Resource
| Id | ATAC-seq/ENCSR174SUM |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR174SUM [biosample_summary="Homo sapiens activated naive CD4-positive, alpha-beta T cell male adult (48 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: male adult (48 years) treated with anti-CD3 and anti-CD28 coated beads for 72 hours, 50 U/mL Interleukin-2 for 72 hours output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN790NYJ|/analyses/ENCAN790NYJ/} 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 {ENCFF914JEV|/files/ENCFF914JEV/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with NRF value of 0.871037. 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 {ENCFF914JEV|/files/ENCFF914JEV/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.89. 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 {ENCFF354BOL|/files/ENCFF354BOL/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with NRF value of 0.866076. 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 {ENCFF354BOL|/files/ENCFF354BOL/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.88. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR174SUM | float |
ATAC-seq_ENCSR174SUM |
ATAC-seq ENCSR174SUM [biosample_summary="Homo sapiens activated naive CD4-positive, alpha-beta T cell male adult (48 years) treated with anti-CD3 and anti-CD28 coated beads for 72 hours, 50 U/mL Interleukin-2 for 72 hours"]
|
 |
[1.23, 43.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 67781554 | 2.11% | 112901 |
| chr1 | 6647822 | 2.67% | 10931 |
| chr2 | 5522392 | 2.28% | 9428 |
| chr3 | 4338665 | 2.19% | 7453 |
| chr4 | 2959539 | 1.56% | 5143 |
| chr5 | 3415865 | 1.88% | 5796 |
| chr6 | 4151723 | 2.43% | 6911 |
| chr7 | 3408978 | 2.14% | 5762 |
| chr8 | 2962221 | 2.04% | 5064 |
| chr9 | 2702165 | 1.95% | 4543 |
| chr10 | 3178327 | 2.38% | 5306 |
| chr11 | 3295630 | 2.44% | 5380 |
| chr12 | 3364614 | 2.52% | 5559 |
| chr13 | 1679890 | 1.47% | 2938 |
| chr14 | 2269205 | 2.12% | 3783 |
| chr15 | 2249668 | 2.21% | 3798 |
| chr16 | 2343782 | 2.59% | 3698 |
| chr17 | 3210035 | 3.86% | 5040 |
| chr18 | 1284268 | 1.60% | 2287 |
| chr19 | 2661208 | 4.54% | 3962 |
| chr20 | 1718918 | 2.67% | 2867 |
| chr21 | 882814 | 1.89% | 1474 |
| chr22 | 1319035 | 2.60% | 2054 |
| chrX | 2045311 | 1.31% | 3420 |
| chrY | 169479 | 0.30% | 304 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 112901 | 150 | 3743 | 600.36 | 516 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF049DNM.bed.gz | 4.69 MB | 45dc681b2e375b85841ea2d304f235ab |
| ENCFF049DNM.tabix.bed.gz | 1.25 MB | 8e625bcc98dca34b4624f2e001af10ed |
| ENCFF049DNM.tabix.bed.gz.tbi | 430.38 KB | c84d6a9c5e357e840453666f6c6f021e |
| genomic_resource.yaml | 4.31 KB | acaa78458113bd18a52e0d3796e1c0cd |
| statistics/ |