Resource
| Id | DNase-seq/ENCSR650TZF |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR650TZF [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 {ENCFF072OFG|/files/ENCFF072OFG/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 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_ENCSR650TZF | float |
DNase-seq_ENCSR650TZF |
DNase-seq ENCSR650TZF [biosample_summary="Homo sapiens with Alzheimer''s disease; head of caudate nucleus tissue female adult (90 or above years)"]
|
 |
[0.11, 16.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 10047005 | 0.31% | 56943 |
| chr1 | 996995 | 0.40% | 5633 |
| chr2 | 720640 | 0.30% | 4156 |
| chr3 | 574015 | 0.29% | 3260 |
| chr4 | 393690 | 0.21% | 2236 |
| chr5 | 486126 | 0.27% | 2779 |
| chr6 | 540585 | 0.32% | 3070 |
| chr7 | 484644 | 0.30% | 2792 |
| chr8 | 419747 | 0.29% | 2411 |
| chr9 | 436473 | 0.32% | 2460 |
| chr10 | 450899 | 0.34% | 2561 |
| chr11 | 562709 | 0.42% | 3207 |
| chr12 | 512903 | 0.38% | 2890 |
| chr13 | 210997 | 0.18% | 1239 |
| chr14 | 321292 | 0.30% | 1824 |
| chr15 | 328201 | 0.32% | 1874 |
| chr16 | 406766 | 0.45% | 2281 |
| chr17 | 555660 | 0.67% | 3069 |
| chr18 | 179226 | 0.22% | 1058 |
| chr19 | 597025 | 1.02% | 3169 |
| chr20 | 288499 | 0.45% | 1659 |
| chr21 | 104896 | 0.22% | 596 |
| chr22 | 235102 | 0.46% | 1357 |
| chrX | 239397 | 0.15% | 1357 |
| chrY | 518 | <0.01% | 5 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 56943 | 5 | 920 | 176.44 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF653GPF.bed.gz | 629.25 KB | 6f01aab52324f09c35b27021ce7c76e1 |
| ENCFF653GPF.tabix.bed.gz | 569.28 KB | 2540d2f65f9dd23889d456552cc67f66 |
| ENCFF653GPF.tabix.bed.gz.tbi | 281.88 KB | 68caa5cabfd19925e53a99b632f051f0 |
| genomic_resource.yaml | 2.26 KB | 5b5b0eff96c0b63d36d850a1101d31dc |
| statistics/ |