Resource
| Id | ATAC-seq/ENCSR513EVP |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR513EVP [biosample_summary="Homo sapiens naive thymus-derived CD8-positive, alpha-beta T cell male adult (42 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (42 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN372DPK|/analyses/ENCAN372DPK/} 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. {ENCFF036OKE|/files/ENCFF036OKE/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has a FRiP score of 0.20. 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) {ENCFF036OKE|/files/ENCFF036OKE/} (overlap peaks) and {ENCFF242BPO|/files/ENCFF242BPO/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline have 76910 and 43467 peaks. audit_warning: Alignment file {ENCFF858GSU|/files/ENCFF858GSU/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has 23191739 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. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR513EVP | float |
ATAC-seq_ENCSR513EVP |
ATAC-seq ENCSR513EVP [biosample_summary="Homo sapiens naive thymus-derived CD8-positive, alpha-beta T cell male adult (42 years)"]
|
 |
[1.63, 33.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 26112152 | 0.81% | 51262 |
| chr1 | 2635065 | 1.06% | 5107 |
| chr2 | 1952986 | 0.81% | 3912 |
| chr3 | 1477465 | 0.75% | 2914 |
| chr4 | 940893 | 0.49% | 1837 |
| chr5 | 1227454 | 0.68% | 2472 |
| chr6 | 1507534 | 0.88% | 2939 |
| chr7 | 1305728 | 0.82% | 2595 |
| chr8 | 1003524 | 0.69% | 1991 |
| chr9 | 1024298 | 0.74% | 1983 |
| chr10 | 1227018 | 0.92% | 2511 |
| chr11 | 1345262 | 1.00% | 2696 |
| chr12 | 1317981 | 0.99% | 2577 |
| chr13 | 548439 | 0.48% | 1075 |
| chr14 | 900190 | 0.84% | 1769 |
| chr15 | 867867 | 0.85% | 1753 |
| chr16 | 1044045 | 1.16% | 1993 |
| chr17 | 1484495 | 1.78% | 2850 |
| chr18 | 466566 | 0.58% | 962 |
| chr19 | 1425862 | 2.43% | 2656 |
| chr20 | 740597 | 1.15% | 1508 |
| chr21 | 367488 | 0.79% | 703 |
| chr22 | 668588 | 1.32% | 1317 |
| chrX | 605663 | 0.39% | 1089 |
| chrY | 27144 | 0.05% | 53 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 51262 | 150 | 2457 | 509.39 | 425 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF036OKE.bed.gz | 1.89 MB | 60f20d33a48fd101271e573bff3cf77b |
| ENCFF036OKE.tabix.bed.gz | 585.1 KB | 3aa3393a41b044cd48e3cb73a211437e |
| ENCFF036OKE.tabix.bed.gz.tbi | 278.93 KB | a6b84da4187c52bd0bc40c332978822b |
| genomic_resource.yaml | 2.9 KB | 975a5d176f3b440612fcf74aaf674859 |
| statistics/ |