Resource
| Id | DNase-seq/ENCSR086PIL |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR086PIL [biosample_summary="Homo sapiens with Alzheimer''s disease; posterior cingulate gyrus tissue female adult (90 or above years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (90 or above 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 {ENCFF259SZT|/files/ENCFF259SZT/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.27. 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_ENCSR086PIL | float |
DNase-seq_ENCSR086PIL |
DNase-seq ENCSR086PIL [biosample_summary="Homo sapiens with Alzheimer''s disease; posterior cingulate gyrus tissue female adult (90 or above years)"]
|
 |
[0.0853, 10.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 9167548 | 0.28% | 49157 |
| chr1 | 849517 | 0.34% | 4508 |
| chr2 | 717153 | 0.30% | 3919 |
| chr3 | 510270 | 0.26% | 2697 |
| chr4 | 306550 | 0.16% | 1629 |
| chr5 | 425922 | 0.23% | 2285 |
| chr6 | 440342 | 0.26% | 2336 |
| chr7 | 446194 | 0.28% | 2430 |
| chr8 | 365479 | 0.25% | 2007 |
| chr9 | 448583 | 0.32% | 2404 |
| chr10 | 477074 | 0.36% | 2604 |
| chr11 | 528855 | 0.39% | 2859 |
| chr12 | 397764 | 0.30% | 2105 |
| chr13 | 162955 | 0.14% | 868 |
| chr14 | 308410 | 0.29% | 1662 |
| chr15 | 314582 | 0.31% | 1709 |
| chr16 | 346298 | 0.38% | 1858 |
| chr17 | 487798 | 0.59% | 2570 |
| chr18 | 172964 | 0.22% | 952 |
| chr19 | 533640 | 0.91% | 2705 |
| chr20 | 303271 | 0.47% | 1684 |
| chr21 | 121330 | 0.26% | 668 |
| chr22 | 305260 | 0.60% | 1659 |
| chrX | 196867 | 0.13% | 1034 |
| chrY | 470 | <0.01% | 5 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 49157 | 2 | 1080 | 186.5 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF615PSI.bed.gz | 530.6 KB | 905bdc84957951d93e1c082d8415ec42 |
| ENCFF615PSI.tabix.bed.gz | 483.21 KB | aa0c88f57c19380505de802320fb3224 |
| ENCFF615PSI.tabix.bed.gz.tbi | 223.58 KB | 7dc8b56e5cc916fd9d4adba298eeff6b |
| genomic_resource.yaml | 2.25 KB | 8d2be2aa74a77c406ea9a92d180e4437 |
| statistics/ |