Resource
| Id | ATAC-seq/ENCSR425WQW |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR425WQW [biosample_summary="Homo sapiens GM19324"] |
| Description |
status: released biological_replicates: Rep 1 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN677TFR|/analyses/ENCAN677TFR/} 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. {ENCFF968BIR|/files/ENCFF968BIR/} 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 {ENCFF668HHR|/files/ENCFF668HHR/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.866817. 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 {ENCFF668HHR|/files/ENCFF668HHR/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.87. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR425WQW | float |
ATAC-seq_ENCSR425WQW |
ATAC-seq ENCSR425WQW [biosample_summary="Homo sapiens GM19324"]
|
 |
[1.47, 26.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 48468244 | 1.51% | 87579 |
| chr1 | 4328210 | 1.74% | 7681 |
| chr2 | 4229665 | 1.75% | 7884 |
| chr3 | 3377654 | 1.70% | 6252 |
| chr4 | 2966847 | 1.56% | 5608 |
| chr5 | 2986481 | 1.65% | 5570 |
| chr6 | 3296695 | 1.93% | 6021 |
| chr7 | 2643554 | 1.66% | 4909 |
| chr8 | 2421283 | 1.67% | 4558 |
| chr9 | 1902848 | 1.37% | 3486 |
| chr10 | 2263820 | 1.69% | 4162 |
| chr11 | 2302368 | 1.70% | 4165 |
| chr12 | 2403940 | 1.80% | 4325 |
| chr13 | 1355033 | 1.18% | 2498 |
| chr14 | 1432237 | 1.34% | 2494 |
| chr15 | 1340987 | 1.31% | 2361 |
| chr16 | 1305583 | 1.45% | 2152 |
| chr17 | 1617124 | 1.94% | 2618 |
| chr18 | 1104066 | 1.37% | 2091 |
| chr19 | 1346086 | 2.30% | 1977 |
| chr20 | 996010 | 1.55% | 1768 |
| chr21 | 492520 | 1.05% | 835 |
| chr22 | 678143 | 1.33% | 1087 |
| chrX | 1674979 | 1.07% | 3068 |
| chrY | 2111 | <0.01% | 9 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 87579 | 150 | 3549 | 553.42 | 460 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF968BIR.bed.gz | 3.5 MB | ae7c1ec96c47955d589874034268c840 |
| ENCFF968BIR.tabix.bed.gz | 986.37 KB | c4c50e9288d42cd4eb4c9da68638df6b |
| ENCFF968BIR.tabix.bed.gz.tbi | 429.03 KB | f90202356c0c9be3c1d60e30de8d2681 |
| genomic_resource.yaml | 2.91 KB | b8755bde22e1fa33c526c637a7d77642 |
| statistics/ |