Resource
| Id | ATAC-seq/ENCSR647AOY |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR647AOY [biosample_summary="Homo sapiens lung tissue female adult (47 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (47 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN079QLM|/analyses/ENCAN079QLM/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_internal_action: Released analysis {ENCAN079QLM|/analyses/ENCAN079QLM/} has in progress subobject document {50503732-021d-48d5-992a-6017f3c3ef03|/documents/50503732-021d-48d5-992a-6017f3c3ef03/} audit_not_compliant: Alignment file {ENCFF810ZGD|/files/ENCFF810ZGD/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has 18425763 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_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. {ENCFF818EYD|/files/ENCFF818EYD/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a FRiP score of 0.18. 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) {ENCFF818EYD|/files/ENCFF818EYD/} (overlap peaks) and {ENCFF068ZZZ|/files/ENCFF068ZZZ/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have 107260 and 48163 peaks. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR647AOY | float |
ATAC-seq_ENCSR647AOY |
ATAC-seq ENCSR647AOY [biosample_summary="Homo sapiens lung tissue female adult (47 years)"]
|
 |
[1.6, 31.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 35959049 | 1.12% | 72892 |
| chr1 | 3503281 | 1.41% | 7029 |
| chr2 | 2846700 | 1.18% | 5876 |
| chr3 | 2363209 | 1.19% | 4855 |
| chr4 | 1683013 | 0.88% | 3482 |
| chr5 | 1893718 | 1.04% | 3901 |
| chr6 | 2176490 | 1.27% | 4420 |
| chr7 | 1840545 | 1.16% | 3797 |
| chr8 | 1614649 | 1.11% | 3336 |
| chr9 | 1552854 | 1.12% | 3164 |
| chr10 | 1698191 | 1.27% | 3548 |
| chr11 | 1869443 | 1.38% | 3766 |
| chr12 | 1740557 | 1.31% | 3498 |
| chr13 | 866066 | 0.76% | 1778 |
| chr14 | 1150276 | 1.07% | 2310 |
| chr15 | 1151140 | 1.13% | 2276 |
| chr16 | 1280653 | 1.42% | 2498 |
| chr17 | 1672722 | 2.01% | 3288 |
| chr18 | 753347 | 0.94% | 1596 |
| chr19 | 1396532 | 2.38% | 2607 |
| chr20 | 877872 | 1.36% | 1825 |
| chr21 | 431153 | 0.92% | 878 |
| chr22 | 670142 | 1.32% | 1324 |
| chrX | 926496 | 0.59% | 1840 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 72892 | 150 | 2489 | 493.32 | 402 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF818EYD.bed.gz | 2.56 MB | 7de2eebc81542ddc47b11c6feaaa724b |
| ENCFF818EYD.tabix.bed.gz | 811.48 KB | 9691431875a0e84c0d37e3b33ae8d272 |
| ENCFF818EYD.tabix.bed.gz.tbi | 371.87 KB | 6adfe757629cf0b51e51d5483d0d1dba |
| genomic_resource.yaml | 2.93 KB | efb2f8bf4c362251c46d6a7ee77c3d51 |
| statistics/ |