Resource
| Id | ATAC-seq/ENCSR291GJU |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR291GJU [biosample_summary="Homo sapiens HepG2"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2, Rep 3 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN877DUG|/analyses/ENCAN877DUG/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} 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 {ENCFF990VCP|/files/ENCFF990VCP/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.890721. 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 {ENCFF990VCP|/files/ENCFF990VCP/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.90. 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 {ENCFF624SON|/files/ENCFF624SON/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.898935. 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 {ENCFF926KFU|/files/ENCFF926KFU/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.813992. 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 {ENCFF926KFU|/files/ENCFF926KFU/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.82. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR291GJU | float |
ATAC-seq_ENCSR291GJU |
ATAC-seq ENCSR291GJU [biosample_summary="Homo sapiens HepG2"]
|
 |
[1.2, 40] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 112741044 | 3.50% | 149268 |
| chr1 | 9748629 | 3.92% | 12798 |
| chr2 | 11700194 | 4.83% | 15332 |
| chr3 | 6580001 | 3.32% | 9096 |
| chr4 | 4560934 | 2.40% | 6452 |
| chr5 | 5253888 | 2.89% | 7185 |
| chr6 | 7353190 | 4.30% | 9896 |
| chr7 | 5699093 | 3.58% | 7574 |
| chr8 | 4390519 | 3.03% | 6043 |
| chr9 | 4419709 | 3.19% | 5875 |
| chr10 | 5051591 | 3.78% | 6738 |
| chr11 | 5162970 | 3.82% | 6700 |
| chr12 | 4822081 | 3.62% | 6469 |
| chr13 | 2588480 | 2.26% | 3646 |
| chr14 | 4289054 | 4.01% | 5565 |
| chr15 | 3276327 | 3.21% | 4368 |
| chr16 | 5204425 | 5.76% | 6524 |
| chr17 | 5674709 | 6.82% | 7009 |
| chr18 | 2162933 | 2.69% | 3123 |
| chr19 | 3993390 | 6.81% | 4797 |
| chr20 | 4454927 | 6.91% | 5686 |
| chr21 | 1348783 | 2.89% | 1689 |
| chr22 | 2391517 | 4.71% | 3027 |
| chrX | 2479154 | 1.59% | 3476 |
| chrY | 134546 | 0.24% | 200 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 149268 | 150 | 4499 | 755.29 | 635 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF439EIO.bed.gz | 6.91 MB | c7e08900ba86556a2f5c460039060c10 |
| ENCFF439EIO.tabix.bed.gz | 1.68 MB | 6705241b2fe7bff5edb21aaaf8e0b500 |
| ENCFF439EIO.tabix.bed.gz.tbi | 483.91 KB | d144ffccc7d6a0fdbf64896a446ce9bb |
| genomic_resource.yaml | 4.22 KB | c8ebceb7c65edea6bf563d35d1a2e28c |
| statistics/ |