Resource
| Id | DNase-seq/ENCSR599JZA |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR599JZA [biosample_summary="Homo sapiens with Alzheimer''s disease; posterior cingulate gyrus tissue female adult (86 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (86 years) with Alzheimer's disease output_type: peaks audit_warning: Signal Portion of Tags (SPOT) is a measure of enrichment, analogous to the commonly used fraction of reads in peaks metric. ENCODE processed alignment files {ENCFF928JSC|/files/ENCFF928JSC/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.33. According to ENCODE standards, SPOT1 score of 0.4 or higher is considered a product of high quality data. Any sample with a SPOT1 score <0.3 should be targeted for replacement with a higher quality sample, and a SPOT1 score of 0.25 is considered minimally acceptable SPOT1 score of 0.25 is considered minimally acceptable for rare and hard to find primary tissues. (See {ENCODE DNase-seq data standards|/data-standards/dnase-seq-encode4/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR599JZA | float |
DNase-seq_ENCSR599JZA |
DNase-seq ENCSR599JZA [biosample_summary="Homo sapiens with Alzheimer''s disease; posterior cingulate gyrus tissue female adult (86 years)"]
|
 |
[0.0534, 12.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 12838301 | 0.40% | 67545 |
| chr1 | 1210229 | 0.49% | 6352 |
| chr2 | 1031475 | 0.43% | 5467 |
| chr3 | 655788 | 0.33% | 3464 |
| chr4 | 504676 | 0.27% | 2606 |
| chr5 | 603374 | 0.33% | 3185 |
| chr6 | 539643 | 0.32% | 2884 |
| chr7 | 635876 | 0.40% | 3392 |
| chr8 | 576787 | 0.40% | 3036 |
| chr9 | 621888 | 0.45% | 3243 |
| chr10 | 753073 | 0.56% | 3976 |
| chr11 | 711454 | 0.53% | 3820 |
| chr12 | 527217 | 0.40% | 2767 |
| chr13 | 273970 | 0.24% | 1397 |
| chr14 | 448868 | 0.42% | 2357 |
| chr15 | 435635 | 0.43% | 2348 |
| chr16 | 454877 | 0.50% | 2419 |
| chr17 | 645630 | 0.78% | 3396 |
| chr18 | 274673 | 0.34% | 1416 |
| chr19 | 573428 | 0.98% | 2925 |
| chr20 | 368781 | 0.57% | 1963 |
| chr21 | 234681 | 0.50% | 1210 |
| chr22 | 459528 | 0.90% | 2401 |
| chrX | 295988 | 0.19% | 1515 |
| chrY | 762 | <0.01% | 6 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 67545 | 2 | 1060 | 190.07 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF235PNM.bed.gz | 715.49 KB | 6b5d6e821dbe9be619f0877082d2b531 |
| ENCFF235PNM.tabix.bed.gz | 656.39 KB | be856b9afb61bee70fbf810e28b5ccd8 |
| ENCFF235PNM.tabix.bed.gz.tbi | 232.36 KB | 202897eeb2de487deb50b844ba67a2ec |
| genomic_resource.yaml | 2.21 KB | f93d3e7ab93c84920ceb2f2d98b630b3 |
| statistics/ |