Resource
| Id | ATAC-seq/ENCSR854ZBA |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR854ZBA [biosample_summary="Homo sapiens HG02840"] |
| Description |
status: released biological_replicates: Rep 1 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN613OKR|/analyses/ENCAN613OKR/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_not_compliant: According to ENCODE4 standards, overlap peaks files in ATAC-seq assays processed by the uniform processing pipeline should have FRiP (fraction of reads in called peak regions) scores > 0.3. FRiP scores 0.2-0.3 are acceptable, and < 0.2 are not compliant. {ENCFF117XXG|/files/ENCFF117XXG/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a FRiP score of 0.19. 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 {ENCFF720BLR|/files/ENCFF720BLR/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.865315. 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 {ENCFF720BLR|/files/ENCFF720BLR/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.88. audit_warning: According to ENCODE4 standards, ATAC-seq assays processed by the uniform processing pipeline should have either >150k reproducible peaks in an overlap peaks file, or >70k in an IDR thresholded peaks file. 100-150k or 50-70k peaks respectively is acceptable, and <100k or <50k respectively is not compliant. File(s) {ENCFF117XXG|/files/ENCFF117XXG/} (overlap peaks) and {ENCFF340FLI|/files/ENCFF340FLI/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have 119715 and 68698 peaks. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR854ZBA | float |
ATAC-seq_ENCSR854ZBA |
ATAC-seq ENCSR854ZBA [biosample_summary="Homo sapiens HG02840"]
|
 |
[1.6, 33] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 40481837 | 1.26% | 69475 |
| chr1 | 3606448 | 1.45% | 6025 |
| chr2 | 3440455 | 1.42% | 6092 |
| chr3 | 2794671 | 1.41% | 5023 |
| chr4 | 2273466 | 1.20% | 4172 |
| chr5 | 2404275 | 1.32% | 4272 |
| chr6 | 2751064 | 1.61% | 4815 |
| chr7 | 2215284 | 1.39% | 3903 |
| chr8 | 1971451 | 1.36% | 3539 |
| chr9 | 1582054 | 1.14% | 2727 |
| chr10 | 1860770 | 1.39% | 3206 |
| chr11 | 1935510 | 1.43% | 3315 |
| chr12 | 2030908 | 1.52% | 3439 |
| chr13 | 1069387 | 0.94% | 1909 |
| chr14 | 1277409 | 1.19% | 2119 |
| chr15 | 1157477 | 1.13% | 1955 |
| chr16 | 1214062 | 1.34% | 1891 |
| chr17 | 1523640 | 1.83% | 2327 |
| chr18 | 883314 | 1.10% | 1606 |
| chr19 | 1308482 | 2.23% | 1841 |
| chr20 | 860080 | 1.33% | 1432 |
| chr21 | 402448 | 0.86% | 643 |
| chr22 | 585340 | 1.15% | 886 |
| chrX | 1333321 | 0.85% | 2336 |
| chrY | 521 | <0.01% | 2 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 69475 | 150 | 2833 | 582.68 | 486 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF117XXG.bed.gz | 2.87 MB | 3dfdba48a3cb8f1fdec1a4f63154e24e |
| ENCFF117XXG.tabix.bed.gz | 792.86 KB | 70fc96642ad0e63a71be1b4d8902f3d3 |
| ENCFF117XXG.tabix.bed.gz.tbi | 345.18 KB | c2bf17c02d3fdb37359087c1372243f3 |
| genomic_resource.yaml | 3.47 KB | 0f0314ba79d2a6ff18d03c7007936047 |
| statistics/ |