Resource
| Id | DNase-seq/ENCSR856XGY |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR856XGY [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 {ENCFF241GPY|/files/ENCFF241GPY/} 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_ENCSR856XGY | float |
DNase-seq_ENCSR856XGY |
DNase-seq ENCSR856XGY [biosample_summary="Homo sapiens with Alzheimer''s disease; head of caudate nucleus tissue female adult (89 years)"]
|
 |
[0.0543, 23.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 17158916 | 0.53% | 91838 |
| chr1 | 1621487 | 0.65% | 8580 |
| chr2 | 1352288 | 0.56% | 7291 |
| chr3 | 933927 | 0.47% | 4998 |
| chr4 | 644046 | 0.34% | 3380 |
| chr5 | 844874 | 0.47% | 4496 |
| chr6 | 853847 | 0.50% | 4550 |
| chr7 | 850466 | 0.53% | 4553 |
| chr8 | 716127 | 0.49% | 3889 |
| chr9 | 740834 | 0.54% | 4016 |
| chr10 | 901216 | 0.67% | 4831 |
| chr11 | 961756 | 0.71% | 5168 |
| chr12 | 771273 | 0.58% | 4065 |
| chr13 | 340854 | 0.30% | 1818 |
| chr14 | 589687 | 0.55% | 3173 |
| chr15 | 600747 | 0.59% | 3279 |
| chr16 | 661149 | 0.73% | 3596 |
| chr17 | 896489 | 1.08% | 4781 |
| chr18 | 329456 | 0.41% | 1786 |
| chr19 | 885532 | 1.51% | 4621 |
| chr20 | 544620 | 0.85% | 2964 |
| chr21 | 231179 | 0.49% | 1229 |
| chr22 | 490829 | 0.97% | 2632 |
| chrX | 396004 | 0.25% | 2140 |
| chrY | 229 | <0.01% | 2 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 91838 | 1 | 940 | 186.84 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF532EQE.bed.gz | 1002.61 KB | 7940fa710e9bd013cd968b061eed3106 |
| ENCFF532EQE.tabix.bed.gz | 916.82 KB | 785e94f6d3bb09df0b6307dd31b5c606 |
| ENCFF532EQE.tabix.bed.gz.tbi | 327.16 KB | 6f5432864d15577be1bac76613860c9b |
| genomic_resource.yaml | 2.21 KB | ca94f155511a01cfcecfdddcdcf0e15c |
| statistics/ |