Resource
| Id | ATAC-seq/ENCSR117PYB |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR117PYB [biosample_summary="Homo sapiens heart left ventricle tissue female adult (51 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (51 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN325VHG|/analyses/ENCAN325VHG/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_internal_action: Released analysis {ENCAN325VHG|/analyses/ENCAN325VHG/} has in progress subobject document {1fb078ac-8be3-4516-8b6d-5934412c6ecc|/documents/1fb078ac-8be3-4516-8b6d-5934412c6ecc/} 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. {ENCFF544RZR|/files/ENCFF544RZR/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a FRiP score of 0.07. 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) {ENCFF544RZR|/files/ENCFF544RZR/} (overlap peaks) and {ENCFF174HPZ|/files/ENCFF174HPZ/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have 84725 and 26918 peaks. audit_warning: Alignment file {ENCFF713UOC|/files/ENCFF713UOC/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has 24932595 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_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 {ENCFF713UOC|/files/ENCFF713UOC/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.824226. 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 {ENCFF713UOC|/files/ENCFF713UOC/} 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_ENCSR117PYB | float |
ATAC-seq_ENCSR117PYB |
ATAC-seq ENCSR117PYB [biosample_summary="Homo sapiens heart left ventricle tissue female adult (51 years)"]
|
 |
[1.62, 19.7] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 27649959 | 0.86% | 48780 |
| chr1 | 2693062 | 1.08% | 4645 |
| chr2 | 2106015 | 0.87% | 3867 |
| chr3 | 1693999 | 0.85% | 3062 |
| chr4 | 1219871 | 0.64% | 2248 |
| chr5 | 1422696 | 0.78% | 2637 |
| chr6 | 1509447 | 0.88% | 2747 |
| chr7 | 1447570 | 0.91% | 2588 |
| chr8 | 1141674 | 0.79% | 2071 |
| chr9 | 1168051 | 0.84% | 2018 |
| chr10 | 1316345 | 0.98% | 2435 |
| chr11 | 1464459 | 1.08% | 2488 |
| chr12 | 1314884 | 0.99% | 2261 |
| chr13 | 651337 | 0.57% | 1206 |
| chr14 | 851273 | 0.80% | 1473 |
| chr15 | 978004 | 0.96% | 1734 |
| chr16 | 1057518 | 1.17% | 1759 |
| chr17 | 1354240 | 1.63% | 2223 |
| chr18 | 573313 | 0.71% | 1102 |
| chr19 | 1336311 | 2.28% | 2059 |
| chr20 | 716944 | 1.11% | 1285 |
| chr21 | 323505 | 0.69% | 560 |
| chr22 | 642495 | 1.26% | 1108 |
| chrX | 666008 | 0.43% | 1200 |
| chrY | 938 | <0.01% | 4 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 48780 | 150 | 3008 | 566.83 | 452 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF544RZR.bed.gz | 1.95 MB | 4c79c86b2843c1f8a9aafc59accb32a5 |
| ENCFF544RZR.tabix.bed.gz | 554.67 KB | 1d60db582cf99bbd97745f292b3c6a9a |
| ENCFF544RZR.tabix.bed.gz.tbi | 288.35 KB | 30883aa3bf9a13fc7619126a115543e8 |
| genomic_resource.yaml | 4.14 KB | d81be50224b6a71c39b5474a3040ee2a |
| statistics/ |