Resource
| Id | DNase-seq/ENCSR646JBR |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR646JBR [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 {ENCFF989COB|/files/ENCFF989COB/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.36. 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_ENCSR646JBR | float |
DNase-seq_ENCSR646JBR |
DNase-seq ENCSR646JBR [biosample_summary="Homo sapiens with Alzheimer''s disease; head of caudate nucleus tissue female adult (90 or above years)"]
|
 |
[0.0895, 21] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 8399088 | 0.26% | 46024 |
| chr1 | 845101 | 0.34% | 4646 |
| chr2 | 580848 | 0.24% | 3230 |
| chr3 | 479102 | 0.24% | 2594 |
| chr4 | 328317 | 0.17% | 1776 |
| chr5 | 407138 | 0.22% | 2274 |
| chr6 | 447662 | 0.26% | 2463 |
| chr7 | 400160 | 0.25% | 2240 |
| chr8 | 336265 | 0.23% | 1898 |
| chr9 | 365868 | 0.26% | 1977 |
| chr10 | 389777 | 0.29% | 2148 |
| chr11 | 478601 | 0.35% | 2630 |
| chr12 | 426541 | 0.32% | 2285 |
| chr13 | 172491 | 0.15% | 945 |
| chr14 | 275765 | 0.26% | 1514 |
| chr15 | 265679 | 0.26% | 1488 |
| chr16 | 339330 | 0.38% | 1859 |
| chr17 | 462726 | 0.56% | 2511 |
| chr18 | 146091 | 0.18% | 815 |
| chr19 | 518037 | 0.88% | 2687 |
| chr20 | 225248 | 0.35% | 1279 |
| chr21 | 96956 | 0.21% | 535 |
| chr22 | 194554 | 0.38% | 1067 |
| chrX | 216630 | 0.14% | 1161 |
| chrY | 201 | <0.01% | 2 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 46024 | 3 | 729 | 182.49 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF438WFB.bed.gz | 505.67 KB | 079055bdf280a80aa538867dde129020 |
| ENCFF438WFB.tabix.bed.gz | 456.88 KB | e07017eb5279e1865bb623afe5ac5e64 |
| ENCFF438WFB.tabix.bed.gz.tbi | 236.64 KB | ca8198b6bffe4143896f86420d6adacc |
| genomic_resource.yaml | 2.26 KB | a16af30ed6afefb9e0e8d28e158f84d2 |
| statistics/ |