Resource
| Id | ATAC-seq/ENCSR335XRZ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR335XRZ [biosample_summary="Homo sapiens stimulated activated effector memory CD8-positive, alpha-beta T cell male adult (36 years) treated with 100 ng/mL Interleukin-12 subunit alpha for 72 hours, 100 ng/mL Interleukin-12 subunit beta for 72 hours, anti-CD3 and anti-CD28 coated beads for 72 hours"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: male adult (36 years) treated with 100 ng/mL Interleukin-12 subunit alpha for 72 hours, 100 ng/mL Interleukin-12 subunit beta for 72 hours, anti-CD3 and anti-CD28 coated beads for 72 hours output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN673BMZ|/analyses/ENCAN673BMZ/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_not_compliant: Alignment file {ENCFF551AJL|/files/ENCFF551AJL/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has 19338751 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_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 {ENCFF551AJL|/files/ENCFF551AJL/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with NRF value of 0.600727. 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 {ENCFF551AJL|/files/ENCFF551AJL/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.57. 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 {ENCFF551AJL|/files/ENCFF551AJL/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with a PBC2 value of 2.14. 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 {ENCFF741HOD|/files/ENCFF741HOD/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with NRF value of 0.749362. 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 {ENCFF741HOD|/files/ENCFF741HOD/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.75. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR335XRZ | float |
ATAC-seq_ENCSR335XRZ |
ATAC-seq ENCSR335XRZ [biosample_summary="Homo sapiens stimulated activated effector memory CD8-positive, alpha-beta T cell male adult (36 years) treated with 100 ng/mL Interleukin-12 subunit alpha for 72 hours, 100 ng/mL Interleukin-12 subunit beta for 72 hours, anti-CD3 and anti-CD28 coated beads for 72 hours"]
|
 |
[1.43, 32.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 46861882 | 1.46% | 88348 |
| chr1 | 4603623 | 1.85% | 8543 |
| chr2 | 3800033 | 1.57% | 7401 |
| chr3 | 3031494 | 1.53% | 5891 |
| chr4 | 1908363 | 1.00% | 3750 |
| chr5 | 2397240 | 1.32% | 4646 |
| chr6 | 2995185 | 1.75% | 5671 |
| chr7 | 2392884 | 1.50% | 4588 |
| chr8 | 2011983 | 1.39% | 3899 |
| chr9 | 1908004 | 1.38% | 3631 |
| chr10 | 2261073 | 1.69% | 4305 |
| chr11 | 2289695 | 1.69% | 4274 |
| chr12 | 2319602 | 1.74% | 4275 |
| chr13 | 1119067 | 0.98% | 2202 |
| chr14 | 1624416 | 1.52% | 3017 |
| chr15 | 1587177 | 1.56% | 3077 |
| chr16 | 1647366 | 1.82% | 2965 |
| chr17 | 2215751 | 2.66% | 3919 |
| chr18 | 887763 | 1.10% | 1788 |
| chr19 | 1845729 | 3.15% | 3050 |
| chr20 | 1193987 | 1.85% | 2255 |
| chr21 | 576886 | 1.24% | 1078 |
| chr22 | 979043 | 1.93% | 1752 |
| chrX | 1114117 | 0.71% | 2060 |
| chrY | 151401 | 0.26% | 311 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 88348 | 150 | 2698 | 530.42 | 434 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF211AMR.bed.gz | 3.46 MB | ec36c8af0a7f1adc9a72c5655875d413 |
| ENCFF211AMR.tabix.bed.gz | 995.82 KB | bf28ff348285c7a332836572e81ecf49 |
| ENCFF211AMR.tabix.bed.gz.tbi | 405.98 KB | 738a0ba4e0bb2c928dd08246a5b38720 |
| genomic_resource.yaml | 5.78 KB | 49b8f15b337c1fcfa3abd13ecd311e38 |
| statistics/ |