Resource
| Id | DNase-seq/ENCSR628GQE |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR628GQE [biosample_summary="Homo sapiens with Alzheimer''s disease; posterior cingulate gyrus tissue female adult (88 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (88 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 {ENCFF221QFW|/files/ENCFF221QFW/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.31. 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_ENCSR628GQE | float |
DNase-seq_ENCSR628GQE |
DNase-seq ENCSR628GQE [biosample_summary="Homo sapiens with Alzheimer''s disease; posterior cingulate gyrus tissue female adult (88 years)"]
|
 |
[0.0482, 10.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 26160292 | 0.81% | 132880 |
| chr1 | 2315738 | 0.93% | 11718 |
| chr2 | 2175567 | 0.90% | 10950 |
| chr3 | 1094683 | 0.55% | 5591 |
| chr4 | 840256 | 0.44% | 4098 |
| chr5 | 1123808 | 0.62% | 5714 |
| chr6 | 827136 | 0.48% | 4276 |
| chr7 | 1500091 | 0.94% | 7535 |
| chr8 | 1070829 | 0.74% | 5343 |
| chr9 | 1201513 | 0.87% | 6106 |
| chr10 | 1630817 | 1.22% | 8279 |
| chr11 | 1567523 | 1.16% | 7922 |
| chr12 | 1013191 | 0.76% | 5232 |
| chr13 | 483237 | 0.42% | 2474 |
| chr14 | 943794 | 0.88% | 4747 |
| chr15 | 909854 | 0.89% | 4746 |
| chr16 | 1156446 | 1.28% | 6096 |
| chr17 | 1693224 | 2.03% | 8632 |
| chr18 | 442542 | 0.55% | 2255 |
| chr19 | 1067275 | 1.82% | 5424 |
| chr20 | 945065 | 1.47% | 4847 |
| chr21 | 457181 | 0.98% | 2300 |
| chr22 | 1222194 | 2.41% | 6066 |
| chrX | 475667 | 0.30% | 2507 |
| chrY | 2661 | <0.01% | 22 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 132880 | 1 | 1080 | 196.87 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF971WVB.bed.gz | 1.26 MB | 1d042a010da3d76ea3e369abde679f1b |
| ENCFF971WVB.tabix.bed.gz | 1.18 MB | a1910b1a7e400240a73965074a3533d6 |
| ENCFF971WVB.tabix.bed.gz.tbi | 228.45 KB | ad1e2a523ebbe84087cae287a5c6ca12 |
| genomic_resource.yaml | 2.21 KB | 8c45ba44920f3d4a94045029370980c5 |
| statistics/ |