Resource
| Id | ATAC-seq/ENCSR603LVR |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR603LVR [biosample_summary="Homo sapiens B cell male adult (22 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (22 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN851QNO|/analyses/ENCAN851QNO/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_warning: Alignment file {ENCFF060ZGV|/files/ENCFF060ZGV/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has 21836765 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 {ENCFF060ZGV|/files/ENCFF060ZGV/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with NRF value of 0.730072. 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 {ENCFF060ZGV|/files/ENCFF060ZGV/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.75. 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) {ENCFF421XIL|/files/ENCFF421XIL/} (overlap peaks) and {ENCFF390ASB|/files/ENCFF390ASB/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline have 100655 and 68214 peaks. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR603LVR | float |
ATAC-seq_ENCSR603LVR |
ATAC-seq ENCSR603LVR [biosample_summary="Homo sapiens B cell male adult (22 years)"]
|
 |
[1.39, 43.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 34825728 | 1.08% | 62919 |
| chr1 | 3455017 | 1.39% | 6197 |
| chr2 | 2569760 | 1.06% | 4739 |
| chr3 | 2003094 | 1.01% | 3706 |
| chr4 | 1257443 | 0.66% | 2294 |
| chr5 | 1597359 | 0.88% | 2923 |
| chr6 | 2118913 | 1.24% | 3859 |
| chr7 | 1750974 | 1.10% | 3215 |
| chr8 | 1373726 | 0.95% | 2587 |
| chr9 | 1405608 | 1.02% | 2577 |
| chr10 | 1546107 | 1.16% | 2829 |
| chr11 | 1744182 | 1.29% | 3088 |
| chr12 | 1769087 | 1.33% | 3156 |
| chr13 | 710445 | 0.62% | 1297 |
| chr14 | 1194682 | 1.12% | 2150 |
| chr15 | 1121329 | 1.10% | 2061 |
| chr16 | 1410855 | 1.56% | 2447 |
| chr17 | 1972816 | 2.37% | 3449 |
| chr18 | 624781 | 0.78% | 1200 |
| chr19 | 1853701 | 3.16% | 3128 |
| chr20 | 963110 | 1.49% | 1777 |
| chr21 | 455810 | 0.98% | 821 |
| chr22 | 884976 | 1.74% | 1586 |
| chrX | 995252 | 0.64% | 1743 |
| chrY | 46701 | 0.08% | 90 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 62919 | 150 | 2996 | 553.5 | 455 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF421XIL.bed.gz | 2.39 MB | 9ffe976e631111e8155a16401208e890 |
| ENCFF421XIL.tabix.bed.gz | 706.34 KB | dd01cb545d2ed99068543448d1187131 |
| ENCFF421XIL.tabix.bed.gz.tbi | 290.85 KB | 49a06804632643bd258d300a5fed3eed |
| genomic_resource.yaml | 3.45 KB | 6eb51a8c86ea459da134be93410f67df |
| statistics/ |