Resource
| Id | ATAC-seq/ENCSR115OIV |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR115OIV [biosample_summary="Homo sapiens activated T-helper 17 cell male adult (50 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 (50 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 {ENCAN746JJI|/analyses/ENCAN746JJI/} 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 {ENCFF932ZST|/files/ENCFF932ZST/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with NRF value of 0.827891. 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 {ENCFF932ZST|/files/ENCFF932ZST/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.83. 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 {ENCFF825QCZ|/files/ENCFF825QCZ/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with NRF value of 0.839611. 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 {ENCFF825QCZ|/files/ENCFF825QCZ/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.84. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR115OIV | float |
ATAC-seq_ENCSR115OIV |
ATAC-seq ENCSR115OIV [biosample_summary="Homo sapiens activated T-helper 17 cell male adult (50 years) treated with anti-CD3 and anti-CD28 coated beads for 72 hours, 50 U/mL Interleukin-2 for 72 hours"]
|
 |
[1.22, 42.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 65073258 | 2.02% | 122817 |
| chr1 | 6356370 | 2.55% | 11872 |
| chr2 | 5216121 | 2.15% | 10097 |
| chr3 | 4156111 | 2.10% | 8026 |
| chr4 | 2649502 | 1.39% | 5162 |
| chr5 | 3205168 | 1.77% | 6225 |
| chr6 | 4135552 | 2.42% | 7895 |
| chr7 | 3213676 | 2.02% | 6111 |
| chr8 | 2810231 | 1.94% | 5441 |
| chr9 | 2561462 | 1.85% | 4815 |
| chr10 | 3162445 | 2.36% | 6059 |
| chr11 | 3103086 | 2.30% | 5824 |
| chr12 | 3224928 | 2.42% | 6008 |
| chr13 | 1609960 | 1.41% | 3168 |
| chr14 | 2261564 | 2.11% | 4328 |
| chr15 | 2213285 | 2.17% | 4207 |
| chr16 | 2309224 | 2.56% | 4134 |
| chr17 | 3160549 | 3.80% | 5603 |
| chr18 | 1197716 | 1.49% | 2378 |
| chr19 | 2525279 | 4.31% | 4291 |
| chr20 | 1664585 | 2.58% | 3137 |
| chr21 | 866330 | 1.85% | 1612 |
| chr22 | 1309840 | 2.58% | 2341 |
| chrX | 1981686 | 1.27% | 3728 |
| chrY | 178588 | 0.31% | 355 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 122817 | 150 | 3147 | 529.84 | 429 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF123QHV.bed.gz | 4.67 MB | 99726b560ed9eea7e2362f21ad11d555 |
| ENCFF123QHV.tabix.bed.gz | 1.34 MB | 9ade2a53f72961c9cd367ccd1ef335d0 |
| ENCFF123QHV.tabix.bed.gz.tbi | 427.75 KB | f83dbbf49fa02f0cee30421a3f0e08f0 |
| genomic_resource.yaml | 4.25 KB | f22f5faa068ac7904a0eca2b720de542 |
| statistics/ |