Resource
| Id | ATAC-seq/ENCSR659SFK |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR659SFK [biosample_summary="Homo sapiens activated B cell male adult\ \ (22 years) treated with 0.5 \u03BCM CpG ODN for 24 hours"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (22 years) treated with 0.5 μM CpG ODN for 24 hours output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN661DOR|/analyses/ENCAN661DOR/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_warning: Alignment file {ENCFF547RWX|/files/ENCFF547RWX/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has 22451903 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 {ENCFF547RWX|/files/ENCFF547RWX/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with NRF value of 0.728279. 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 {ENCFF547RWX|/files/ENCFF547RWX/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.74. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR659SFK | float |
ATAC-seq_ENCSR659SFK |
ATAC-seq ENCSR659SFK [biosample_summary="Homo sapiens activated B cell male adult\ \ (22 years) treated with 0.5 \u03BCM CpG ODN for 24 hours"]
|
 |
[1.35, 43.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 40210699 | 1.25% | 73028 |
| chr1 | 3990425 | 1.60% | 7194 |
| chr2 | 3034843 | 1.25% | 5639 |
| chr3 | 2359591 | 1.19% | 4445 |
| chr4 | 1454386 | 0.76% | 2649 |
| chr5 | 1869048 | 1.03% | 3487 |
| chr6 | 2463829 | 1.44% | 4556 |
| chr7 | 2025247 | 1.27% | 3756 |
| chr8 | 1610998 | 1.11% | 3003 |
| chr9 | 1625523 | 1.17% | 3006 |
| chr10 | 1816460 | 1.36% | 3378 |
| chr11 | 2003565 | 1.48% | 3562 |
| chr12 | 2072702 | 1.56% | 3696 |
| chr13 | 826284 | 0.72% | 1541 |
| chr14 | 1383856 | 1.29% | 2478 |
| chr15 | 1294961 | 1.27% | 2381 |
| chr16 | 1578006 | 1.75% | 2734 |
| chr17 | 2223401 | 2.67% | 3887 |
| chr18 | 733476 | 0.91% | 1408 |
| chr19 | 2046144 | 3.49% | 3445 |
| chr20 | 1107593 | 1.72% | 2064 |
| chr21 | 506353 | 1.08% | 870 |
| chr22 | 995332 | 1.96% | 1743 |
| chrX | 1135481 | 0.73% | 2005 |
| chrY | 53195 | 0.09% | 101 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 73028 | 150 | 3068 | 550.62 | 449 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF958SXF.bed.gz | 2.83 MB | 7173735ce4504aa497dcd8d015457601 |
| ENCFF958SXF.tabix.bed.gz | 819.03 KB | 414e3ce73dbd07ab8831179de8a4cdad |
| ENCFF958SXF.tabix.bed.gz.tbi | 315.79 KB | e1211f01b67af4917f77e61a63ffbbf0 |
| genomic_resource.yaml | 3.25 KB | 6a036194d6ee93b00917f2546e90e8ae |
| statistics/ |