Resource
| Id | ATAC-seq/ENCSR019XCN |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR019XCN [biosample_summary="Homo sapiens effector memory CD8-positive, alpha-beta T cell male adult (36 years)"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: male adult (36 years) output_type: pseudoreplicated peaks audit_error: Alignment file {ENCFF364RYN|/files/ENCFF364RYN/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has 12745523 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 {ENCAN077FIR|/analyses/ENCAN077FIR/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_not_compliant: 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 {ENCFF364RYN|/files/ENCFF364RYN/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with NRF value of 0.538814. audit_not_compliant: 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 {ENCFF364RYN|/files/ENCFF364RYN/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.50. 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. {ENCFF929NTI|/files/ENCFF929NTI/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has a FRiP score of 0.16. audit_warning: PBC2 (PCR Bottlenecking Coefficient 2, M1/M2) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where two reads map uniquely (M2). A PBC2 value in the range 0 - 1 is severe bottlenecking, 1 - 3 is moderate bottlenecking, 3 - 10 is mild bottlenecking, > 10 is no bottlenecking. PBC2 value > 10 is recommended, but > 3 is acceptable. ENCODE processed file {ENCFF364RYN|/files/ENCFF364RYN/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with a PBC2 value of 1.78. 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 {ENCFF347LNL|/files/ENCFF347LNL/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with NRF value of 0.833455. 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 {ENCFF347LNL|/files/ENCFF347LNL/} processed by ATAC-seq ENCODE4 v1.10.0 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) {ENCFF929NTI|/files/ENCFF929NTI/} (overlap peaks) and {ENCFF603GBI|/files/ENCFF603GBI/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline have 89161 and 56932 peaks. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR019XCN | float |
ATAC-seq_ENCSR019XCN |
ATAC-seq ENCSR019XCN [biosample_summary="Homo sapiens effector memory CD8-positive, alpha-beta T cell male adult (36 years)"]
|
 |
[1.41, 33.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 29234502 | 0.91% | 54160 |
| chr1 | 2813391 | 1.13% | 5102 |
| chr2 | 2309511 | 0.95% | 4452 |
| chr3 | 1788538 | 0.90% | 3394 |
| chr4 | 1195729 | 0.63% | 2241 |
| chr5 | 1503926 | 0.83% | 2820 |
| chr6 | 1799187 | 1.05% | 3339 |
| chr7 | 1484334 | 0.93% | 2812 |
| chr8 | 1213625 | 0.84% | 2311 |
| chr9 | 1183402 | 0.86% | 2227 |
| chr10 | 1429311 | 1.07% | 2721 |
| chr11 | 1444094 | 1.07% | 2686 |
| chr12 | 1452311 | 1.09% | 2659 |
| chr13 | 682934 | 0.60% | 1303 |
| chr14 | 995849 | 0.93% | 1797 |
| chr15 | 912681 | 0.89% | 1704 |
| chr16 | 1100674 | 1.22% | 1944 |
| chr17 | 1439042 | 1.73% | 2543 |
| chr18 | 571264 | 0.71% | 1156 |
| chr19 | 1367537 | 2.33% | 2321 |
| chr20 | 753365 | 1.17% | 1439 |
| chr21 | 376378 | 0.81% | 695 |
| chr22 | 614127 | 1.21% | 1109 |
| chrX | 686434 | 0.44% | 1158 |
| chrY | 116858 | 0.20% | 227 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 54160 | 150 | 2791 | 539.78 | 447 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF929NTI.bed.gz | 2.14 MB | 695007603d004fcb8c9858f8e4b3702c |
| ENCFF929NTI.tabix.bed.gz | 621.24 KB | 82065f2a9346df24b62c9bb6ff28fcf6 |
| ENCFF929NTI.tabix.bed.gz.tbi | 292.66 KB | 6814a92a58c2624faf9d22fe6df330d0 |
| genomic_resource.yaml | 5.96 KB | 2bba7bd92d0ab3761783c4cf173acb0f |
| statistics/ |