Resource
| Id | DNase-seq/ENCSR805RJA |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR805RJA [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 {ENCFF120BYB|/files/ENCFF120BYB/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.30. 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_ENCSR805RJA | float |
DNase-seq_ENCSR805RJA |
DNase-seq ENCSR805RJA [biosample_summary="Homo sapiens with Alzheimer''s disease; dorsolateral prefrontal cortex tissue female adult (90 or above years)"]
|
 |
[0.0655, 17.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 11288367 | 0.35% | 59463 |
| chr1 | 1097221 | 0.44% | 5788 |
| chr2 | 844388 | 0.35% | 4501 |
| chr3 | 658784 | 0.33% | 3466 |
| chr4 | 443365 | 0.23% | 2365 |
| chr5 | 574415 | 0.32% | 3073 |
| chr6 | 596285 | 0.35% | 3140 |
| chr7 | 563542 | 0.35% | 2991 |
| chr8 | 468849 | 0.32% | 2535 |
| chr9 | 508546 | 0.37% | 2639 |
| chr10 | 556644 | 0.42% | 2925 |
| chr11 | 620566 | 0.46% | 3298 |
| chr12 | 531168 | 0.40% | 2763 |
| chr13 | 238109 | 0.21% | 1241 |
| chr14 | 360747 | 0.34% | 1912 |
| chr15 | 396058 | 0.39% | 2081 |
| chr16 | 434805 | 0.48% | 2267 |
| chr17 | 604723 | 0.73% | 3153 |
| chr18 | 196524 | 0.24% | 1057 |
| chr19 | 595445 | 1.02% | 2980 |
| chr20 | 329232 | 0.51% | 1789 |
| chr21 | 117953 | 0.25% | 629 |
| chr22 | 266223 | 0.52% | 1386 |
| chrX | 284513 | 0.18% | 1482 |
| chrY | 262 | <0.01% | 2 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 59463 | 2 | 860 | 189.84 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF712KXT.bed.gz | 658.2 KB | 5fee5fa1981fba8d89ca0a01587c9913 |
| ENCFF712KXT.tabix.bed.gz | 599.33 KB | d46c4a5b7fa7ff1e621ab85f650dc146 |
| ENCFF712KXT.tabix.bed.gz.tbi | 283.23 KB | fecb4b93405aec4e95620e4921bd6800 |
| genomic_resource.yaml | 2.27 KB | 34c4272750d2f0870a227c3f922c5a5a |
| statistics/ |