Resource
| Id | ATAC-seq/ENCSR297VGU |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR297VGU [biosample_summary="Homo sapiens kidney tissue female adult (47 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (47 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN588LOR|/analyses/ENCAN588LOR/} 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. {ENCFF845OZO|/files/ENCFF845OZO/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a FRiP score of 0.20. 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 {ENCFF136AEE|/files/ENCFF136AEE/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.875879. 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 {ENCFF136AEE|/files/ENCFF136AEE/} 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_ENCSR297VGU | float |
ATAC-seq_ENCSR297VGU |
ATAC-seq ENCSR297VGU [biosample_summary="Homo sapiens kidney tissue female adult (47 years)"]
|
 |
[1.4, 37] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 86817624 | 2.70% | 148859 |
| chr1 | 8200569 | 3.29% | 13814 |
| chr2 | 7143925 | 2.95% | 12502 |
| chr3 | 5613679 | 2.83% | 9909 |
| chr4 | 4024565 | 2.12% | 7253 |
| chr5 | 4702237 | 2.59% | 8338 |
| chr6 | 5204470 | 3.05% | 9069 |
| chr7 | 4487294 | 2.82% | 7779 |
| chr8 | 3875891 | 2.67% | 6733 |
| chr9 | 3809564 | 2.75% | 6560 |
| chr10 | 4296006 | 3.21% | 7504 |
| chr11 | 4357990 | 3.23% | 7321 |
| chr12 | 4275791 | 3.21% | 7287 |
| chr13 | 2235883 | 1.96% | 4002 |
| chr14 | 2703959 | 2.53% | 4660 |
| chr15 | 2883559 | 2.83% | 5014 |
| chr16 | 2947703 | 3.26% | 4822 |
| chr17 | 3833729 | 4.60% | 6130 |
| chr18 | 1904589 | 2.37% | 3398 |
| chr19 | 3013733 | 5.14% | 4479 |
| chr20 | 2283440 | 3.54% | 3956 |
| chr21 | 1223711 | 2.62% | 2080 |
| chr22 | 1749032 | 3.44% | 2843 |
| chrX | 2046060 | 1.31% | 3405 |
| chrY | 245 | <0.01% | 1 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 148859 | 150 | 3254 | 583.22 | 460 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF845OZO.bed.gz | 5.67 MB | d6176244150fc7caa3fba648f9cd483e |
| ENCFF845OZO.tabix.bed.gz | 1.62 MB | 47778933798ac4917fcf875e2f4000ed |
| ENCFF845OZO.tabix.bed.gz.tbi | 506.76 KB | d0be0ccc83d12bfe11c8f00919b4ead4 |
| genomic_resource.yaml | 3.32 KB | f25be627e05291e50bd93909c8ec427d |
| statistics/ |