Resource
| Id | ATAC-seq/ENCSR032RGS |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR032RGS [biosample_summary="Homo sapiens A549"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2, Rep 3 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN065GGH|/analyses/ENCAN065GGH/} 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 {ENCFF607DTB|/files/ENCFF607DTB/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.865913. 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 {ENCFF607DTB|/files/ENCFF607DTB/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.87. 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 {ENCFF701BDT|/files/ENCFF701BDT/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.857486. 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 {ENCFF701BDT|/files/ENCFF701BDT/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.87. 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 {ENCFF616DYV|/files/ENCFF616DYV/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.844336. 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 {ENCFF616DYV|/files/ENCFF616DYV/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.86. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR032RGS | float |
ATAC-seq_ENCSR032RGS |
ATAC-seq ENCSR032RGS [biosample_summary="Homo sapiens A549"]
|
 |
[1.23, 41.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 107778547 | 3.35% | 138825 |
| chr1 | 9394091 | 3.77% | 11930 |
| chr2 | 10107251 | 4.17% | 13011 |
| chr3 | 5942247 | 3.00% | 7953 |
| chr4 | 3645125 | 1.92% | 5097 |
| chr5 | 5853904 | 3.22% | 7778 |
| chr6 | 4765963 | 2.79% | 6290 |
| chr7 | 6069302 | 3.81% | 7872 |
| chr8 | 5004960 | 3.45% | 6571 |
| chr9 | 4910260 | 3.55% | 6191 |
| chr10 | 5326625 | 3.98% | 6855 |
| chr11 | 5253759 | 3.89% | 6614 |
| chr12 | 6320674 | 4.74% | 8094 |
| chr13 | 1712858 | 1.50% | 2426 |
| chr14 | 3420376 | 3.20% | 4362 |
| chr15 | 4323666 | 4.24% | 5450 |
| chr16 | 4016152 | 4.45% | 4979 |
| chr17 | 6474667 | 7.78% | 7863 |
| chr18 | 1505099 | 1.87% | 2134 |
| chr19 | 4622153 | 7.89% | 5562 |
| chr20 | 3326334 | 5.16% | 4324 |
| chr21 | 930162 | 1.99% | 1176 |
| chr22 | 1974305 | 3.89% | 2505 |
| chrX | 2752010 | 1.76% | 3595 |
| chrY | 126604 | 0.22% | 193 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 138825 | 150 | 4525 | 776.36 | 655 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF899OMR.bed.gz | 6.82 MB | feed36997c097111e6dd09cd4c29109c |
| ENCFF899OMR.tabix.bed.gz | 1.56 MB | 820138e9ab7bc7024e443fb55dbcb604 |
| ENCFF899OMR.tabix.bed.gz.tbi | 453.25 KB | 3551ca18ab85ea728fced3f8181cd75a |
| genomic_resource.yaml | 4.88 KB | 917dce350603f066b6d434df1fa246d1 |
| statistics/ |