Resource
| Id | ATAC-seq/ENCSR857MCZ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR857MCZ [biosample_summary="Homo sapiens HG02970"] |
| Description |
status: released biological_replicates: Rep 1 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN246BLF|/analyses/ENCAN246BLF/} 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. {ENCFF901SKJ|/files/ENCFF901SKJ/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a FRiP score of 0.15. audit_warning: NRF (Non Redundant Fraction) is equal to the result of the division of the number of reads after duplicates removal by the total number of reads. An NRF value < 0.7 is poor complexity, between 0.7 and 0.9 is moderate complexity, and >= 0.9 high complexity. NRF value > 0.9 is recommended, but > 0.7 is acceptable. ENCODE processed file {ENCFF320DVY|/files/ENCFF320DVY/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.820248. audit_warning: PBC1 (PCR Bottlenecking Coefficient 1, M1/M_distinct) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where some reads map (M_distinct). A PBC1 value in the range 0 - 0.5 is severe bottlenecking, 0.5 - 0.8 is moderate bottlenecking, 0.8 - 0.9 is mild bottlenecking, and > 0.9 is no bottlenecking. PBC1 value > 0.9 is recommended, but > 0.7 is acceptable. ENCODE processed file {ENCFF320DVY|/files/ENCFF320DVY/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.82. 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) {ENCFF901SKJ|/files/ENCFF901SKJ/} (overlap peaks) and {ENCFF256UDE|/files/ENCFF256UDE/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have 110564 and 59100 peaks. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR857MCZ | float |
ATAC-seq_ENCSR857MCZ |
ATAC-seq ENCSR857MCZ [biosample_summary="Homo sapiens HG02970"]
|
 |
[1.37, 30.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 38023168 | 1.18% | 67135 |
| chr1 | 3542398 | 1.42% | 6132 |
| chr2 | 3215522 | 1.33% | 5939 |
| chr3 | 2530837 | 1.28% | 4605 |
| chr4 | 2143565 | 1.13% | 4085 |
| chr5 | 2236341 | 1.23% | 4097 |
| chr6 | 2534981 | 1.48% | 4544 |
| chr7 | 2042337 | 1.28% | 3719 |
| chr8 | 1856033 | 1.28% | 3444 |
| chr9 | 1520117 | 1.10% | 2707 |
| chr10 | 1779414 | 1.33% | 3184 |
| chr11 | 1874058 | 1.39% | 3323 |
| chr12 | 1883569 | 1.41% | 3262 |
| chr13 | 976172 | 0.85% | 1790 |
| chr14 | 1126603 | 1.05% | 1870 |
| chr15 | 1063893 | 1.04% | 1818 |
| chr16 | 1173002 | 1.30% | 1868 |
| chr17 | 1452561 | 1.74% | 2279 |
| chr18 | 812647 | 1.01% | 1507 |
| chr19 | 1309103 | 2.23% | 1903 |
| chr20 | 798349 | 1.24% | 1375 |
| chr21 | 377132 | 0.81% | 623 |
| chr22 | 584567 | 1.15% | 896 |
| chrX | 1188729 | 0.76% | 2160 |
| chrY | 1238 | <0.01% | 5 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 67135 | 150 | 2807 | 566.37 | 472 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF901SKJ.bed.gz | 2.63 MB | df42dbbf65d234e7e88f5723ecf49fd9 |
| ENCFF901SKJ.tabix.bed.gz | 763.18 KB | f9736b80b78e81b01eff33eb294d5519 |
| ENCFF901SKJ.tabix.bed.gz.tbi | 363.89 KB | 833deb411ccc03a4c94636cd51363833 |
| genomic_resource.yaml | 3.47 KB | 62fb96b1447868c4f18e96c7aceac596 |
| statistics/ |