Resource
| Id | DNase-seq/ENCSR057GPV |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR057GPV [biosample_summary="Homo sapiens with mild 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 mild 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 {ENCFF733XEA|/files/ENCFF733XEA/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.28. 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_ENCSR057GPV | float |
DNase-seq_ENCSR057GPV |
DNase-seq ENCSR057GPV [biosample_summary="Homo sapiens with mild cognitive impairment; head of caudate nucleus tissue female adult (90 or above years)"]
|
 |
[0.0715, 12.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 16621703 | 0.52% | 90073 |
| chr1 | 1576151 | 0.63% | 8468 |
| chr2 | 1251979 | 0.52% | 6862 |
| chr3 | 1026348 | 0.52% | 5596 |
| chr4 | 731155 | 0.38% | 4044 |
| chr5 | 862513 | 0.48% | 4760 |
| chr6 | 932053 | 0.55% | 5067 |
| chr7 | 841668 | 0.53% | 4617 |
| chr8 | 729372 | 0.50% | 3999 |
| chr9 | 715603 | 0.52% | 3848 |
| chr10 | 770593 | 0.58% | 4157 |
| chr11 | 916600 | 0.68% | 4956 |
| chr12 | 834328 | 0.63% | 4472 |
| chr13 | 398357 | 0.35% | 2196 |
| chr14 | 548830 | 0.51% | 2990 |
| chr15 | 550042 | 0.54% | 2985 |
| chr16 | 629482 | 0.70% | 3340 |
| chr17 | 795187 | 0.96% | 4219 |
| chr18 | 340656 | 0.42% | 1905 |
| chr19 | 763705 | 1.30% | 3846 |
| chr20 | 464934 | 0.72% | 2563 |
| chr21 | 181066 | 0.39% | 1003 |
| chr22 | 346315 | 0.68% | 1872 |
| chrX | 414424 | 0.27% | 2305 |
| chrY | 342 | <0.01% | 3 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 90073 | 1 | 820 | 184.54 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF385SUY.bed.gz | 983.12 KB | 95746e6b5873a1faddac3334796e4597 |
| ENCFF385SUY.tabix.bed.gz | 891.31 KB | f38a1af74e1281756154fe8828472651 |
| ENCFF385SUY.tabix.bed.gz.tbi | 423.84 KB | 2e85be053b4c9f5b6f83258a8ad1cb38 |
| genomic_resource.yaml | 2.28 KB | 3129dea27a312db35c5493ee29a5aff6 |
| statistics/ |