Resource
| Id | ATAC-seq/ENCSR096BPX |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR096BPX [biosample_summary="Homo sapiens esophagus squamous epithelium tissue female adult (51 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (51 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN473YZI|/analyses/ENCAN473YZI/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_internal_action: Released analysis {ENCAN473YZI|/analyses/ENCAN473YZI/} has in progress subobject document {eb17df69-73f3-43d7-9e49-6138149efd94|/documents/eb17df69-73f3-43d7-9e49-6138149efd94/} 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. {ENCFF181DWD|/files/ENCFF181DWD/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a FRiP score of 0.05. 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) {ENCFF181DWD|/files/ENCFF181DWD/} (overlap peaks) and {ENCFF984VPG|/files/ENCFF984VPG/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have 63096 and 20473 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 {ENCFF479ISR|/files/ENCFF479ISR/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a TSS enrichment value of 6.583807805114838. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR096BPX | float |
ATAC-seq_ENCSR096BPX |
ATAC-seq ENCSR096BPX [biosample_summary="Homo sapiens esophagus squamous epithelium tissue female adult (51 years)"]
|
 |
[1.62, 28.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 19398941 | 0.60% | 49311 |
| chr1 | 1804530 | 0.72% | 4508 |
| chr2 | 1572679 | 0.65% | 4039 |
| chr3 | 1270055 | 0.64% | 3195 |
| chr4 | 1041050 | 0.55% | 2647 |
| chr5 | 1086185 | 0.60% | 2802 |
| chr6 | 1178323 | 0.69% | 3008 |
| chr7 | 1043826 | 0.66% | 2655 |
| chr8 | 861352 | 0.59% | 2220 |
| chr9 | 827158 | 0.60% | 2110 |
| chr10 | 920488 | 0.69% | 2348 |
| chr11 | 971811 | 0.72% | 2500 |
| chr12 | 940936 | 0.71% | 2360 |
| chr13 | 496055 | 0.43% | 1259 |
| chr14 | 604189 | 0.56% | 1472 |
| chr15 | 616639 | 0.60% | 1576 |
| chr16 | 625216 | 0.69% | 1638 |
| chr17 | 778814 | 0.94% | 1951 |
| chr18 | 442591 | 0.55% | 1128 |
| chr19 | 672232 | 1.15% | 1639 |
| chr20 | 463574 | 0.72% | 1195 |
| chr21 | 249709 | 0.53% | 612 |
| chr22 | 330061 | 0.65% | 844 |
| chrX | 600000 | 0.38% | 1599 |
| chrY | 1468 | <0.01% | 6 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 49311 | 150 | 1939 | 393.4 | 332 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF181DWD.bed.gz | 1.48 MB | 47b57a3158d935d3f3000b891d3c136b |
| ENCFF181DWD.tabix.bed.gz | 540.15 KB | 5a8596230d3d34265ccaa4b47fbddcbb |
| ENCFF181DWD.tabix.bed.gz.tbi | 298.83 KB | 4d59ebca4eb1845e4dc33d772f489190 |
| genomic_resource.yaml | 3.0 KB | 48440822c7ced6c174df9635325cd1f9 |
| statistics/ |