Resource
| Id | ATAC-seq/ENCSR062SVK |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR062SVK [biosample_summary="Homo sapiens right atrium auricular region 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 {ENCAN905NGK|/analyses/ENCAN905NGK/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_internal_action: Released analysis {ENCAN905NGK|/analyses/ENCAN905NGK/} has in progress subobject document {f8476621-0eb6-4171-85f0-d9ba2054bbc7|/documents/f8476621-0eb6-4171-85f0-d9ba2054bbc7/} 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. {ENCFF705YSI|/files/ENCFF705YSI/} 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) {ENCFF705YSI|/files/ENCFF705YSI/} (overlap peaks) and {ENCFF675UHQ|/files/ENCFF675UHQ/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have 73431 and 25006 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 {ENCFF122ENK|/files/ENCFF122ENK/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a TSS enrichment value of 6.658336425673424. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR062SVK | float |
ATAC-seq_ENCSR062SVK |
ATAC-seq ENCSR062SVK [biosample_summary="Homo sapiens right atrium auricular region tissue female adult (51 years)"]
|
 |
[1.77, 16.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 23867150 | 0.74% | 50293 |
| chr1 | 2207843 | 0.89% | 4464 |
| chr2 | 1823332 | 0.75% | 3934 |
| chr3 | 1467473 | 0.74% | 3103 |
| chr4 | 1168727 | 0.61% | 2658 |
| chr5 | 1226055 | 0.68% | 2683 |
| chr6 | 1355933 | 0.79% | 2938 |
| chr7 | 1290753 | 0.81% | 2733 |
| chr8 | 1062533 | 0.73% | 2364 |
| chr9 | 1038049 | 0.75% | 2166 |
| chr10 | 1087326 | 0.81% | 2344 |
| chr11 | 1199869 | 0.89% | 2458 |
| chr12 | 1159229 | 0.87% | 2411 |
| chr13 | 597800 | 0.52% | 1339 |
| chr14 | 724531 | 0.68% | 1461 |
| chr15 | 769095 | 0.75% | 1587 |
| chr16 | 862703 | 0.95% | 1716 |
| chr17 | 1064893 | 1.28% | 2039 |
| chr18 | 526543 | 0.66% | 1198 |
| chr19 | 1094590 | 1.87% | 2041 |
| chr20 | 617423 | 0.96% | 1296 |
| chr21 | 290798 | 0.62% | 639 |
| chr22 | 494834 | 0.97% | 998 |
| chrX | 734058 | 0.47% | 1711 |
| chrY | 2760 | <0.01% | 12 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 50293 | 150 | 2855 | 474.56 | 377 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF705YSI.bed.gz | 1.62 MB | 03a3c18e95188ee582d38955f672aa30 |
| ENCFF705YSI.tabix.bed.gz | 543.53 KB | 3adacd339cf674a17c65b0eb15fcd2b7 |
| ENCFF705YSI.tabix.bed.gz.tbi | 318.15 KB | 5bdbc0b4c2baf39b07ceaf77097a9d0c |
| genomic_resource.yaml | 3.0 KB | 48b64a29638167300169f11a9a403292 |
| statistics/ |