Resource
| Id | DNase-seq/ENCSR516RTV |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR516RTV [biosample_summary="Homo sapiens with Cognitive impairment; 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 Cognitive impairment 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 {ENCFF196CBF|/files/ENCFF196CBF/} 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_ENCSR516RTV | float |
DNase-seq_ENCSR516RTV |
DNase-seq ENCSR516RTV [biosample_summary="Homo sapiens with Cognitive impairment; head of caudate nucleus tissue female adult (90 or above years)"]
|
 |
[0.0654, 20] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 16323322 | 0.51% | 87074 |
| chr1 | 1452564 | 0.58% | 7755 |
| chr2 | 1377842 | 0.57% | 7373 |
| chr3 | 794198 | 0.40% | 4207 |
| chr4 | 546468 | 0.29% | 2868 |
| chr5 | 751865 | 0.41% | 4053 |
| chr6 | 750640 | 0.44% | 4005 |
| chr7 | 797440 | 0.50% | 4298 |
| chr8 | 690727 | 0.48% | 3716 |
| chr9 | 747824 | 0.54% | 4002 |
| chr10 | 920506 | 0.69% | 4994 |
| chr11 | 896617 | 0.66% | 4745 |
| chr12 | 719129 | 0.54% | 3809 |
| chr13 | 337224 | 0.29% | 1784 |
| chr14 | 565687 | 0.53% | 2985 |
| chr15 | 669893 | 0.66% | 3630 |
| chr16 | 632697 | 0.70% | 3415 |
| chr17 | 882456 | 1.06% | 4669 |
| chr18 | 286278 | 0.36% | 1587 |
| chr19 | 799201 | 1.36% | 4079 |
| chr20 | 529459 | 0.82% | 2883 |
| chr21 | 230086 | 0.49% | 1232 |
| chr22 | 582809 | 1.15% | 3074 |
| chrX | 360340 | 0.23% | 1900 |
| chrY | 1372 | <0.01% | 11 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 87074 | 1 | 1020 | 187.46 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF221IWR.bed.gz | 925.43 KB | b9bf773947c30606ae09166a21a84f20 |
| ENCFF221IWR.tabix.bed.gz | 852.71 KB | a86fc613c9b3f699260c74b4d6ae27ab |
| ENCFF221IWR.tabix.bed.gz.tbi | 286.34 KB | 681fe2c1b715924cce1a241691d56a61 |
| genomic_resource.yaml | 2.25 KB | 8b8ba96f74db9f058797ec92a186e8fe |
| statistics/ |