Resource
| Id | DNase-seq/ENCSR483HUW |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR483HUW [biosample_summary="Homo sapiens with Alzheimer''s disease; head of caudate nucleus 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 {ENCFF589HKG|/files/ENCFF589HKG/} 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_ENCSR483HUW | float |
DNase-seq_ENCSR483HUW |
DNase-seq ENCSR483HUW [biosample_summary="Homo sapiens with Alzheimer''s disease; head of caudate nucleus tissue female adult (90 or above years)"]
|
 |
[0.0749, 15.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 11332978 | 0.35% | 60763 |
| chr1 | 1107032 | 0.44% | 5879 |
| chr2 | 804256 | 0.33% | 4375 |
| chr3 | 650441 | 0.33% | 3500 |
| chr4 | 465722 | 0.24% | 2470 |
| chr5 | 555582 | 0.31% | 3041 |
| chr6 | 610944 | 0.36% | 3284 |
| chr7 | 566065 | 0.36% | 3060 |
| chr8 | 475903 | 0.33% | 2593 |
| chr9 | 490871 | 0.35% | 2643 |
| chr10 | 529928 | 0.40% | 2861 |
| chr11 | 627981 | 0.46% | 3364 |
| chr12 | 559174 | 0.42% | 2953 |
| chr13 | 246032 | 0.22% | 1363 |
| chr14 | 378257 | 0.35% | 2015 |
| chr15 | 372459 | 0.37% | 2003 |
| chr16 | 443104 | 0.49% | 2391 |
| chr17 | 600539 | 0.72% | 3161 |
| chr18 | 213436 | 0.27% | 1179 |
| chr19 | 642309 | 1.10% | 3245 |
| chr20 | 323365 | 0.50% | 1776 |
| chr21 | 123257 | 0.26% | 657 |
| chr22 | 257807 | 0.51% | 1399 |
| chrX | 288046 | 0.18% | 1547 |
| chrY | 468 | <0.01% | 4 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 60763 | 2 | 874 | 186.51 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF046BNJ.bed.gz | 672.34 KB | 09b13fb1675fd52d4af1a7b0e73fb2ed |
| ENCFF046BNJ.tabix.bed.gz | 611.17 KB | 3328ae8fac5eae6c528deed426875953 |
| ENCFF046BNJ.tabix.bed.gz.tbi | 290.57 KB | 501b60820f485a24bff065d539a3cd61 |
| genomic_resource.yaml | 2.25 KB | b7f66d1887e99903c053a792f98610d5 |
| statistics/ |