Resource
| Id | ATAC-seq/ENCSR452OSK |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR452OSK [biosample_summary="Homo sapiens right cardiac atrium tissue male adult (40 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (40 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN237QKD|/analyses/ENCAN237QKD/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_internal_action: Released analysis {ENCAN237QKD|/analyses/ENCAN237QKD/} has in progress subobject document {fbb28048-cfb5-40f1-8245-dce1e3c0fa31|/documents/fbb28048-cfb5-40f1-8245-dce1e3c0fa31/} 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. {ENCFF092BBF|/files/ENCFF092BBF/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline has a FRiP score of 0.07. 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) {ENCFF092BBF|/files/ENCFF092BBF/} (overlap peaks) and {ENCFF820DKN|/files/ENCFF820DKN/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline have 70107 and 31063 peaks. audit_warning: Alignment file {ENCFF637IKR|/files/ENCFF637IKR/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline has 24239506 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 {ENCFF637IKR|/files/ENCFF637IKR/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with NRF value of 0.863969. 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 {ENCFF637IKR|/files/ENCFF637IKR/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.87. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR452OSK | float |
ATAC-seq_ENCSR452OSK |
ATAC-seq ENCSR452OSK [biosample_summary="Homo sapiens right cardiac atrium tissue male adult (40 years)"]
|
 |
[1.41, 18.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 22771387 | 0.71% | 47279 |
| chr1 | 2256663 | 0.91% | 4644 |
| chr2 | 1725832 | 0.71% | 3626 |
| chr3 | 1411377 | 0.71% | 2942 |
| chr4 | 963663 | 0.51% | 1997 |
| chr5 | 1157933 | 0.64% | 2434 |
| chr6 | 1311121 | 0.77% | 2738 |
| chr7 | 1121324 | 0.70% | 2295 |
| chr8 | 970368 | 0.67% | 2043 |
| chr9 | 995314 | 0.72% | 2061 |
| chr10 | 1046401 | 0.78% | 2200 |
| chr11 | 1222137 | 0.90% | 2533 |
| chr12 | 1131106 | 0.85% | 2328 |
| chr13 | 516292 | 0.45% | 1097 |
| chr14 | 748467 | 0.70% | 1553 |
| chr15 | 785818 | 0.77% | 1628 |
| chr16 | 844625 | 0.93% | 1744 |
| chr17 | 1187003 | 1.43% | 2451 |
| chr18 | 441228 | 0.55% | 974 |
| chr19 | 1104050 | 1.88% | 2159 |
| chr20 | 617842 | 0.96% | 1349 |
| chr21 | 295233 | 0.63% | 628 |
| chr22 | 466142 | 0.92% | 1000 |
| chrX | 436413 | 0.28% | 825 |
| chrY | 15035 | 0.03% | 30 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 47279 | 150 | 2551 | 481.64 | 404 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF092BBF.bed.gz | 1.69 MB | d5db70b6ac32242469ee5007aa96c0a6 |
| ENCFF092BBF.tabix.bed.gz | 536.12 KB | 803173215ae0fead592cc6b739f38f83 |
| ENCFF092BBF.tabix.bed.gz.tbi | 270.06 KB | 027165dd74d36c7cfafee7c12f0be36b |
| genomic_resource.yaml | 4.13 KB | d4aa027692d367c02f4ba1212a8ed38f |
| statistics/ |