Resource
| Id | ATAC-seq/ENCSR637OPZ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR637OPZ [biosample_summary="Homo sapiens stimulated activated naive CD8-positive, alpha-beta T cell male adult (36 years) treated with 100 ng/mL Interleukin-15 for 72 hours, anti-CD3 and anti-CD28 coated beads for 72 hours"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: male adult (36 years) treated with 100 ng/mL Interleukin-15 for 72 hours, anti-CD3 and anti-CD28 coated beads for 72 hours output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN478FMJ|/analyses/ENCAN478FMJ/} 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 {ENCFF218IMC|/files/ENCFF218IMC/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with NRF value of 0.852658. 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 {ENCFF218IMC|/files/ENCFF218IMC/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.86. 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 {ENCFF960TBS|/files/ENCFF960TBS/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with NRF value of 0.84677. 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 {ENCFF960TBS|/files/ENCFF960TBS/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.85. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR637OPZ | float |
ATAC-seq_ENCSR637OPZ |
ATAC-seq ENCSR637OPZ [biosample_summary="Homo sapiens stimulated activated naive CD8-positive, alpha-beta T cell male adult (36 years) treated with 100 ng/mL Interleukin-15 for 72 hours, anti-CD3 and anti-CD28 coated beads for 72 hours"]
|
 |
[1.27, 42.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 67894161 | 2.11% | 116509 |
| chr1 | 6470159 | 2.60% | 10952 |
| chr2 | 5729422 | 2.37% | 10099 |
| chr3 | 4272433 | 2.15% | 7599 |
| chr4 | 2885325 | 1.52% | 5154 |
| chr5 | 3506782 | 1.93% | 6201 |
| chr6 | 4078042 | 2.39% | 7101 |
| chr7 | 3742904 | 2.35% | 6410 |
| chr8 | 2951938 | 2.03% | 5232 |
| chr9 | 2722074 | 1.97% | 4660 |
| chr10 | 3327804 | 2.49% | 5831 |
| chr11 | 3428223 | 2.54% | 5846 |
| chr12 | 3249905 | 2.44% | 5517 |
| chr13 | 1614670 | 1.41% | 2911 |
| chr14 | 2215489 | 2.07% | 3838 |
| chr15 | 2015599 | 1.98% | 3474 |
| chr16 | 2333843 | 2.58% | 3803 |
| chr17 | 3089926 | 3.71% | 4970 |
| chr18 | 1393451 | 1.73% | 2521 |
| chr19 | 2764550 | 4.72% | 4186 |
| chr20 | 1734307 | 2.69% | 2937 |
| chr21 | 854742 | 1.83% | 1438 |
| chr22 | 1376294 | 2.71% | 2191 |
| chrX | 1894376 | 1.21% | 3191 |
| chrY | 241903 | 0.42% | 447 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 116509 | 150 | 3362 | 582.74 | 476 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF955PTL.bed.gz | 4.98 MB | f3e0e5fcf4359cb0ca0131c00090b1a9 |
| ENCFF955PTL.tabix.bed.gz | 1.29 MB | 831ee074183c12821df6dc59291b14eb |
| ENCFF955PTL.tabix.bed.gz.tbi | 439.01 KB | 7599fa82475e4972a608cb59ae350080 |
| genomic_resource.yaml | 4.36 KB | e76a8196a1d6b94c07dd166c5e617481 |
| statistics/ |