Resource
| Id | DNase-seq/ENCSR839GHA |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR839GHA [biosample_summary="Homo sapiens with Alzheimer''s disease; head of caudate nucleus 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 {ENCFF038WEZ|/files/ENCFF038WEZ/} processed by DNase-seq ENCODE4 v3.0.0 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_ENCSR839GHA | float |
DNase-seq_ENCSR839GHA |
DNase-seq ENCSR839GHA [biosample_summary="Homo sapiens with Alzheimer''s disease; head of caudate nucleus tissue female adult (89 years)"]
|
 |
[0.0607, 21.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 13942540 | 0.43% | 75782 |
| chr1 | 1320269 | 0.53% | 7126 |
| chr2 | 1079201 | 0.45% | 5968 |
| chr3 | 794181 | 0.40% | 4315 |
| chr4 | 549057 | 0.29% | 3013 |
| chr5 | 685634 | 0.38% | 3786 |
| chr6 | 706819 | 0.41% | 3855 |
| chr7 | 677067 | 0.42% | 3736 |
| chr8 | 594840 | 0.41% | 3250 |
| chr9 | 639965 | 0.46% | 3475 |
| chr10 | 653443 | 0.49% | 3575 |
| chr11 | 811256 | 0.60% | 4386 |
| chr12 | 662802 | 0.50% | 3553 |
| chr13 | 305529 | 0.27% | 1697 |
| chr14 | 459524 | 0.43% | 2490 |
| chr15 | 492571 | 0.48% | 2653 |
| chr16 | 555307 | 0.61% | 2999 |
| chr17 | 726497 | 0.87% | 3918 |
| chr18 | 276872 | 0.34% | 1550 |
| chr19 | 704484 | 1.20% | 3587 |
| chr20 | 400757 | 0.62% | 2226 |
| chr21 | 155117 | 0.33% | 876 |
| chr22 | 368099 | 0.72% | 1994 |
| chrX | 322630 | 0.21% | 1749 |
| chrY | 619 | <0.01% | 5 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 75782 | 1 | 920 | 183.98 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF558YOL.bed.gz | 835.31 KB | 75dfc4b4703effe21312ad9667bb26a7 |
| ENCFF558YOL.tabix.bed.gz | 756.38 KB | fcad96d6f62f89fbdeb2cdfa76522d12 |
| ENCFF558YOL.tabix.bed.gz.tbi | 330.55 KB | 988e680b21a423ffd43b7261fbd87ba9 |
| genomic_resource.yaml | 2.21 KB | 0b4a2265bc1fab80d950228db26da290 |
| statistics/ |