Resource
| Id | ATAC-seq/ENCSR260ZIV |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR260ZIV [biosample_summary="Homo sapiens gastroesophageal sphincter 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 {ENCAN850AHB|/analyses/ENCAN850AHB/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_internal_action: Released analysis {ENCAN850AHB|/analyses/ENCAN850AHB/} has in progress subobject document {321f70ec-2b4f-4b46-a505-d98e090642c4|/documents/321f70ec-2b4f-4b46-a505-d98e090642c4/} 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. {ENCFF401GGO|/files/ENCFF401GGO/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a FRiP score of 0.10. 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 {ENCFF558QLX|/files/ENCFF558QLX/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.879083. 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 {ENCFF558QLX|/files/ENCFF558QLX/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.88. audit_warning: 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) {ENCFF401GGO|/files/ENCFF401GGO/} (overlap peaks) and {ENCFF580UXE|/files/ENCFF580UXE/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have 137173 and 69556 peaks. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR260ZIV | float |
ATAC-seq_ENCSR260ZIV |
ATAC-seq ENCSR260ZIV [biosample_summary="Homo sapiens gastroesophageal sphincter tissue female adult (51 years)"]
|
 |
[1.59, 27] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 43527751 | 1.35% | 75161 |
| chr1 | 4079092 | 1.64% | 6643 |
| chr2 | 3475283 | 1.43% | 6219 |
| chr3 | 2826528 | 1.43% | 5063 |
| chr4 | 2185637 | 1.15% | 4117 |
| chr5 | 2332204 | 1.28% | 4208 |
| chr6 | 2568397 | 1.50% | 4639 |
| chr7 | 2308165 | 1.45% | 4170 |
| chr8 | 2018405 | 1.39% | 3775 |
| chr9 | 1933996 | 1.40% | 3311 |
| chr10 | 2049831 | 1.53% | 3572 |
| chr11 | 2169827 | 1.61% | 3561 |
| chr12 | 2135009 | 1.60% | 3630 |
| chr13 | 1153792 | 1.01% | 2172 |
| chr14 | 1375838 | 1.29% | 2336 |
| chr15 | 1402086 | 1.37% | 2300 |
| chr16 | 1420327 | 1.57% | 2212 |
| chr17 | 1933235 | 2.32% | 2951 |
| chr18 | 953824 | 1.19% | 1832 |
| chr19 | 1569746 | 2.68% | 2253 |
| chr20 | 1043300 | 1.62% | 1744 |
| chr21 | 551056 | 1.18% | 974 |
| chr22 | 836297 | 1.65% | 1300 |
| chrX | 1204618 | 0.77% | 2174 |
| chrY | 1258 | <0.01% | 5 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 75161 | 150 | 3032 | 579.13 | 464 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF401GGO.bed.gz | 3.16 MB | 4c14c0db0f8834a79edf4a89b62781a1 |
| ENCFF401GGO.tabix.bed.gz | 850.99 KB | 24b2b62562630a01852bd725295ed3ff |
| ENCFF401GGO.tabix.bed.gz.tbi | 389.14 KB | 2e8c0a5233ff5c71efadfaca08a050fa |
| genomic_resource.yaml | 3.79 KB | 54726402a962133214f58d63c10bf8ef |
| statistics/ |