Resource
| Id | ATAC-seq/ENCSR078EBD |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR078EBD [biosample_summary="Homo sapiens spleen 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 {ENCAN568UNO|/analyses/ENCAN568UNO/} has in progress subobject document {e9268c3a-09b2-4c49-9551-5bbb4fe42be4|/documents/e9268c3a-09b2-4c49-9551-5bbb4fe42be4/} audit_internal_action: Released analysis {ENCAN568UNO|/analyses/ENCAN568UNO/} 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. {ENCFF727IIE|/files/ENCFF727IIE/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a FRiP score of 0.13. 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 {ENCFF159BUD|/files/ENCFF159BUD/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.884059. 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 {ENCFF159BUD|/files/ENCFF159BUD/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.89. 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) {ENCFF727IIE|/files/ENCFF727IIE/} (overlap peaks) and {ENCFF105FRE|/files/ENCFF105FRE/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have 128539 and 59146 peaks. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR078EBD | float |
ATAC-seq_ENCSR078EBD |
ATAC-seq ENCSR078EBD [biosample_summary="Homo sapiens spleen tissue female adult (51 years)"]
|
 |
[1.58, 32.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 43582363 | 1.35% | 84854 |
| chr1 | 3922273 | 1.58% | 7545 |
| chr2 | 3489276 | 1.44% | 6876 |
| chr3 | 2680197 | 1.35% | 5249 |
| chr4 | 2060267 | 1.08% | 4017 |
| chr5 | 2310038 | 1.27% | 4595 |
| chr6 | 2477645 | 1.45% | 4755 |
| chr7 | 2401775 | 1.51% | 4736 |
| chr8 | 1970057 | 1.36% | 3902 |
| chr9 | 1814696 | 1.31% | 3541 |
| chr10 | 2093857 | 1.56% | 4206 |
| chr11 | 2242810 | 1.66% | 4355 |
| chr12 | 2023231 | 1.52% | 3925 |
| chr13 | 1140558 | 1.00% | 2216 |
| chr14 | 1366787 | 1.28% | 2641 |
| chr15 | 1336376 | 1.31% | 2603 |
| chr16 | 1502048 | 1.66% | 2864 |
| chr17 | 2014752 | 2.42% | 3863 |
| chr18 | 968947 | 1.21% | 1968 |
| chr19 | 1835582 | 3.13% | 3353 |
| chr20 | 1128723 | 1.75% | 2297 |
| chr21 | 593951 | 1.27% | 1158 |
| chr22 | 946023 | 1.86% | 1835 |
| chrX | 1261993 | 0.81% | 2352 |
| chrY | 501 | <0.01% | 2 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 84854 | 150 | 2969 | 513.62 | 431 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF727IIE.bed.gz | 3.04 MB | 87691852a9ec994bd261549056f12c3d |
| ENCFF727IIE.tabix.bed.gz | 952.32 KB | cd55db6d9042721f0bfa57845c7256ca |
| ENCFF727IIE.tabix.bed.gz.tbi | 412.9 KB | d6ce51a246314ef342214055fceb41f5 |
| genomic_resource.yaml | 3.72 KB | 08ccc15287d90d96efcecbd8709612c2 |
| statistics/ |