Resource
| Id | ATAC-seq/ENCSR685OFR |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR685OFR [biosample_summary="Homo sapiens naive B cell female adult (39 years)"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: female adult (39 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN160XVS|/analyses/ENCAN160XVS/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_warning: Alignment file {ENCFF402TQJ|/files/ENCFF402TQJ/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has 22532527 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: Alignment file {ENCFF271LEW|/files/ENCFF271LEW/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has 21039551 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 {ENCFF402TQJ|/files/ENCFF402TQJ/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with NRF value of 0.847443. 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 {ENCFF402TQJ|/files/ENCFF402TQJ/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.87. 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 {ENCFF271LEW|/files/ENCFF271LEW/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with NRF value of 0.848575. 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 {ENCFF271LEW|/files/ENCFF271LEW/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.88. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR685OFR | float |
ATAC-seq_ENCSR685OFR |
ATAC-seq ENCSR685OFR [biosample_summary="Homo sapiens naive B cell female adult (39 years)"]
|
 |
[1.25, 46.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 39209596 | 1.22% | 75935 |
| chr1 | 3853301 | 1.55% | 7409 |
| chr2 | 2928106 | 1.21% | 5810 |
| chr3 | 2268385 | 1.14% | 4482 |
| chr4 | 1497674 | 0.79% | 2968 |
| chr5 | 1824429 | 1.00% | 3629 |
| chr6 | 2422352 | 1.42% | 4781 |
| chr7 | 1976781 | 1.24% | 3848 |
| chr8 | 1572906 | 1.08% | 3144 |
| chr9 | 1593621 | 1.15% | 3135 |
| chr10 | 1722968 | 1.29% | 3379 |
| chr11 | 1932269 | 1.43% | 3657 |
| chr12 | 2006606 | 1.51% | 3894 |
| chr13 | 845326 | 0.74% | 1684 |
| chr14 | 1337009 | 1.25% | 2558 |
| chr15 | 1251000 | 1.23% | 2453 |
| chr16 | 1520102 | 1.68% | 2838 |
| chr17 | 2134063 | 2.56% | 3961 |
| chr18 | 725188 | 0.90% | 1493 |
| chr19 | 2073278 | 3.54% | 3714 |
| chr20 | 1047464 | 1.63% | 2056 |
| chr21 | 520904 | 1.12% | 974 |
| chr22 | 963996 | 1.90% | 1827 |
| chrX | 1190833 | 0.76% | 2237 |
| chrY | 1035 | <0.01% | 4 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 75935 | 150 | 2582 | 516.36 | 406 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF424JEX.bed.gz | 2.94 MB | 7b7dc1898bdd4b3db5934132ac7bda25 |
| ENCFF424JEX.tabix.bed.gz | 855.33 KB | 1f9adc00b5ebd661b66612162367bbc2 |
| ENCFF424JEX.tabix.bed.gz.tbi | 318.82 KB | 58d26d9596a2bb8a0b9950abe3441f94 |
| genomic_resource.yaml | 4.45 KB | f264a800458fafbbdc26c1b99594de65 |
| statistics/ |