Resource
| Id | ATAC-seq/ENCSR086OGH |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR086OGH [biosample_summary="Homo sapiens sigmoid 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 {ENCAN657AGV|/analyses/ENCAN657AGV/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_internal_action: Released analysis {ENCAN657AGV|/analyses/ENCAN657AGV/} has in progress subobject document {35df17fc-b139-4395-9a89-85afc3648f31|/documents/35df17fc-b139-4395-9a89-85afc3648f31/} 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. {ENCFF270JNZ|/files/ENCFF270JNZ/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a FRiP score of 0.12. 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 {ENCFF182ZGK|/files/ENCFF182ZGK/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.874348. 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 {ENCFF182ZGK|/files/ENCFF182ZGK/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.88. 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) {ENCFF270JNZ|/files/ENCFF270JNZ/} (overlap peaks) and {ENCFF697MUB|/files/ENCFF697MUB/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have 110999 and 60532 peaks. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR086OGH | float |
ATAC-seq_ENCSR086OGH |
ATAC-seq ENCSR086OGH [biosample_summary="Homo sapiens sigmoid colon tissue male adult (54 years)"]
|
 |
[1.5, 28.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 34966918 | 1.09% | 66250 |
| chr1 | 3379525 | 1.36% | 6214 |
| chr2 | 2765605 | 1.14% | 5353 |
| chr3 | 2176199 | 1.10% | 4185 |
| chr4 | 1627532 | 0.86% | 3275 |
| chr5 | 1823364 | 1.00% | 3589 |
| chr6 | 2002585 | 1.17% | 3875 |
| chr7 | 1814366 | 1.14% | 3532 |
| chr8 | 1531793 | 1.06% | 3055 |
| chr9 | 1593482 | 1.15% | 3027 |
| chr10 | 1700632 | 1.27% | 3280 |
| chr11 | 1843616 | 1.36% | 3424 |
| chr12 | 1688790 | 1.27% | 3136 |
| chr13 | 813833 | 0.71% | 1647 |
| chr14 | 1120564 | 1.05% | 2139 |
| chr15 | 1115405 | 1.09% | 2059 |
| chr16 | 1277538 | 1.41% | 2297 |
| chr17 | 1678978 | 2.02% | 2966 |
| chr18 | 712828 | 0.89% | 1467 |
| chr19 | 1467816 | 2.50% | 2502 |
| chr20 | 931304 | 1.45% | 1781 |
| chr21 | 453118 | 0.97% | 858 |
| chr22 | 737763 | 1.45% | 1352 |
| chrX | 676772 | 0.43% | 1161 |
| chrY | 33510 | 0.06% | 76 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 66250 | 150 | 2902 | 527.8 | 424 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF270JNZ.bed.gz | 2.63 MB | 527acde68e0be423b391318d071243cb |
| ENCFF270JNZ.tabix.bed.gz | 751.53 KB | 370567116ff1f7c7a7e13b993638594c |
| ENCFF270JNZ.tabix.bed.gz.tbi | 351.83 KB | a3a56568436112a5b0e4ee80c7f09c7f |
| genomic_resource.yaml | 3.74 KB | 108f0f69e09775530d2b8f0564af4cba |
| statistics/ |