Resource
| Id | ATAC-seq/ENCSR304ZDQ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR304ZDQ [biosample_summary="Homo sapiens GM18873"] |
| Description |
status: released biological_replicates: Rep 1 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN746KGZ|/analyses/ENCAN746KGZ/} 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. {ENCFF719MMH|/files/ENCFF719MMH/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a FRiP score of 0.16. 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 {ENCFF589DFL|/files/ENCFF589DFL/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.814406. 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 {ENCFF589DFL|/files/ENCFF589DFL/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.89. audit_warning: 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) {ENCFF719MMH|/files/ENCFF719MMH/} (overlap peaks) and {ENCFF557BSF|/files/ENCFF557BSF/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have 121078 and 69897 peaks. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR304ZDQ | float |
ATAC-seq_ENCSR304ZDQ |
ATAC-seq ENCSR304ZDQ [biosample_summary="Homo sapiens GM18873"]
|
 |
[1.47, 29.7] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 40409524 | 1.26% | 77764 |
| chr1 | 3515528 | 1.41% | 6609 |
| chr2 | 3532328 | 1.46% | 7015 |
| chr3 | 2842153 | 1.43% | 5651 |
| chr4 | 2388570 | 1.26% | 4860 |
| chr5 | 2494449 | 1.37% | 4930 |
| chr6 | 2789831 | 1.63% | 5466 |
| chr7 | 2292222 | 1.44% | 4523 |
| chr8 | 2023904 | 1.39% | 4049 |
| chr9 | 1591825 | 1.15% | 3082 |
| chr10 | 1908378 | 1.43% | 3714 |
| chr11 | 1862220 | 1.38% | 3557 |
| chr12 | 2046257 | 1.54% | 3903 |
| chr13 | 1106598 | 0.97% | 2182 |
| chr14 | 1233079 | 1.15% | 2300 |
| chr15 | 1069371 | 1.05% | 2008 |
| chr16 | 1109308 | 1.23% | 1944 |
| chr17 | 1389706 | 1.67% | 2368 |
| chr18 | 921648 | 1.15% | 1868 |
| chr19 | 1163990 | 1.99% | 1796 |
| chr20 | 814125 | 1.26% | 1545 |
| chr21 | 400070 | 0.86% | 737 |
| chr22 | 501399 | 0.99% | 825 |
| chrX | 1411384 | 0.90% | 2827 |
| chrY | 1181 | <0.01% | 5 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 77764 | 150 | 3146 | 519.64 | 436 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF719MMH.bed.gz | 2.87 MB | 48db02ace0d477881b15d02b1a601eea |
| ENCFF719MMH.tabix.bed.gz | 870.68 KB | 74f6ece63bddac74695dc017b2c3c561 |
| ENCFF719MMH.tabix.bed.gz.tbi | 376.26 KB | f537d8f37eca434905a252aa8af8c7ae |
| genomic_resource.yaml | 3.47 KB | 58ce2ef4defb9491db52e54c24a8e637 |
| statistics/ |