Resource
| Id | ATAC-seq/ENCSR802GEV |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR802GEV [biosample_summary="Homo sapiens cerebellum tissue male adult (20 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (20 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN059BTS|/analyses/ENCAN059BTS/} 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. {ENCFF081WNU|/files/ENCFF081WNU/} processed by ATAC-seq ENCODE4 v1.9.2 GRCh38 pipeline has a FRiP score of 0.08. audit_not_compliant: 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) {ENCFF081WNU|/files/ENCFF081WNU/} (overlap peaks) and {ENCFF858CCP|/files/ENCFF858CCP/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.2 GRCh38 pipeline have 55243 and 26034 peaks. audit_warning: Alignment file {ENCFF111JBV|/files/ENCFF111JBV/} processed by ATAC-seq ENCODE4 v1.9.2 GRCh38 pipeline has 24700277 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 {ENCFF111JBV|/files/ENCFF111JBV/} processed by ATAC-seq ENCODE4 v1.9.2 GRCh38 pipeline was generated from a library with NRF value of 0.84668. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR802GEV | float |
ATAC-seq_ENCSR802GEV |
ATAC-seq ENCSR802GEV [biosample_summary="Homo sapiens cerebellum tissue male adult (20 years)"]
|
 |
[1.73, 19] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 18432154 | 0.57% | 42908 |
| chr1 | 1068709 | 0.43% | 2503 |
| chr2 | 1721966 | 0.71% | 3917 |
| chr3 | 1449797 | 0.73% | 3338 |
| chr4 | 1443687 | 0.76% | 3411 |
| chr5 | 1510824 | 0.83% | 3454 |
| chr6 | 1379738 | 0.81% | 3170 |
| chr7 | 1262647 | 0.79% | 2916 |
| chr8 | 1191769 | 0.82% | 2736 |
| chr9 | 617160 | 0.45% | 1438 |
| chr10 | 1067090 | 0.80% | 2447 |
| chr11 | 701549 | 0.52% | 1656 |
| chr12 | 1039741 | 0.78% | 2341 |
| chr13 | 739819 | 0.65% | 1702 |
| chr14 | 496740 | 0.46% | 1152 |
| chr15 | 277068 | 0.27% | 679 |
| chr16 | 227866 | 0.25% | 587 |
| chr17 | 212941 | 0.26% | 560 |
| chr18 | 683216 | 0.85% | 1565 |
| chr19 | 176439 | 0.30% | 452 |
| chr20 | 315098 | 0.49% | 765 |
| chr21 | 231465 | 0.50% | 575 |
| chr22 | 101786 | 0.20% | 285 |
| chrX | 490736 | 0.31% | 1181 |
| chrY | 24303 | 0.04% | 78 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 42908 | 150 | 2308 | 429.57 | 350 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF081WNU.bed.gz | 1.26 MB | 97317bfa6775175703088eeacacdd6b1 |
| ENCFF081WNU.tabix.bed.gz | 463.55 KB | c91bc9b1082d6c3c33641991a2696064 |
| ENCFF081WNU.tabix.bed.gz.tbi | 284.08 KB | a7906732b29ba8df8f3fe07c3c685434 |
| genomic_resource.yaml | 3.25 KB | c549830dc9631ec1284edc45b3118dde |
| statistics/ |