Resource
| Id | ATAC-seq/ENCSR025MEO |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR025MEO [biosample_summary="Homo sapiens HG03354"] |
| Description |
status: released biological_replicates: Rep 1 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN363NRV|/analyses/ENCAN363NRV/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} 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 {ENCFF132WNX|/files/ENCFF132WNX/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.693678. 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 {ENCFF132WNX|/files/ENCFF132WNX/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.68. 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 {ENCFF132WNX|/files/ENCFF132WNX/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC2 value of 2.87. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR025MEO | float |
ATAC-seq_ENCSR025MEO |
ATAC-seq ENCSR025MEO [biosample_summary="Homo sapiens HG03354"]
|
 |
[1.4, 37.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 65261426 | 2.03% | 113899 |
| chr1 | 5836450 | 2.34% | 10054 |
| chr2 | 5807298 | 2.40% | 10458 |
| chr3 | 4539936 | 2.29% | 8145 |
| chr4 | 4019216 | 2.11% | 7358 |
| chr5 | 4088267 | 2.25% | 7297 |
| chr6 | 4442444 | 2.60% | 7882 |
| chr7 | 3699756 | 2.32% | 6554 |
| chr8 | 3297712 | 2.27% | 5918 |
| chr9 | 2595508 | 1.88% | 4523 |
| chr10 | 3073414 | 2.30% | 5364 |
| chr11 | 3092219 | 2.29% | 5346 |
| chr12 | 3259149 | 2.45% | 5607 |
| chr13 | 1817213 | 1.59% | 3280 |
| chr14 | 1954870 | 1.83% | 3329 |
| chr15 | 1802206 | 1.77% | 3063 |
| chr16 | 1716731 | 1.90% | 2767 |
| chr17 | 2066207 | 2.48% | 3335 |
| chr18 | 1509266 | 1.88% | 2729 |
| chr19 | 1635351 | 2.79% | 2349 |
| chr20 | 1307377 | 2.03% | 2257 |
| chr21 | 616396 | 1.32% | 1030 |
| chr22 | 756943 | 1.49% | 1169 |
| chrX | 2325925 | 1.49% | 4079 |
| chrY | 1572 | <0.01% | 6 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 113899 | 150 | 3207 | 572.98 | 471 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF429JRQ.bed.gz | 4.76 MB | 016b55eeedcb018e18ec3bfffc0b97d8 |
| ENCFF429JRQ.tabix.bed.gz | 1.26 MB | fc7b44e6df533421a1df2e6f2e39e9f9 |
| ENCFF429JRQ.tabix.bed.gz.tbi | 475.03 KB | b9fcf3db428138eb4c0e155042a2f0e3 |
| genomic_resource.yaml | 3.13 KB | a1570d22f4d9d4a37173829aea0fbc7e |
| statistics/ |