Resource
| Id | ATAC-seq/ENCSR729FNL |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR729FNL [biosample_summary="Homo sapiens posterior cingulate cortex 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 {ENCAN343RLI|/analyses/ENCAN343RLI/} 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. {ENCFF129OYC|/files/ENCFF129OYC/} processed by ATAC-seq ENCODE4 v1.9.2 GRCh38 pipeline has a FRiP score of 0.04. 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) {ENCFF129OYC|/files/ENCFF129OYC/} (overlap peaks) and {ENCFF221FSW|/files/ENCFF221FSW/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.2 GRCh38 pipeline have 39396 and 11331 peaks. audit_warning: Transcription Start Site (TSS) enrichment values for alignments to the human genome GRCh38 are concerning when < 5, acceptable between 5 and 7, and ideal when > 7. ENCODE processed file {ENCFF876ELG|/files/ENCFF876ELG/} processed by ATAC-seq ENCODE4 v1.9.2 GRCh38 pipeline has a TSS enrichment value of 5.992365727913902. 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 {ENCFF876ELG|/files/ENCFF876ELG/} processed by ATAC-seq ENCODE4 v1.9.2 GRCh38 pipeline was generated from a library with NRF value of 0.857676. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR729FNL | float |
ATAC-seq_ENCSR729FNL |
ATAC-seq ENCSR729FNL [biosample_summary="Homo sapiens posterior cingulate cortex tissue male adult (20 years)"]
|
 |
[2.01, 16.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 12668871 | 0.39% | 32177 |
| chr1 | 1088843 | 0.44% | 2747 |
| chr2 | 1035206 | 0.43% | 2592 |
| chr3 | 889939 | 0.45% | 2249 |
| chr4 | 817070 | 0.43% | 2072 |
| chr5 | 853900 | 0.47% | 2167 |
| chr6 | 889019 | 0.52% | 2222 |
| chr7 | 796714 | 0.50% | 2028 |
| chr8 | 658400 | 0.45% | 1700 |
| chr9 | 549416 | 0.40% | 1382 |
| chr10 | 588915 | 0.44% | 1491 |
| chr11 | 690706 | 0.51% | 1727 |
| chr12 | 683775 | 0.51% | 1706 |
| chr13 | 403896 | 0.35% | 1049 |
| chr14 | 473258 | 0.44% | 1144 |
| chr15 | 383863 | 0.38% | 939 |
| chr16 | 244869 | 0.27% | 635 |
| chr17 | 256406 | 0.31% | 710 |
| chr18 | 348871 | 0.43% | 921 |
| chr19 | 211254 | 0.36% | 566 |
| chr20 | 227273 | 0.35% | 625 |
| chr21 | 141459 | 0.30% | 375 |
| chr22 | 113566 | 0.22% | 312 |
| chrX | 308394 | 0.20% | 776 |
| chrY | 13859 | 0.02% | 42 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 32177 | 150 | 1691 | 393.72 | 326 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF129OYC.bed.gz | 885.51 KB | f7ca540719874aa003fd85e53634814b |
| ENCFF129OYC.tabix.bed.gz | 345.09 KB | 080bafc9c47af58ba43aff44b4d177b7 |
| ENCFF129OYC.tabix.bed.gz.tbi | 228.84 KB | bbb3877dfe60ac20b7d731f5e44eff76 |
| genomic_resource.yaml | 3.29 KB | 3d7c0c94990ed0ae2442ddea94a0711f |
| statistics/ |