Resource
| Id | DNase-seq/ENCSR340XQX |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR340XQX [biosample_summary="Homo sapiens with Alzheimer''s disease; dorsolateral prefrontal cortex 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 {ENCFF669HSH|/files/ENCFF669HSH/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.37. 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_ENCSR340XQX | float |
DNase-seq_ENCSR340XQX |
DNase-seq ENCSR340XQX [biosample_summary="Homo sapiens with Alzheimer''s disease; dorsolateral prefrontal cortex tissue female adult (90 or above years)"]
|
 |
[0.0762, 19.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 12707568 | 0.39% | 68700 |
| chr1 | 1212536 | 0.49% | 6604 |
| chr2 | 1004242 | 0.41% | 5413 |
| chr3 | 698802 | 0.35% | 3785 |
| chr4 | 494433 | 0.26% | 2632 |
| chr5 | 611539 | 0.34% | 3387 |
| chr6 | 599396 | 0.35% | 3269 |
| chr7 | 623512 | 0.39% | 3405 |
| chr8 | 601819 | 0.41% | 3227 |
| chr9 | 579748 | 0.42% | 3098 |
| chr10 | 659022 | 0.49% | 3579 |
| chr11 | 724222 | 0.54% | 3925 |
| chr12 | 577795 | 0.43% | 3100 |
| chr13 | 264223 | 0.23% | 1450 |
| chr14 | 435752 | 0.41% | 2355 |
| chr15 | 429887 | 0.42% | 2328 |
| chr16 | 462858 | 0.51% | 2517 |
| chr17 | 646903 | 0.78% | 3489 |
| chr18 | 263201 | 0.33% | 1430 |
| chr19 | 611997 | 1.04% | 3156 |
| chr20 | 388685 | 0.60% | 2131 |
| chr21 | 163088 | 0.35% | 871 |
| chr22 | 377407 | 0.74% | 2043 |
| chrX | 275794 | 0.18% | 1499 |
| chrY | 707 | <0.01% | 7 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 68700 | 1 | 900 | 184.97 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF135AQL.bed.gz | 746.77 KB | c61bb56479b313a18dcc80be4776c5c5 |
| ENCFF135AQL.tabix.bed.gz | 680.95 KB | 6f9fc62246745fd2e4526cbe7668e091 |
| ENCFF135AQL.tabix.bed.gz.tbi | 284.19 KB | 799a29cba241afe2bc776944afe9a0c6 |
| genomic_resource.yaml | 2.27 KB | 479146fc08c4a7f9f93627d320bdcea0 |
| statistics/ |