Resource
| Id | ATAC-seq/ENCSR558ZSN |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR558ZSN [biosample_summary="Homo sapiens activated T-cell female adult (21 years) treated with anti-CD3 and anti-CD28 coated beads for 72 hours, 50 U/mL Interleukin-2 for 72 hours"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: female adult (21 years) treated with anti-CD3 and anti-CD28 coated beads for 72 hours, 50 U/mL Interleukin-2 for 72 hours output_type: replicated peaks audit_internal_action: Released analysis {ENCAN936YOF|/analyses/ENCAN936YOF/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} 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 {ENCFF218OSF|/files/ENCFF218OSF/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with NRF value of 0.883735. 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 {ENCFF287DFF|/files/ENCFF287DFF/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with NRF value of 0.882192. 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 {ENCFF287DFF|/files/ENCFF287DFF/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.90. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR558ZSN | float |
ATAC-seq_ENCSR558ZSN |
ATAC-seq ENCSR558ZSN [biosample_summary="Homo sapiens activated T-cell female adult (21 years) treated with anti-CD3 and anti-CD28 coated beads for 72 hours, 50 U/mL Interleukin-2 for 72 hours"]
|
 |
[1.17, 47.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 58954107 | 1.83% | 97092 |
| chr1 | 5779487 | 2.32% | 9432 |
| chr2 | 4787749 | 1.98% | 8028 |
| chr3 | 3701064 | 1.87% | 6285 |
| chr4 | 2378054 | 1.25% | 4045 |
| chr5 | 2916466 | 1.61% | 4903 |
| chr6 | 3600605 | 2.11% | 5944 |
| chr7 | 2957267 | 1.86% | 4925 |
| chr8 | 2517631 | 1.73% | 4239 |
| chr9 | 2322918 | 1.68% | 3872 |
| chr10 | 2742661 | 2.05% | 4579 |
| chr11 | 2843304 | 2.10% | 4646 |
| chr12 | 2882800 | 2.16% | 4690 |
| chr13 | 1403564 | 1.23% | 2388 |
| chr14 | 2009254 | 1.88% | 3318 |
| chr15 | 1954283 | 1.92% | 3268 |
| chr16 | 2123605 | 2.35% | 3335 |
| chr17 | 2903872 | 3.49% | 4516 |
| chr18 | 1080570 | 1.34% | 1870 |
| chr19 | 2475557 | 4.22% | 3690 |
| chr20 | 1565736 | 2.43% | 2597 |
| chr21 | 809555 | 1.73% | 1341 |
| chr22 | 1231370 | 2.42% | 1912 |
| chrX | 1966469 | 1.26% | 3268 |
| chrY | 266 | <0.01% | 1 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 97092 | 150 | 3291 | 607.2 | 521 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF381CVI.bed.gz | 4.09 MB | 12e1d8e90e28f56dcef0951d6851b72c |
| ENCFF381CVI.tabix.bed.gz | 1.08 MB | e5be6b50b98b60c251ad31082bc88167 |
| ENCFF381CVI.tabix.bed.gz.tbi | 388.5 KB | 3f58fcc5da87bb04f1b59487efbb7a8c |
| genomic_resource.yaml | 3.59 KB | 76d16ab6621b90394779e687ae2fc7f4 |
| statistics/ |