Resource
| Id | DNase-seq/ENCSR577QZP |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR577QZP [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 {ENCFF032RAK|/files/ENCFF032RAK/} 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_ENCSR577QZP | float |
DNase-seq_ENCSR577QZP |
DNase-seq ENCSR577QZP [biosample_summary="Homo sapiens with Alzheimer''s disease; posterior cingulate gyrus tissue female adult (90 or above years)"]
|
 |
[0.0781, 11.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 12390919 | 0.39% | 67067 |
| chr1 | 1156302 | 0.46% | 6163 |
| chr2 | 1077296 | 0.44% | 5866 |
| chr3 | 592030 | 0.30% | 3211 |
| chr4 | 318394 | 0.17% | 1742 |
| chr5 | 583716 | 0.32% | 3212 |
| chr6 | 545175 | 0.32% | 3004 |
| chr7 | 610107 | 0.38% | 3298 |
| chr8 | 502273 | 0.35% | 2757 |
| chr9 | 577625 | 0.42% | 3119 |
| chr10 | 764868 | 0.57% | 4224 |
| chr11 | 711673 | 0.53% | 3885 |
| chr12 | 507013 | 0.38% | 2697 |
| chr13 | 220188 | 0.19% | 1205 |
| chr14 | 445328 | 0.42% | 2363 |
| chr15 | 479826 | 0.47% | 2661 |
| chr16 | 462582 | 0.51% | 2499 |
| chr17 | 667042 | 0.80% | 3553 |
| chr18 | 225437 | 0.28% | 1223 |
| chr19 | 605686 | 1.03% | 3080 |
| chr20 | 449023 | 0.70% | 2467 |
| chr21 | 185680 | 0.40% | 1035 |
| chr22 | 487909 | 0.96% | 2643 |
| chrX | 215294 | 0.14% | 1156 |
| chrY | 452 | <0.01% | 4 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 67067 | 1 | 940 | 184.75 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF189OSV.bed.gz | 692.47 KB | 6851a373fa323d90435eda576f9dc2e5 |
| ENCFF189OSV.tabix.bed.gz | 628.78 KB | e2509f1f2e82a0d5e95722ba65213d71 |
| ENCFF189OSV.tabix.bed.gz.tbi | 219.38 KB | 734119abc55b5447ef1ad2b0011a8e66 |
| genomic_resource.yaml | 2.25 KB | 7b4417dc516cfaa2820fc30a18ff236b |
| statistics/ |