Resource
| Id | ATAC-seq/ENCSR895SEG |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR895SEG [biosample_summary="Homo sapiens upper lobe of left lung tissue male adult (60 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (60 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN251ASB|/analyses/ENCAN251ASB/} 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. {ENCFF537TOU|/files/ENCFF537TOU/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a FRiP score of 0.18. 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 {ENCFF346URV|/files/ENCFF346URV/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.894495. 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 {ENCFF346URV|/files/ENCFF346URV/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.90. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR895SEG | float |
ATAC-seq_ENCSR895SEG |
ATAC-seq ENCSR895SEG [biosample_summary="Homo sapiens upper lobe of left lung tissue male adult (60 years)"]
|
 |
[1.33, 31.7] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 83105508 | 2.58% | 140816 |
| chr1 | 7853592 | 3.15% | 13176 |
| chr2 | 6820290 | 2.82% | 11815 |
| chr3 | 5283282 | 2.66% | 9161 |
| chr4 | 3741355 | 1.97% | 6558 |
| chr5 | 4470873 | 2.46% | 7746 |
| chr6 | 4924787 | 2.88% | 8395 |
| chr7 | 4456415 | 2.80% | 7640 |
| chr8 | 3878640 | 2.67% | 6707 |
| chr9 | 3561749 | 2.57% | 6002 |
| chr10 | 4260684 | 3.18% | 7408 |
| chr11 | 4209209 | 3.12% | 7026 |
| chr12 | 3972656 | 2.98% | 6793 |
| chr13 | 2109294 | 1.84% | 3660 |
| chr14 | 2676962 | 2.50% | 4536 |
| chr15 | 2795230 | 2.74% | 4673 |
| chr16 | 2910289 | 3.22% | 4759 |
| chr17 | 3774055 | 4.53% | 5995 |
| chr18 | 1829984 | 2.28% | 3218 |
| chr19 | 3051625 | 5.21% | 4621 |
| chr20 | 2212731 | 3.43% | 3757 |
| chr21 | 1154376 | 2.47% | 1942 |
| chr22 | 1649175 | 3.25% | 2646 |
| chrX | 1435943 | 0.92% | 2447 |
| chrY | 72312 | 0.13% | 135 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 140816 | 150 | 3962 | 590.17 | 475 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF537TOU.bed.gz | 5.38 MB | c828d9b160f00ce1f37e0d02da19f4a5 |
| ENCFF537TOU.tabix.bed.gz | 1.54 MB | 7ef248a66c27351408e594c69ecbd7f7 |
| ENCFF537TOU.tabix.bed.gz.tbi | 501.83 KB | 718c9273011575ba7ef78e7e54d3ed57 |
| genomic_resource.yaml | 3.37 KB | 25d77f85df3c7b75eb9df6a9766e4518 |
| statistics/ |