Resource
| Id | ATAC-seq/ENCSR451JSB |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR451JSB [biosample_summary="Homo sapiens heart left ventricle tissue female adult (56 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (56 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN599GXH|/analyses/ENCAN599GXH/} 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. {ENCFF343GGF|/files/ENCFF343GGF/} 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 {ENCFF987YOH|/files/ENCFF987YOH/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.875307. 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 {ENCFF987YOH|/files/ENCFF987YOH/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.89. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR451JSB | float |
ATAC-seq_ENCSR451JSB |
ATAC-seq ENCSR451JSB [biosample_summary="Homo sapiens heart left ventricle tissue female adult (56 years)"]
|
 |
[1.38, 27.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 77528032 | 2.41% | 146703 |
| chr1 | 7460823 | 3.00% | 13945 |
| chr2 | 6213428 | 2.57% | 11992 |
| chr3 | 4891978 | 2.47% | 9498 |
| chr4 | 3211935 | 1.69% | 6355 |
| chr5 | 4054281 | 2.23% | 7991 |
| chr6 | 4430612 | 2.59% | 8517 |
| chr7 | 3838563 | 2.41% | 7381 |
| chr8 | 3340732 | 2.30% | 6480 |
| chr9 | 3391382 | 2.45% | 6389 |
| chr10 | 3884364 | 2.90% | 7548 |
| chr11 | 4005212 | 2.96% | 7392 |
| chr12 | 3776627 | 2.83% | 7117 |
| chr13 | 1808380 | 1.58% | 3604 |
| chr14 | 2476807 | 2.31% | 4653 |
| chr15 | 2695697 | 2.64% | 5133 |
| chr16 | 2773161 | 3.07% | 5068 |
| chr17 | 3795157 | 4.56% | 6775 |
| chr18 | 1602955 | 1.99% | 3181 |
| chr19 | 3048004 | 5.20% | 5094 |
| chr20 | 2198626 | 3.41% | 4164 |
| chr21 | 1094314 | 2.34% | 2018 |
| chr22 | 1737226 | 3.42% | 3126 |
| chrX | 1796830 | 1.15% | 3278 |
| chrY | 938 | <0.01% | 4 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 146703 | 150 | 3076 | 528.47 | 430 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF343GGF.bed.gz | 5.26 MB | 5e9d032ba7968de5fcecc0d02b1f605b |
| ENCFF343GGF.tabix.bed.gz | 1.59 MB | d2a8f5096bb12c5f62ce0d66d46b7101 |
| ENCFF343GGF.tabix.bed.gz.tbi | 474.31 KB | 27d3dca3a0e7b3a510eb6fab16ba73bc |
| genomic_resource.yaml | 3.36 KB | 683b3b5f78e314f3e579fb662c89f95c |
| statistics/ |