Resource
| Id | ATAC-seq/ENCSR903WVU |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR903WVU [biosample_summary="Homo sapiens naive 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 {ENCAN213BBL|/analyses/ENCAN213BBL/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_warning: Alignment file {ENCFF244SND|/files/ENCFF244SND/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has 23463576 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 {ENCFF501GZR|/files/ENCFF501GZR/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has 23408617 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 {ENCFF244SND|/files/ENCFF244SND/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with NRF value of 0.846287. 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 {ENCFF244SND|/files/ENCFF244SND/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.88. 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 {ENCFF501GZR|/files/ENCFF501GZR/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with NRF value of 0.847939. 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 {ENCFF501GZR|/files/ENCFF501GZR/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.87. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR903WVU | float |
ATAC-seq_ENCSR903WVU |
ATAC-seq ENCSR903WVU [biosample_summary="Homo sapiens naive B cell male adult (40 years)"]
|
 |
[1.29, 48.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 41389613 | 1.29% | 79310 |
| chr1 | 4051635 | 1.63% | 7699 |
| chr2 | 3146065 | 1.30% | 6150 |
| chr3 | 2467552 | 1.24% | 4855 |
| chr4 | 1628097 | 0.86% | 3217 |
| chr5 | 1955859 | 1.08% | 3846 |
| chr6 | 2582646 | 1.51% | 5057 |
| chr7 | 2106980 | 1.32% | 4051 |
| chr8 | 1666065 | 1.15% | 3297 |
| chr9 | 1676271 | 1.21% | 3225 |
| chr10 | 1855511 | 1.39% | 3616 |
| chr11 | 2041753 | 1.51% | 3821 |
| chr12 | 2114295 | 1.59% | 4044 |
| chr13 | 914000 | 0.80% | 1805 |
| chr14 | 1369772 | 1.28% | 2603 |
| chr15 | 1317466 | 1.29% | 2532 |
| chr16 | 1525518 | 1.69% | 2812 |
| chr17 | 2205295 | 2.65% | 4015 |
| chr18 | 768301 | 0.96% | 1550 |
| chr19 | 2079548 | 3.55% | 3665 |
| chr20 | 1083471 | 1.68% | 2088 |
| chr21 | 541477 | 1.16% | 1002 |
| chr22 | 988809 | 1.95% | 1840 |
| chrX | 1234453 | 0.79% | 2372 |
| chrY | 68774 | 0.12% | 148 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 79310 | 150 | 2903 | 521.87 | 421 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF839DEM.bed.gz | 3.07 MB | 89887425ad2cef7b1d63ecfb7b9d3477 |
| ENCFF839DEM.tabix.bed.gz | 892.62 KB | a9aa9431848d3b6239f8e89c76901ed0 |
| ENCFF839DEM.tabix.bed.gz.tbi | 340.64 KB | 8210c3389e100d1f664dc665f6a03700 |
| genomic_resource.yaml | 4.44 KB | ece14200d4a1d47e80bc78bf44ef81db |
| statistics/ |