Resource
| Id | ATAC-seq/ENCSR182VGJ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR182VGJ [biosample_summary="Homo sapiens spleen tissue female adult (59 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (59 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN343IES|/analyses/ENCAN343IES/} 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. {ENCFF214HLR|/files/ENCFF214HLR/} 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 {ENCFF358QFM|/files/ENCFF358QFM/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.890348. 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 {ENCFF358QFM|/files/ENCFF358QFM/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.89. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR182VGJ | float |
ATAC-seq_ENCSR182VGJ |
ATAC-seq ENCSR182VGJ [biosample_summary="Homo sapiens spleen tissue female adult (59 years)"]
|
 |
[1.37, 23.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 93665069 | 2.91% | 136067 |
| chr1 | 7329644 | 2.94% | 10955 |
| chr2 | 8359140 | 3.45% | 12006 |
| chr3 | 6754084 | 3.41% | 9617 |
| chr4 | 5725912 | 3.01% | 7796 |
| chr5 | 6064952 | 3.34% | 8566 |
| chr6 | 5938807 | 3.48% | 8550 |
| chr7 | 5654942 | 3.55% | 8005 |
| chr8 | 4897488 | 3.37% | 6948 |
| chr9 | 3814451 | 2.76% | 5609 |
| chr10 | 4576410 | 3.42% | 6705 |
| chr11 | 4460847 | 3.30% | 6579 |
| chr12 | 4415202 | 3.31% | 6491 |
| chr13 | 2865535 | 2.51% | 4020 |
| chr14 | 2840931 | 2.65% | 4248 |
| chr15 | 2386730 | 2.34% | 3681 |
| chr16 | 2296017 | 2.54% | 3606 |
| chr17 | 2849520 | 3.42% | 4479 |
| chr18 | 2601203 | 3.24% | 3683 |
| chr19 | 2305183 | 3.93% | 3617 |
| chr20 | 1972759 | 3.06% | 3125 |
| chr21 | 1131943 | 2.42% | 1670 |
| chr22 | 1270844 | 2.50% | 2014 |
| chrX | 3151409 | 2.02% | 4092 |
| chrY | 1116 | <0.01% | 5 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 136067 | 150 | 4004 | 688.37 | 592 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF214HLR.bed.gz | 5.05 MB | f9045c7401ba057f86709b67c0b3e9c3 |
| ENCFF214HLR.tabix.bed.gz | 1.49 MB | e4344accdd32e48d232863c96253edcd |
| ENCFF214HLR.tabix.bed.gz.tbi | 560.1 KB | 9141cac60e0a9e616c60b152819dc75e |
| genomic_resource.yaml | 3.32 KB | 1f5483060b257034b25ec523ad24fc37 |
| statistics/ |