Resource
| Id | ATAC-seq/ENCSR123WME |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR123WME [biosample_summary="Homo sapiens HG02943"] |
| Description |
status: released biological_replicates: Rep 1 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN469ZFM|/analyses/ENCAN469ZFM/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_warning: Alignment file {ENCFF657AXO|/files/ENCFF657AXO/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has 24650809 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 {ENCFF657AXO|/files/ENCFF657AXO/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.884005. 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 {ENCFF657AXO|/files/ENCFF657AXO/} processed by ATAC-seq ENCODE4 v1.9.1 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_ENCSR123WME | float |
ATAC-seq_ENCSR123WME |
ATAC-seq ENCSR123WME [biosample_summary="Homo sapiens HG02943"]
|
 |
[1.39, 36.7] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 42442836 | 1.32% | 74200 |
| chr1 | 3796590 | 1.53% | 6485 |
| chr2 | 3613425 | 1.49% | 6513 |
| chr3 | 2938984 | 1.48% | 5289 |
| chr4 | 2446418 | 1.29% | 4526 |
| chr5 | 2546957 | 1.40% | 4571 |
| chr6 | 2836173 | 1.66% | 5036 |
| chr7 | 2358233 | 1.48% | 4219 |
| chr8 | 2095602 | 1.44% | 3782 |
| chr9 | 1699408 | 1.23% | 2967 |
| chr10 | 2050841 | 1.53% | 3618 |
| chr11 | 2019625 | 1.50% | 3518 |
| chr12 | 2094306 | 1.57% | 3632 |
| chr13 | 1152790 | 1.01% | 2066 |
| chr14 | 1270419 | 1.19% | 2155 |
| chr15 | 1197337 | 1.17% | 2063 |
| chr16 | 1231097 | 1.36% | 1983 |
| chr17 | 1479713 | 1.78% | 2366 |
| chr18 | 983722 | 1.22% | 1786 |
| chr19 | 1256491 | 2.14% | 1824 |
| chr20 | 904744 | 1.40% | 1582 |
| chr21 | 401740 | 0.86% | 659 |
| chr22 | 568375 | 1.12% | 900 |
| chrX | 1499282 | 0.96% | 2658 |
| chrY | 564 | <0.01% | 2 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 74200 | 150 | 2823 | 572.01 | 473 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF304OUP.bed.gz | 3.09 MB | 7fed5bcfc43a9fd1265004498ca3fb8e |
| ENCFF304OUP.tabix.bed.gz | 848.6 KB | 94e1783d1324993f111e3c3107611bae |
| ENCFF304OUP.tabix.bed.gz.tbi | 370.13 KB | e1aa2328ba5e8c4fc1625b66495199af |
| genomic_resource.yaml | 2.86 KB | 9b4582d30287d22b1a45689b35c66346 |
| statistics/ |