Resource
| Id | ATAC-seq/ENCSR823ZCR |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR823ZCR [biosample_summary="Homo sapiens gastrocnemius medialis 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 {ENCAN748YVM|/analyses/ENCAN748YVM/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_internal_action: Released analysis {ENCAN748YVM|/analyses/ENCAN748YVM/} has in progress subobject document {c8de691e-72b2-4d8f-b9b4-ee0e42ee4a91|/documents/c8de691e-72b2-4d8f-b9b4-ee0e42ee4a91/} 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. {ENCFF751EAY|/files/ENCFF751EAY/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a FRiP score of 0.10. audit_not_compliant: According to ENCODE4 standards, ATAC-seq assays processed by the uniform processing pipeline should have either >150k reproducible peaks in an overlap peaks file, or >70k in an IDR thresholded peaks file. 100-150k or 50-70k peaks respectively is acceptable, and <100k or <50k respectively is not compliant. File(s) {ENCFF751EAY|/files/ENCFF751EAY/} (overlap peaks) and {ENCFF953QCT|/files/ENCFF953QCT/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have 88946 and 44214 peaks. 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 {ENCFF125LEJ|/files/ENCFF125LEJ/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.842976. 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 {ENCFF125LEJ|/files/ENCFF125LEJ/} 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_ENCSR823ZCR | float |
ATAC-seq_ENCSR823ZCR |
ATAC-seq ENCSR823ZCR [biosample_summary="Homo sapiens gastrocnemius medialis tissue female adult (51 years)"]
|
 |
[1.6, 22.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 29949119 | 0.93% | 53982 |
| chr1 | 2864494 | 1.15% | 5096 |
| chr2 | 2407207 | 0.99% | 4468 |
| chr3 | 1929061 | 0.97% | 3510 |
| chr4 | 1252418 | 0.66% | 2269 |
| chr5 | 1531785 | 0.84% | 2821 |
| chr6 | 1723369 | 1.01% | 3193 |
| chr7 | 1590983 | 1.00% | 2844 |
| chr8 | 1254128 | 0.86% | 2367 |
| chr9 | 1348660 | 0.97% | 2433 |
| chr10 | 1427702 | 1.07% | 2627 |
| chr11 | 1562279 | 1.16% | 2778 |
| chr12 | 1382380 | 1.04% | 2435 |
| chr13 | 695715 | 0.61% | 1275 |
| chr14 | 942965 | 0.88% | 1633 |
| chr15 | 1048422 | 1.03% | 1930 |
| chr16 | 1115187 | 1.23% | 1929 |
| chr17 | 1497643 | 1.80% | 2573 |
| chr18 | 577660 | 0.72% | 1085 |
| chr19 | 1227772 | 2.09% | 2054 |
| chr20 | 769406 | 1.19% | 1451 |
| chr21 | 371159 | 0.79% | 674 |
| chr22 | 663737 | 1.31% | 1186 |
| chrX | 763801 | 0.49% | 1346 |
| chrY | 1186 | <0.01% | 5 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 53982 | 150 | 2952 | 554.8 | 448 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF751EAY.bed.gz | 2.11 MB | eeb9d0d96202b38cb0b75dee7c0c76ff |
| ENCFF751EAY.tabix.bed.gz | 612.74 KB | f245392a6bab0032bc581167865fda0e |
| ENCFF751EAY.tabix.bed.gz.tbi | 296.22 KB | 9a775ed520b9b1b41c457bfbea116cb3 |
| genomic_resource.yaml | 3.78 KB | 8b345841ab67686daf207283e5479301 |
| statistics/ |