Resource
| Id | ATAC-seq/ENCSR851SBY |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR851SBY [biosample_summary="Homo sapiens stomach tissue male adult (54 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (54 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN924FND|/analyses/ENCAN924FND/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_internal_action: Released analysis {ENCAN924FND|/analyses/ENCAN924FND/} has in progress subobject document {f73153a5-f608-49c9-9325-08cc6157d579|/documents/f73153a5-f608-49c9-9325-08cc6157d579/} 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. {ENCFF028CAI|/files/ENCFF028CAI/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a FRiP score of 0.09. 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 {ENCFF858TZP|/files/ENCFF858TZP/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.881097. 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 {ENCFF858TZP|/files/ENCFF858TZP/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.89. 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) {ENCFF028CAI|/files/ENCFF028CAI/} (overlap peaks) and {ENCFF430VEQ|/files/ENCFF430VEQ/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have 103609 and 48990 peaks. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR851SBY | float |
ATAC-seq_ENCSR851SBY |
ATAC-seq ENCSR851SBY [biosample_summary="Homo sapiens stomach tissue male adult (54 years)"]
|
 |
[1.47, 29.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 32946590 | 1.02% | 66897 |
| chr1 | 3218637 | 1.29% | 6423 |
| chr2 | 2562192 | 1.06% | 5334 |
| chr3 | 2031644 | 1.02% | 4224 |
| chr4 | 1497305 | 0.79% | 3120 |
| chr5 | 1687098 | 0.93% | 3480 |
| chr6 | 1929737 | 1.13% | 3991 |
| chr7 | 1741178 | 1.09% | 3568 |
| chr8 | 1447396 | 1.00% | 3031 |
| chr9 | 1459030 | 1.05% | 2934 |
| chr10 | 1530771 | 1.14% | 3216 |
| chr11 | 1729986 | 1.28% | 3501 |
| chr12 | 1556677 | 1.17% | 3087 |
| chr13 | 786614 | 0.69% | 1627 |
| chr14 | 1057306 | 0.99% | 2157 |
| chr15 | 1059057 | 1.04% | 2129 |
| chr16 | 1266454 | 1.40% | 2523 |
| chr17 | 1630372 | 1.96% | 3174 |
| chr18 | 666847 | 0.83% | 1416 |
| chr19 | 1430470 | 2.44% | 2665 |
| chr20 | 867686 | 1.35% | 1809 |
| chr21 | 462160 | 0.99% | 929 |
| chr22 | 722599 | 1.42% | 1433 |
| chrX | 576629 | 0.37% | 1059 |
| chrY | 28745 | 0.05% | 67 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 66897 | 150 | 2602 | 492.5 | 398 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF028CAI.bed.gz | 2.48 MB | 60a1926a8abb58c8943f5a66a9215d62 |
| ENCFF028CAI.tabix.bed.gz | 755.19 KB | 73aaed44f3daf2ac61d0f78a16c6ae66 |
| ENCFF028CAI.tabix.bed.gz.tbi | 345.01 KB | 42c5e1ac4b95ddacf98a1eac8beb6e8d |
| genomic_resource.yaml | 3.72 KB | 57d581678ada85479425c5b6e6052d4d |
| statistics/ |