Resource
| Id | ATAC-seq/ENCSR610AQP |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR610AQP [biosample_summary="Homo sapiens memory B cell male adult (40 years)"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: male adult (40 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN563GAD|/analyses/ENCAN563GAD/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_warning: Alignment file {ENCFF458RBY|/files/ENCFF458RBY/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has 23145584 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 {ENCFF661VAK|/files/ENCFF661VAK/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has 21940107 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 {ENCFF458RBY|/files/ENCFF458RBY/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with NRF value of 0.857935. 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 {ENCFF458RBY|/files/ENCFF458RBY/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.89. 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 {ENCFF661VAK|/files/ENCFF661VAK/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with NRF value of 0.844812. 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 {ENCFF661VAK|/files/ENCFF661VAK/} 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_ENCSR610AQP | float |
ATAC-seq_ENCSR610AQP |
ATAC-seq ENCSR610AQP [biosample_summary="Homo sapiens memory B cell male adult (40 years)"]
|
 |
[1.27, 48.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 43528338 | 1.35% | 84511 |
| chr1 | 4318641 | 1.73% | 8266 |
| chr2 | 3286918 | 1.36% | 6555 |
| chr3 | 2570757 | 1.30% | 5163 |
| chr4 | 1660004 | 0.87% | 3326 |
| chr5 | 2050800 | 1.13% | 4081 |
| chr6 | 2635923 | 1.54% | 5178 |
| chr7 | 2220916 | 1.39% | 4358 |
| chr8 | 1803011 | 1.24% | 3605 |
| chr9 | 1767798 | 1.28% | 3460 |
| chr10 | 1983373 | 1.48% | 3889 |
| chr11 | 2144746 | 1.59% | 4095 |
| chr12 | 2232194 | 1.67% | 4314 |
| chr13 | 938370 | 0.82% | 1893 |
| chr14 | 1465611 | 1.37% | 2818 |
| chr15 | 1412787 | 1.39% | 2763 |
| chr16 | 1660928 | 1.84% | 3098 |
| chr17 | 2312992 | 2.78% | 4243 |
| chr18 | 836153 | 1.04% | 1699 |
| chr19 | 2119116 | 3.62% | 3807 |
| chr20 | 1215451 | 1.89% | 2396 |
| chr21 | 550517 | 1.18% | 1026 |
| chr22 | 1029987 | 2.03% | 1930 |
| chrX | 1243968 | 0.80% | 2404 |
| chrY | 67377 | 0.12% | 144 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 84511 | 150 | 3407 | 515.06 | 417 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF888IRH.bed.gz | 3.27 MB | 59770ceecfebde3a4a15d041c95c0796 |
| ENCFF888IRH.tabix.bed.gz | 952.07 KB | 13b7cfc59f202cca3028251fe8d008f5 |
| ENCFF888IRH.tabix.bed.gz.tbi | 354.57 KB | 6586df6fea5ce9b84f4b6ae8630d4a1c |
| genomic_resource.yaml | 4.45 KB | 62b7de656126de48a69ab9e5c13ecb82 |
| statistics/ |