Resource
| Id | ATAC-seq/ENCSR124NNL |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR124NNL [biosample_summary="Homo sapiens liver tissue male adult (67 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (67 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN568CIG|/analyses/ENCAN568CIG/} 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. {ENCFF488BRH|/files/ENCFF488BRH/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a FRiP score of 0.14. 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 {ENCFF640ZNR|/files/ENCFF640ZNR/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.892239. 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 {ENCFF640ZNR|/files/ENCFF640ZNR/} 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_ENCSR124NNL | float |
ATAC-seq_ENCSR124NNL |
ATAC-seq ENCSR124NNL [biosample_summary="Homo sapiens liver tissue male adult (67 years)"]
|
 |
[1.35, 33.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 71064127 | 2.21% | 136959 |
| chr1 | 6712385 | 2.70% | 12781 |
| chr2 | 5657408 | 2.34% | 11120 |
| chr3 | 4306995 | 2.17% | 8554 |
| chr4 | 3086834 | 1.62% | 6132 |
| chr5 | 3688336 | 2.03% | 7297 |
| chr6 | 4016976 | 2.35% | 7921 |
| chr7 | 3765203 | 2.36% | 7311 |
| chr8 | 3136073 | 2.16% | 6233 |
| chr9 | 3191896 | 2.31% | 6141 |
| chr10 | 3577159 | 2.67% | 7023 |
| chr11 | 3679210 | 2.72% | 6978 |
| chr12 | 3281465 | 2.46% | 6365 |
| chr13 | 1772515 | 1.55% | 3453 |
| chr14 | 2249580 | 2.10% | 4289 |
| chr15 | 2430712 | 2.38% | 4698 |
| chr16 | 2720677 | 3.01% | 5065 |
| chr17 | 3359156 | 4.03% | 6111 |
| chr18 | 1636470 | 2.04% | 3308 |
| chr19 | 2854591 | 4.87% | 4898 |
| chr20 | 2010727 | 3.12% | 3896 |
| chr21 | 1031023 | 2.21% | 1897 |
| chr22 | 1782052 | 3.51% | 3236 |
| chrX | 1032979 | 0.66% | 2062 |
| chrY | 83705 | 0.15% | 190 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 136959 | 150 | 3382 | 518.87 | 429 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF488BRH.bed.gz | 4.7 MB | b381f3c92a566de0df2457e0c939b497 |
| ENCFF488BRH.tabix.bed.gz | 1.48 MB | 1aa97d6741fb57fbb72f5f29ade45ce5 |
| ENCFF488BRH.tabix.bed.gz.tbi | 487.93 KB | 964fb894b1fd56a8b3915f7fbd8e0c22 |
| genomic_resource.yaml | 3.31 KB | 8a7403b2571d78fe47c43a2709b6d3ac |
| statistics/ |