Resource
| Id | ATAC-seq/ENCSR414DVK |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR414DVK [biosample_summary="Homo sapiens adrenal gland tissue female adult (51 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (51 years) output_type: pseudoreplicated peaks audit_error: Alignment file {ENCFF946URK|/files/ENCFF946URK/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has 12122240 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 {ENCAN481VYZ|/analyses/ENCAN481VYZ/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_internal_action: Released analysis {ENCAN481VYZ|/analyses/ENCAN481VYZ/} has in progress subobject document {49215c69-33db-4187-b5f6-c9c77a2cafb7|/documents/49215c69-33db-4187-b5f6-c9c77a2cafb7/} 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. {ENCFF296LMD|/files/ENCFF296LMD/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a FRiP score of 0.12. 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) {ENCFF296LMD|/files/ENCFF296LMD/} (overlap peaks) and {ENCFF663KQH|/files/ENCFF663KQH/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have 81117 and 32318 peaks. 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 {ENCFF946URK|/files/ENCFF946URK/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.896244. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR414DVK | float |
ATAC-seq_ENCSR414DVK |
ATAC-seq ENCSR414DVK [biosample_summary="Homo sapiens adrenal gland tissue female adult (51 years)"]
|
 |
[1.88, 31.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 26678023 | 0.83% | 61010 |
| chr1 | 2457476 | 0.99% | 5514 |
| chr2 | 2110799 | 0.87% | 4909 |
| chr3 | 1707172 | 0.86% | 3938 |
| chr4 | 1263533 | 0.66% | 2980 |
| chr5 | 1497238 | 0.82% | 3496 |
| chr6 | 1497966 | 0.88% | 3399 |
| chr7 | 1446314 | 0.91% | 3331 |
| chr8 | 1237098 | 0.85% | 2871 |
| chr9 | 1178853 | 0.85% | 2706 |
| chr10 | 1270580 | 0.95% | 2935 |
| chr11 | 1467488 | 1.09% | 3314 |
| chr12 | 1338398 | 1.00% | 2984 |
| chr13 | 679862 | 0.59% | 1648 |
| chr14 | 873633 | 0.82% | 1942 |
| chr15 | 864043 | 0.85% | 1913 |
| chr16 | 939311 | 1.04% | 2107 |
| chr17 | 1022892 | 1.23% | 2318 |
| chr18 | 625385 | 0.78% | 1487 |
| chr19 | 943906 | 1.61% | 1969 |
| chr20 | 691289 | 1.07% | 1616 |
| chr21 | 348773 | 0.75% | 797 |
| chr22 | 485184 | 0.95% | 1118 |
| chrX | 730376 | 0.47% | 1716 |
| chrY | 454 | <0.01% | 2 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 61010 | 150 | 2122 | 437.27 | 356 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF296LMD.bed.gz | 1.88 MB | 94213d6eceb5ac0ecc37417c2d00b2c8 |
| ENCFF296LMD.tabix.bed.gz | 662.63 KB | 254d480ce585fed5c998ae65c469e9be |
| ENCFF296LMD.tabix.bed.gz.tbi | 359.84 KB | d24c956a7d56895a58667d45990b63ed |
| genomic_resource.yaml | 3.48 KB | 432d37fb62d659409c685952b5c16288 |
| statistics/ |