Resource
| Id | ATAC-seq/ENCSR700HPA |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR700HPA [biosample_summary="Homo sapiens GM18499"] |
| Description |
status: released biological_replicates: Rep 1 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN833QRG|/analyses/ENCAN833QRG/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_not_compliant: Alignment file {ENCFF617WPF|/files/ENCFF617WPF/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has 17107587 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. audit_warning: 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) {ENCFF647UDQ|/files/ENCFF647UDQ/} (overlap peaks) and {ENCFF452XUT|/files/ENCFF452XUT/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have 118210 and 56440 peaks. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR700HPA | float |
ATAC-seq_ENCSR700HPA |
ATAC-seq ENCSR700HPA [biosample_summary="Homo sapiens GM18499"]
|
 |
[1.6, 32.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 40663174 | 1.26% | 84599 |
| chr1 | 3550142 | 1.43% | 7273 |
| chr2 | 3589253 | 1.48% | 7646 |
| chr3 | 2968976 | 1.50% | 6322 |
| chr4 | 2477556 | 1.30% | 5361 |
| chr5 | 2553754 | 1.41% | 5431 |
| chr6 | 2816877 | 1.65% | 5922 |
| chr7 | 2333864 | 1.46% | 4883 |
| chr8 | 2110542 | 1.45% | 4485 |
| chr9 | 1577292 | 1.14% | 3286 |
| chr10 | 1984522 | 1.48% | 4141 |
| chr11 | 1913147 | 1.42% | 3963 |
| chr12 | 2037201 | 1.53% | 4176 |
| chr13 | 1141293 | 1.00% | 2420 |
| chr14 | 1184282 | 1.11% | 2391 |
| chr15 | 1088139 | 1.07% | 2219 |
| chr16 | 1065846 | 1.18% | 2066 |
| chr17 | 1259690 | 1.51% | 2415 |
| chr18 | 951511 | 1.18% | 2064 |
| chr19 | 1007093 | 1.72% | 1779 |
| chr20 | 800399 | 1.24% | 1646 |
| chr21 | 391617 | 0.84% | 769 |
| chr22 | 439331 | 0.86% | 838 |
| chrX | 1420068 | 0.91% | 3100 |
| chrY | 779 | <0.01% | 3 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 84599 | 150 | 2706 | 480.66 | 414 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF647UDQ.bed.gz | 2.89 MB | ac13a52e3d21eaf1187b08f46305d271 |
| ENCFF647UDQ.tabix.bed.gz | 945.8 KB | 87ba5233023d971c187407b8e36dc970 |
| ENCFF647UDQ.tabix.bed.gz.tbi | 411.9 KB | 1645a1173e6c19b4f4bf063d83237c49 |
| genomic_resource.yaml | 2.23 KB | 44a3a9f70977e67e1b04add8b0f9982a |
| statistics/ |