Resource
| Id | ATAC-seq/ENCSR373TDL |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR373TDL [biosample_summary="Homo sapiens right lobe of liver tissue female adult (53 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (53 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN907OKQ|/analyses/ENCAN907OKQ/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_internal_action: Released analysis {ENCAN907OKQ|/analyses/ENCAN907OKQ/} has in progress subobject document {f217c95d-6106-41a8-b512-046998322662|/documents/f217c95d-6106-41a8-b512-046998322662/} 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. {ENCFF360SWK|/files/ENCFF360SWK/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a FRiP score of 0.08. 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 {ENCFF205LVV|/files/ENCFF205LVV/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.872159. 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 {ENCFF205LVV|/files/ENCFF205LVV/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.89. 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) {ENCFF360SWK|/files/ENCFF360SWK/} (overlap peaks) and {ENCFF522FNJ|/files/ENCFF522FNJ/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have 104179 and 39822 peaks. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR373TDL | float |
ATAC-seq_ENCSR373TDL |
ATAC-seq ENCSR373TDL [biosample_summary="Homo sapiens right lobe of liver tissue female adult (53 years)"]
|
 |
[1.66, 30.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 31550255 | 0.98% | 75931 |
| chr1 | 2823631 | 1.13% | 6607 |
| chr2 | 2536332 | 1.05% | 6248 |
| chr3 | 1908941 | 0.96% | 4667 |
| chr4 | 1531355 | 0.81% | 3856 |
| chr5 | 1656836 | 0.91% | 4104 |
| chr6 | 1768682 | 1.04% | 4333 |
| chr7 | 1766006 | 1.11% | 4283 |
| chr8 | 1438581 | 0.99% | 3556 |
| chr9 | 1383484 | 1.00% | 3318 |
| chr10 | 1506506 | 1.13% | 3652 |
| chr11 | 1646697 | 1.22% | 3884 |
| chr12 | 1434819 | 1.08% | 3397 |
| chr13 | 832274 | 0.73% | 2045 |
| chr14 | 990426 | 0.93% | 2346 |
| chr15 | 961425 | 0.94% | 2269 |
| chr16 | 1170042 | 1.30% | 2712 |
| chr17 | 1302276 | 1.56% | 2943 |
| chr18 | 730332 | 0.91% | 1841 |
| chr19 | 1294811 | 2.21% | 2791 |
| chr20 | 789573 | 1.23% | 1920 |
| chr21 | 422344 | 0.90% | 1032 |
| chr22 | 611341 | 1.20% | 1442 |
| chrX | 1042217 | 0.67% | 2680 |
| chrY | 1324 | <0.01% | 5 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 75931 | 150 | 2422 | 415.51 | 328 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF360SWK.bed.gz | 2.42 MB | 58df987dbd2c8853a378b7102cc99198 |
| ENCFF360SWK.tabix.bed.gz | 824.78 KB | aa7881c84f3c6f48759ba95f2e66632f |
| ENCFF360SWK.tabix.bed.gz.tbi | 401.1 KB | af8caf0991522ebeb9514c55c5a0e3ae |
| genomic_resource.yaml | 3.76 KB | 37251a645703c9ff3b9941521b20996f |
| statistics/ |