Resource
| Id | ATAC-seq/ENCSR851EBF |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR851EBF [biosample_summary="Homo sapiens heart left ventricle tissue female adult (53 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (53 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN243PUK|/analyses/ENCAN243PUK/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_internal_action: Released analysis {ENCAN243PUK|/analyses/ENCAN243PUK/} has in progress subobject document {5142f7ef-af77-45be-8c0e-f92a55721b84|/documents/5142f7ef-af77-45be-8c0e-f92a55721b84/} audit_not_compliant: Alignment file {ENCFF097EXD|/files/ENCFF097EXD/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has 18512476 usable fragments. According to ENCODE4 standards, ATAC-seq assays processed by the uniform processing pipeline should have > 25 million usable fragments. 20-25 million is acceptable and < 15 million is not compliant. 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. {ENCFF172AHA|/files/ENCFF172AHA/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a FRiP score of 0.12. audit_not_compliant: 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) {ENCFF172AHA|/files/ENCFF172AHA/} (overlap peaks) and {ENCFF560EBG|/files/ENCFF560EBG/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have 90429 and 36864 peaks. 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 {ENCFF097EXD|/files/ENCFF097EXD/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.8126. 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 {ENCFF097EXD|/files/ENCFF097EXD/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.85. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR851EBF | float |
ATAC-seq_ENCSR851EBF |
ATAC-seq ENCSR851EBF [biosample_summary="Homo sapiens heart left ventricle tissue female adult (53 years)"]
|
 |
[1.56, 28.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 29458007 | 0.92% | 63178 |
| chr1 | 2847843 | 1.14% | 6006 |
| chr2 | 2239844 | 0.92% | 4914 |
| chr3 | 1829347 | 0.92% | 3955 |
| chr4 | 1268439 | 0.67% | 2839 |
| chr5 | 1529797 | 0.84% | 3438 |
| chr6 | 1640954 | 0.96% | 3604 |
| chr7 | 1510456 | 0.95% | 3300 |
| chr8 | 1263113 | 0.87% | 2765 |
| chr9 | 1255014 | 0.91% | 2670 |
| chr10 | 1457086 | 1.09% | 3208 |
| chr11 | 1541548 | 1.14% | 3273 |
| chr12 | 1405949 | 1.05% | 2944 |
| chr13 | 690613 | 0.60% | 1532 |
| chr14 | 878248 | 0.82% | 1819 |
| chr15 | 1029000 | 1.01% | 2180 |
| chr16 | 1103878 | 1.22% | 2285 |
| chr17 | 1474868 | 1.77% | 2987 |
| chr18 | 587082 | 0.73% | 1349 |
| chr19 | 1353619 | 2.31% | 2592 |
| chr20 | 791079 | 1.23% | 1724 |
| chr21 | 361177 | 0.77% | 769 |
| chr22 | 683962 | 1.35% | 1435 |
| chrX | 714408 | 0.46% | 1587 |
| chrY | 683 | <0.01% | 3 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 63178 | 150 | 2447 | 466.27 | 380 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF172AHA.bed.gz | 2.15 MB | 375208f1f0d5df5edea52a12af98d9d2 |
| ENCFF172AHA.tabix.bed.gz | 701.83 KB | d198c22fbf6f0f1215fbf73e52d3a2e1 |
| ENCFF172AHA.tabix.bed.gz.tbi | 338.07 KB | c56018f8ceb7cd7ff8981393a5d0e6f1 |
| genomic_resource.yaml | 4.14 KB | dc0aa99650e5b87d8fe6d0bb2cde7de3 |
| statistics/ |