Resource
| Id | ATAC-seq/ENCSR331JFZ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR331JFZ [biosample_summary="Homo sapiens HG03575"] |
| Description |
status: released biological_replicates: Rep 1 summary: output_type: pseudoreplicated peaks audit_error: Alignment file {ENCFF632MBC|/files/ENCFF632MBC/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has 12592755 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_internal_action: Released analysis {ENCAN086FNR|/analyses/ENCAN086FNR/} 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. {ENCFF089MEL|/files/ENCFF089MEL/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a FRiP score of 0.19. 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) {ENCFF089MEL|/files/ENCFF089MEL/} (overlap peaks) and {ENCFF027KMZ|/files/ENCFF027KMZ/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have 98877 and 38973 peaks. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR331JFZ | float |
ATAC-seq_ENCSR331JFZ |
ATAC-seq ENCSR331JFZ [biosample_summary="Homo sapiens HG03575"]
|
 |
[1.77, 27.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 33453198 | 1.04% | 77208 |
| chr1 | 2932840 | 1.18% | 6652 |
| chr2 | 2979958 | 1.23% | 6979 |
| chr3 | 2430459 | 1.23% | 5744 |
| chr4 | 2139204 | 1.12% | 5127 |
| chr5 | 2131730 | 1.17% | 5004 |
| chr6 | 2359071 | 1.38% | 5407 |
| chr7 | 1927408 | 1.21% | 4495 |
| chr8 | 1769127 | 1.22% | 4183 |
| chr9 | 1292285 | 0.93% | 3019 |
| chr10 | 1623166 | 1.21% | 3729 |
| chr11 | 1547083 | 1.15% | 3601 |
| chr12 | 1634595 | 1.23% | 3702 |
| chr13 | 999367 | 0.87% | 2331 |
| chr14 | 995541 | 0.93% | 2242 |
| chr15 | 883017 | 0.87% | 2014 |
| chr16 | 834450 | 0.92% | 1820 |
| chr17 | 957011 | 1.15% | 2070 |
| chr18 | 783145 | 0.97% | 1850 |
| chr19 | 780092 | 1.33% | 1524 |
| chr20 | 616745 | 0.96% | 1424 |
| chr21 | 302585 | 0.65% | 676 |
| chr22 | 323277 | 0.64% | 698 |
| chrX | 1210735 | 0.78% | 2916 |
| chrY | 307 | <0.01% | 1 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 77208 | 150 | 2120 | 433.29 | 374 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF089MEL.bed.gz | 2.36 MB | 0b8a63df89abe0df142ee714f9fc67b2 |
| ENCFF089MEL.tabix.bed.gz | 841.74 KB | 53359925dd4e94e91bec5d7516e0cee5 |
| ENCFF089MEL.tabix.bed.gz.tbi | 402.74 KB | fbddead1fcb8b08b16a550493a13a319 |
| genomic_resource.yaml | 2.65 KB | 379eff02e59967cc4c9afedb14f8d11e |
| statistics/ |