Resource
| Id | ATAC-seq/ENCSR955JSO |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR955JSO [biosample_summary="Homo sapiens breast epithelium tissue male adult (54 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (54 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN362BBC|/analyses/ENCAN362BBC/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_internal_action: Released analysis {ENCAN362BBC|/analyses/ENCAN362BBC/} has in progress subobject document {72e5ee36-e11a-475d-a13a-8bda096d5636|/documents/72e5ee36-e11a-475d-a13a-8bda096d5636/} 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. {ENCFF934JPB|/files/ENCFF934JPB/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a FRiP score of 0.12. 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 {ENCFF344HVC|/files/ENCFF344HVC/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.865547. 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 {ENCFF344HVC|/files/ENCFF344HVC/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.87. 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) {ENCFF934JPB|/files/ENCFF934JPB/} (overlap peaks) and {ENCFF738IZU|/files/ENCFF738IZU/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have 121178 and 62135 peaks. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR955JSO | float |
ATAC-seq_ENCSR955JSO |
ATAC-seq ENCSR955JSO [biosample_summary="Homo sapiens breast epithelium tissue male adult (54 years)"]
|
 |
[1.6, 32.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 39320919 | 1.22% | 74941 |
| chr1 | 3844346 | 1.54% | 7175 |
| chr2 | 3004851 | 1.24% | 5815 |
| chr3 | 2435860 | 1.23% | 4714 |
| chr4 | 1827828 | 0.96% | 3717 |
| chr5 | 2030359 | 1.12% | 4022 |
| chr6 | 2258120 | 1.32% | 4303 |
| chr7 | 1971863 | 1.24% | 3820 |
| chr8 | 1730541 | 1.19% | 3392 |
| chr9 | 1722865 | 1.24% | 3250 |
| chr10 | 1837362 | 1.37% | 3564 |
| chr11 | 2139174 | 1.58% | 4066 |
| chr12 | 1864494 | 1.40% | 3519 |
| chr13 | 885369 | 0.77% | 1744 |
| chr14 | 1254642 | 1.17% | 2338 |
| chr15 | 1245267 | 1.22% | 2332 |
| chr16 | 1466619 | 1.62% | 2727 |
| chr17 | 2002407 | 2.41% | 3662 |
| chr18 | 835460 | 1.04% | 1699 |
| chr19 | 1734520 | 2.96% | 3025 |
| chr20 | 1055459 | 1.64% | 2059 |
| chr21 | 522199 | 1.12% | 988 |
| chr22 | 894915 | 1.76% | 1689 |
| chrX | 718619 | 0.46% | 1238 |
| chrY | 37780 | 0.07% | 83 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 74941 | 150 | 2613 | 524.69 | 432 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF934JPB.bed.gz | 2.88 MB | 3e196ae9513491b5bf997b8a202cc869 |
| ENCFF934JPB.tabix.bed.gz | 848.63 KB | 566cfbe616d66270a9b6eb5122555fb7 |
| ENCFF934JPB.tabix.bed.gz.tbi | 372.49 KB | 10e5dfe17a03c88f44c2bd28a133ae23 |
| genomic_resource.yaml | 3.75 KB | 34ce88bc2a854514720a18c46427012e |
| statistics/ |