Resource
| Id | DNase-seq/ENCSR060UPU |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR060UPU [biosample_summary="Homo sapiens with Alzheimer''s disease; posterior cingulate gyrus tissue female adult (89 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (89 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 {ENCFF261WPP|/files/ENCFF261WPP/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.37. 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_ENCSR060UPU | float |
DNase-seq_ENCSR060UPU |
DNase-seq ENCSR060UPU [biosample_summary="Homo sapiens with Alzheimer''s disease; posterior cingulate gyrus tissue female adult (89 years)"]
|
 |
[0.0757, 16.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 13562125 | 0.42% | 73101 |
| chr1 | 1216954 | 0.49% | 6586 |
| chr2 | 1164267 | 0.48% | 6259 |
| chr3 | 752345 | 0.38% | 4078 |
| chr4 | 516518 | 0.27% | 2787 |
| chr5 | 677222 | 0.37% | 3663 |
| chr6 | 638529 | 0.37% | 3441 |
| chr7 | 666159 | 0.42% | 3617 |
| chr8 | 633595 | 0.44% | 3428 |
| chr9 | 620540 | 0.45% | 3343 |
| chr10 | 689614 | 0.52% | 3697 |
| chr11 | 765622 | 0.57% | 4126 |
| chr12 | 612256 | 0.46% | 3258 |
| chr13 | 268802 | 0.24% | 1482 |
| chr14 | 443865 | 0.41% | 2441 |
| chr15 | 477353 | 0.47% | 2590 |
| chr16 | 469719 | 0.52% | 2564 |
| chr17 | 715853 | 0.86% | 3834 |
| chr18 | 266315 | 0.33% | 1449 |
| chr19 | 669199 | 1.14% | 3443 |
| chr20 | 392059 | 0.61% | 2166 |
| chr21 | 170571 | 0.37% | 922 |
| chr22 | 456973 | 0.90% | 2437 |
| chrX | 277152 | 0.18% | 1484 |
| chrY | 643 | <0.01% | 6 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 73101 | 1 | 940 | 185.53 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF662LUB.bed.gz | 792.19 KB | 2412f9cb6f33cac4754baec9b36833bb |
| ENCFF662LUB.tabix.bed.gz | 721.3 KB | c693e4aaf4f7d6a1d9b7551319de9eee |
| ENCFF662LUB.tabix.bed.gz.tbi | 284.5 KB | a8088e8801451538d38e84584ed02cbf |
| genomic_resource.yaml | 2.21 KB | 742599c9fd5ad5e8f4b9b13c0e425ac3 |
| statistics/ |