ETK|/files/ENCFF456ETK/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has 24322709 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. 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 {ENCFF456ETK|/files/ENCFF456ETK/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with NRF value of 0.897686. audit_warning: 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) {ENCFF364QVY|/files/ENCFF364QVY/} (overlap peaks) and {ENCFF519QMA|/files/ENCFF519QMA/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline have 91414 and 57636 peaks. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR159GFS | float |
ATAC-seq_ENCSR159GFS |
ATAC-seq ENCSR159GFS [biosample_summary="Homo sapiens CD4-positive, CD25-positive, alpha-beta regulatory T cell male adult (42 years)"]
|
 |
[1.3, 41.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 30043458 | 0.93% | 60177 |
| chr1 | 3017844 | 1.21% | 6026 |
| chr2 | 2321325 | 0.96% | 4770 |
| chr3 | 1753737 | 0.88% | 3545 |
| chr4 | 1066058 | 0.56% | 2116 |
| chr5 | 1363110 | 0.75% | 2781 |
| chr6 | 1784525 | 1.04% | 3621 |
| chr7 | 1434207 | 0.90% | 2875 |
| chr8 | 1160735 | 0.80% | 2356 |
| chr9 | 1151850 | 0.83% | 2301 |
| chr10 | 1416802 | 1.06% | 2948 |
| chr11 | 1519417 | 1.12% | 3043 |
| chr12 | 1495373 | 1.12% | 2963 |
| chr13 | 654951 | 0.57% | 1320 |
| chr14 | 1058663 | 0.99% | 2136 |
| chr15 | 1021086 | 1.00% | 2077 |
| chr16 | 1192666 | 1.32% | 2303 |
| chr17 | 1695191 | 2.04% | 3292 |
| chr18 | 514302 | 0.64% | 1103 |
| chr19 | 1564343 | 2.67% | 2901 |
| chr20 | 826385 | 1.28% | 1679 |
| chr21 | 413259 | 0.88% | 818 |
| chr22 | 738598 | 1.45% | 1463 |
| chrX | 836528 | 0.54% | 1649 |
| chrY | 42503 | 0.07% | 91 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 60177 | 150 | 2431 | 499.25 | 416 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF364QVY.bed.gz | 2.25 MB | 3f39c30b1d907aaf7226b9afce5e17a7 |
| ENCFF364QVY.tabix.bed.gz | 682.95 KB | 2b1e011892998904c283d173a6967792 |
| ENCFF364QVY.tabix.bed.gz.tbi | 285.7 KB | c8aee31dcc799828a0eb04b06ff15333 |
| genomic_resource.yaml | 2.96 KB | 4b5f4f5faa37c8da0d276cf7074b6f47 |
| statistics/ |