Resource
| Id | ATAC-seq/ENCSR788TRR |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR788TRR [biosample_summary="Homo sapiens omental fat pad tissue female adult (51 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (51 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN715MTI|/analyses/ENCAN715MTI/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_internal_action: Released analysis {ENCAN715MTI|/analyses/ENCAN715MTI/} has in progress subobject document {693bfc58-5eb9-46e8-8217-59a1ab5b163f|/documents/693bfc58-5eb9-46e8-8217-59a1ab5b163f/} 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. {ENCFF096PUC|/files/ENCFF096PUC/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a FRiP score of 0.15. 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 {ENCFF550OUL|/files/ENCFF550OUL/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.871107. 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 {ENCFF550OUL|/files/ENCFF550OUL/} 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_ENCSR788TRR | float |
ATAC-seq_ENCSR788TRR |
ATAC-seq ENCSR788TRR [biosample_summary="Homo sapiens omental fat pad tissue female adult (51 years)"]
|
 |
[1.45, 23.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 50323008 | 1.56% | 87201 |
| chr1 | 4921276 | 1.98% | 8425 |
| chr2 | 3978302 | 1.64% | 6961 |
| chr3 | 3183185 | 1.61% | 5637 |
| chr4 | 2311178 | 1.22% | 4056 |
| chr5 | 2636961 | 1.45% | 4639 |
| chr6 | 2979045 | 1.74% | 5172 |
| chr7 | 2564133 | 1.61% | 4503 |
| chr8 | 2242658 | 1.55% | 3965 |
| chr9 | 2236654 | 1.62% | 3945 |
| chr10 | 2323354 | 1.74% | 4095 |
| chr11 | 2615192 | 1.94% | 4435 |
| chr12 | 2486718 | 1.87% | 4231 |
| chr13 | 1174592 | 1.03% | 2100 |
| chr14 | 1614581 | 1.51% | 2752 |
| chr15 | 1703502 | 1.67% | 2971 |
| chr16 | 1669228 | 1.85% | 2826 |
| chr17 | 2370347 | 2.85% | 3973 |
| chr18 | 1081390 | 1.35% | 1940 |
| chr19 | 1900130 | 3.24% | 3056 |
| chr20 | 1386210 | 2.15% | 2420 |
| chr21 | 648083 | 1.39% | 1145 |
| chr22 | 1030550 | 2.03% | 1779 |
| chrX | 1264704 | 0.81% | 2171 |
| chrY | 1035 | <0.01% | 4 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 87201 | 150 | 3004 | 577.09 | 480 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF096PUC.bed.gz | 3.6 MB | aa7e7a97cb07133e1e9997486ac5e103 |
| ENCFF096PUC.tabix.bed.gz | 995.27 KB | 799247b51026131f02ae2429054b1612 |
| ENCFF096PUC.tabix.bed.gz.tbi | 397.1 KB | d5f69b82e9301e49929da6385460b813 |
| genomic_resource.yaml | 3.21 KB | 85de7ccdc3ff1e22691c1aadaad8659d |
| statistics/ |