Resource
| Id | DNase-seq/ENCSR101HFF |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR101HFF [biosample_summary="Homo sapiens with Alzheimer''s disease; head of caudate nucleus tissue female adult (81 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (81 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 {ENCFF875ESV|/files/ENCFF875ESV/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.32. 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_ENCSR101HFF | float |
DNase-seq_ENCSR101HFF |
DNase-seq ENCSR101HFF [biosample_summary="Homo sapiens with Alzheimer''s disease; head of caudate nucleus tissue female adult (81 years)"]
|
 |
[0.0409, 23.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 14579811 | 0.45% | 76889 |
| chr1 | 1440816 | 0.58% | 7565 |
| chr2 | 1088729 | 0.45% | 5818 |
| chr3 | 830696 | 0.42% | 4409 |
| chr4 | 559672 | 0.29% | 2914 |
| chr5 | 708037 | 0.39% | 3779 |
| chr6 | 784756 | 0.46% | 4083 |
| chr7 | 708827 | 0.44% | 3757 |
| chr8 | 588817 | 0.41% | 3140 |
| chr9 | 671203 | 0.48% | 3529 |
| chr10 | 715922 | 0.54% | 3811 |
| chr11 | 792918 | 0.59% | 4199 |
| chr12 | 676101 | 0.51% | 3520 |
| chr13 | 310898 | 0.27% | 1634 |
| chr14 | 476917 | 0.45% | 2526 |
| chr15 | 507984 | 0.50% | 2709 |
| chr16 | 569835 | 0.63% | 2993 |
| chr17 | 771493 | 0.93% | 4043 |
| chr18 | 285432 | 0.36% | 1542 |
| chr19 | 758927 | 1.29% | 3892 |
| chr20 | 424633 | 0.66% | 2258 |
| chr21 | 172974 | 0.37% | 927 |
| chr22 | 346067 | 0.68% | 1824 |
| chrX | 387792 | 0.25% | 2014 |
| chrY | 365 | <0.01% | 3 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 76889 | 1 | 1020 | 189.62 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF454EUR.bed.gz | 850.36 KB | 1a07cf2620b373eec908c93e15849069 |
| ENCFF454EUR.tabix.bed.gz | 780.85 KB | 937dfd3163758f5b1623a701a1fc1795 |
| ENCFF454EUR.tabix.bed.gz.tbi | 304.46 KB | 4050390c7c649c6924531b6c41d02e40 |
| genomic_resource.yaml | 2.21 KB | 0a212d863ef0b8bc89a2395850d9b6d2 |
| statistics/ |