Resource
| Id | ATAC-seq/ENCSR635AIF |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR635AIF [biosample_summary="Homo sapiens GM19468"] |
| Description |
status: released biological_replicates: Rep 1 summary: output_type: pseudoreplicated peaks audit_error: Alignment file {ENCFF362ACE|/files/ENCFF362ACE/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has 6496961 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_internal_action: Released analysis {ENCAN496PIY|/analyses/ENCAN496PIY/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} 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 {ENCFF362ACE|/files/ENCFF362ACE/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.834628. 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 {ENCFF362ACE|/files/ENCFF362ACE/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.83. 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) {ENCFF883YXV|/files/ENCFF883YXV/} (overlap peaks) and {ENCFF550WFX|/files/ENCFF550WFX/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have 88727 and 51568 peaks. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR635AIF | float |
ATAC-seq_ENCSR635AIF |
ATAC-seq ENCSR635AIF [biosample_summary="Homo sapiens GM19468"]
|
 |
[1.89, 28.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 30814695 | 0.96% | 73989 |
| chr1 | 2765443 | 1.11% | 6558 |
| chr2 | 2778104 | 1.15% | 6829 |
| chr3 | 2245981 | 1.13% | 5524 |
| chr4 | 1920566 | 1.01% | 4813 |
| chr5 | 1969242 | 1.08% | 4855 |
| chr6 | 2029608 | 1.19% | 4817 |
| chr7 | 1606079 | 1.01% | 3784 |
| chr8 | 1441676 | 0.99% | 3406 |
| chr9 | 1164793 | 0.84% | 2718 |
| chr10 | 1495662 | 1.12% | 3650 |
| chr11 | 1460410 | 1.08% | 3497 |
| chr12 | 1530774 | 1.15% | 3697 |
| chr13 | 917167 | 0.80% | 2274 |
| chr14 | 968856 | 0.91% | 2297 |
| chr15 | 888982 | 0.87% | 2142 |
| chr16 | 844526 | 0.93% | 1921 |
| chr17 | 942296 | 1.13% | 2167 |
| chr18 | 752297 | 0.94% | 1909 |
| chr19 | 784521 | 1.34% | 1633 |
| chr20 | 612790 | 0.95% | 1470 |
| chr21 | 318607 | 0.68% | 744 |
| chr22 | 362231 | 0.71% | 833 |
| chrX | 1013404 | 0.65% | 2449 |
| chrY | 680 | <0.01% | 2 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 73989 | 150 | 2097 | 416.48 | 359 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF883YXV.bed.gz | 2.04 MB | eac315ae545ef50cf08cbc7153dc88c0 |
| ENCFF883YXV.tabix.bed.gz | 782.38 KB | 034d9124b7d1df747229ec7042b9cdd4 |
| ENCFF883YXV.tabix.bed.gz.tbi | 407.9 KB | 705539265644474b0a4a015f53f6e2cd |
| genomic_resource.yaml | 3.42 KB | 11f54923e4279b97fa8d5dc5c62c4186 |
| statistics/ |