Resource
| Id | ATAC-seq/ENCSR242QRV |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR242QRV [biosample_summary="Homo sapiens upper lobe of left lung tissue female adult (61 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (61 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN747ETK|/analyses/ENCAN747ETK/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_not_compliant: According to ENCODE4 standards, overlap peaks files in ATAC-seq assays processed by the uniform processing pipeline should have FRiP (fraction of reads in called peak regions) scores > 0.3. FRiP scores 0.2-0.3 are acceptable, and < 0.2 are not compliant. {ENCFF348XSG|/files/ENCFF348XSG/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a FRiP score of 0.09. 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 {ENCFF225GIF|/files/ENCFF225GIF/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.892108. 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 {ENCFF225GIF|/files/ENCFF225GIF/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.90. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR242QRV | float |
ATAC-seq_ENCSR242QRV |
ATAC-seq ENCSR242QRV [biosample_summary="Homo sapiens upper lobe of left lung tissue female adult (61 years)"]
|
 |
[1.44, 24] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 61352022 | 1.91% | 107784 |
| chr1 | 5624568 | 2.26% | 9874 |
| chr2 | 4924173 | 2.03% | 8849 |
| chr3 | 3501738 | 1.77% | 6226 |
| chr4 | 2631594 | 1.38% | 4628 |
| chr5 | 2983302 | 1.64% | 5335 |
| chr6 | 3310411 | 1.94% | 5831 |
| chr7 | 3175460 | 1.99% | 5583 |
| chr8 | 2652671 | 1.83% | 4731 |
| chr9 | 2550085 | 1.84% | 4445 |
| chr10 | 3058382 | 2.29% | 5536 |
| chr11 | 3100685 | 2.30% | 5324 |
| chr12 | 2799774 | 2.10% | 4967 |
| chr13 | 1601280 | 1.40% | 2882 |
| chr14 | 2013190 | 1.88% | 3509 |
| chr15 | 2155606 | 2.11% | 3820 |
| chr16 | 2286397 | 2.53% | 4011 |
| chr17 | 2949185 | 3.54% | 5024 |
| chr18 | 1405755 | 1.75% | 2605 |
| chr19 | 2607976 | 4.45% | 4287 |
| chr20 | 1684737 | 2.61% | 3074 |
| chr21 | 912166 | 1.95% | 1578 |
| chr22 | 1441915 | 2.84% | 2486 |
| chrX | 1977187 | 1.27% | 3164 |
| chrY | 3785 | 0.01% | 15 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 107784 | 150 | 2961 | 569.21 | 477 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF348XSG.bed.gz | 3.79 MB | dea167ef5a0d82518a459b7c69a1018d |
| ENCFF348XSG.tabix.bed.gz | 1.17 MB | 8c232a105dfaa49b39d5431f5653407f |
| ENCFF348XSG.tabix.bed.gz.tbi | 470.23 KB | 126a7a9f6d923843b7d23baa90270df1 |
| genomic_resource.yaml | 3.38 KB | a95404631a48221dd22d8112e5681c97 |
| statistics/ |