Resource
| Id | ATAC-seq/ENCSR761TKU |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR761TKU [biosample_summary="Homo sapiens transverse colon 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 {ENCAN664RQJ|/analyses/ENCAN664RQJ/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_internal_action: Released analysis {ENCAN664RQJ|/analyses/ENCAN664RQJ/} has in progress subobject document {f2e34401-e046-493f-b7c4-b1ea26f9763c|/documents/f2e34401-e046-493f-b7c4-b1ea26f9763c/} 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. {ENCFF591HMI|/files/ENCFF591HMI/} 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 {ENCFF455YNB|/files/ENCFF455YNB/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.883989. 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 {ENCFF455YNB|/files/ENCFF455YNB/} 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) {ENCFF591HMI|/files/ENCFF591HMI/} (overlap peaks) and {ENCFF668ARP|/files/ENCFF668ARP/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have 106493 and 51803 peaks. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR761TKU | float |
ATAC-seq_ENCSR761TKU |
ATAC-seq ENCSR761TKU [biosample_summary="Homo sapiens transverse colon tissue male adult (54 years)"]
|
 |
[1.54, 28.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 33703806 | 1.05% | 64461 |
| chr1 | 3266145 | 1.31% | 6069 |
| chr2 | 2750180 | 1.14% | 5407 |
| chr3 | 2143032 | 1.08% | 4247 |
| chr4 | 1683350 | 0.88% | 3511 |
| chr5 | 1775608 | 0.98% | 3543 |
| chr6 | 1990379 | 1.17% | 3889 |
| chr7 | 1770990 | 1.11% | 3445 |
| chr8 | 1475740 | 1.02% | 2990 |
| chr9 | 1503233 | 1.09% | 2882 |
| chr10 | 1584709 | 1.18% | 3042 |
| chr11 | 1780641 | 1.32% | 3319 |
| chr12 | 1643501 | 1.23% | 3102 |
| chr13 | 813483 | 0.71% | 1684 |
| chr14 | 1079753 | 1.01% | 2030 |
| chr15 | 1040712 | 1.02% | 1937 |
| chr16 | 1185587 | 1.31% | 2144 |
| chr17 | 1564810 | 1.88% | 2725 |
| chr18 | 695536 | 0.87% | 1433 |
| chr19 | 1392019 | 2.37% | 2334 |
| chr20 | 850608 | 1.32% | 1623 |
| chr21 | 418100 | 0.90% | 785 |
| chr22 | 657050 | 1.29% | 1225 |
| chrX | 609465 | 0.39% | 1026 |
| chrY | 29175 | 0.05% | 69 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 64461 | 150 | 2708 | 522.86 | 411 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF591HMI.bed.gz | 2.48 MB | 4f117fc635261637669d029096222fe8 |
| ENCFF591HMI.tabix.bed.gz | 722.46 KB | 0304001519e6beb1610741a1ab8ac9c9 |
| ENCFF591HMI.tabix.bed.gz.tbi | 354.57 KB | f16efbbbf34386bdaaf1076412df39b8 |
| genomic_resource.yaml | 3.74 KB | 9517bed471eda9641f53067a86e8420c |
| statistics/ |