Resource
| Id | DNase-seq/ENCSR355PNF |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR355PNF [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 {ENCFF885XPI|/files/ENCFF885XPI/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.32. 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_ENCSR355PNF | float |
DNase-seq_ENCSR355PNF |
DNase-seq ENCSR355PNF [biosample_summary="Homo sapiens with Alzheimer''s disease; head of caudate nucleus tissue female adult (90 or above years)"]
|
 |
[0.0703, 53] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 6868384 | 0.21% | 39201 |
| chr1 | 450836 | 0.18% | 2603 |
| chr2 | 547968 | 0.23% | 3156 |
| chr3 | 245047 | 0.12% | 1488 |
| chr4 | 353130 | 0.19% | 2043 |
| chr5 | 368951 | 0.20% | 2184 |
| chr6 | 182161 | 0.11% | 1144 |
| chr7 | 440344 | 0.28% | 2474 |
| chr8 | 332627 | 0.23% | 1850 |
| chr9 | 336792 | 0.24% | 1966 |
| chr10 | 313103 | 0.23% | 1736 |
| chr11 | 456587 | 0.34% | 2541 |
| chr12 | 246636 | 0.19% | 1421 |
| chr13 | 148296 | 0.13% | 905 |
| chr14 | 235978 | 0.22% | 1305 |
| chr15 | 149763 | 0.15% | 900 |
| chr16 | 339955 | 0.38% | 1932 |
| chr17 | 364842 | 0.44% | 2059 |
| chr18 | 87590 | 0.11% | 528 |
| chr19 | 305719 | 0.52% | 1631 |
| chr20 | 250715 | 0.39% | 1335 |
| chr21 | 166509 | 0.36% | 923 |
| chr22 | 340144 | 0.67% | 1851 |
| chrX | 200538 | 0.13% | 1195 |
| chrY | 4153 | 0.01% | 31 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 39201 | 1 | 1360 | 175.21 | 160 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF187DOW.bed.gz | 391.97 KB | d5aaf6b7746e5c014811b0883f4f8d95 |
| ENCFF187DOW.tabix.bed.gz | 359.84 KB | bfff278726f44ed1b60f417a6c9420d4 |
| ENCFF187DOW.tabix.bed.gz.tbi | 135.47 KB | e4c2a26057594b969fddf4f102901dab |
| genomic_resource.yaml | 2.25 KB | 821633e7417294e95e0eee1d6edc40a8 |
| statistics/ |