Resource
| Id | ATAC-seq/ENCSR609GST |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR609GST [biosample_summary="Homo sapiens esophagus muscularis mucosa 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 {ENCAN557MKP|/analyses/ENCAN557MKP/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_internal_action: Released analysis {ENCAN557MKP|/analyses/ENCAN557MKP/} has in progress subobject document {e1600634-d439-4178-b606-cd07b839d04d|/documents/e1600634-d439-4178-b606-cd07b839d04d/} 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. {ENCFF282ETP|/files/ENCFF282ETP/} processed by ATAC-seq ENCODE4 v1.9.1 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) {ENCFF282ETP|/files/ENCFF282ETP/} (overlap peaks) and {ENCFF272UWG|/files/ENCFF272UWG/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have 56673 and 19555 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 {ENCFF210KJO|/files/ENCFF210KJO/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a TSS enrichment value of 6.501619247179108. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR609GST | float |
ATAC-seq_ENCSR609GST |
ATAC-seq ENCSR609GST [biosample_summary="Homo sapiens esophagus muscularis mucosa tissue male adult (54 years)"]
|
 |
[1.74, 27.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 18060619 | 0.56% | 44812 |
| chr1 | 1655264 | 0.66% | 3955 |
| chr2 | 1429766 | 0.59% | 3604 |
| chr3 | 1247387 | 0.63% | 3152 |
| chr4 | 1049361 | 0.55% | 2732 |
| chr5 | 1055659 | 0.58% | 2728 |
| chr6 | 1087345 | 0.64% | 2761 |
| chr7 | 1007944 | 0.63% | 2507 |
| chr8 | 840211 | 0.58% | 2145 |
| chr9 | 789124 | 0.57% | 1966 |
| chr10 | 875147 | 0.65% | 2205 |
| chr11 | 880031 | 0.65% | 2176 |
| chr12 | 882098 | 0.66% | 2167 |
| chr13 | 492079 | 0.43% | 1273 |
| chr14 | 591641 | 0.55% | 1422 |
| chr15 | 561253 | 0.55% | 1355 |
| chr16 | 565647 | 0.63% | 1377 |
| chr17 | 741492 | 0.89% | 1764 |
| chr18 | 410242 | 0.51% | 1083 |
| chr19 | 684424 | 1.17% | 1492 |
| chr20 | 430161 | 0.67% | 1073 |
| chr21 | 208057 | 0.45% | 495 |
| chr22 | 289065 | 0.57% | 727 |
| chrX | 274920 | 0.18% | 623 |
| chrY | 12301 | 0.02% | 30 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 44812 | 150 | 2218 | 403.03 | 342 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF282ETP.bed.gz | 1.27 MB | 989401aa300aa2114aed03e5d577577c |
| ENCFF282ETP.tabix.bed.gz | 480.87 KB | 065572717170da28946739c0403185aa |
| ENCFF282ETP.tabix.bed.gz.tbi | 293.85 KB | 8856ee3da7c2b4ce7467d16a6a44b0ef |
| genomic_resource.yaml | 2.98 KB | f9db9311a24a68d7ab0526f234bf6a67 |
| statistics/ |