Resource
| Id | DNase-seq/ENCSR060MJY |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR060MJY [biosample_summary="Homo sapiens with mild cognitive impairment; dorsolateral prefrontal cortex 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 {ENCFF978AHA|/files/ENCFF978AHA/} 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_ENCSR060MJY | float |
DNase-seq_ENCSR060MJY |
DNase-seq ENCSR060MJY [biosample_summary="Homo sapiens with mild cognitive impairment; dorsolateral prefrontal cortex tissue female adult (90 or above years)"]
|
 |
[0.0632, 20.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 17727193 | 0.55% | 93919 |
| chr1 | 1595948 | 0.64% | 8441 |
| chr2 | 1643026 | 0.68% | 8738 |
| chr3 | 886500 | 0.45% | 4713 |
| chr4 | 546889 | 0.29% | 2886 |
| chr5 | 858564 | 0.47% | 4536 |
| chr6 | 695565 | 0.41% | 3740 |
| chr7 | 879076 | 0.55% | 4672 |
| chr8 | 792447 | 0.55% | 4094 |
| chr9 | 831230 | 0.60% | 4490 |
| chr10 | 1117004 | 0.83% | 5884 |
| chr11 | 972147 | 0.72% | 5148 |
| chr12 | 643767 | 0.48% | 3445 |
| chr13 | 372204 | 0.33% | 1936 |
| chr14 | 635223 | 0.59% | 3411 |
| chr15 | 717214 | 0.70% | 3812 |
| chr16 | 650036 | 0.72% | 3476 |
| chr17 | 984976 | 1.18% | 5221 |
| chr18 | 340286 | 0.42% | 1800 |
| chr19 | 730437 | 1.25% | 3781 |
| chr20 | 557047 | 0.86% | 2981 |
| chr21 | 263555 | 0.56% | 1389 |
| chr22 | 648922 | 1.28% | 3366 |
| chrX | 364120 | 0.23% | 1951 |
| chrY | 1010 | <0.01% | 8 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 93919 | 1 | 1160 | 188.75 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF427NRJ.bed.gz | 966.44 KB | 9beddbd74be4fc83fe25744349374867 |
| ENCFF427NRJ.tabix.bed.gz | 890.12 KB | f6daf988ab0c82ae413809d4525a80eb |
| ENCFF427NRJ.tabix.bed.gz.tbi | 258.64 KB | 9d7ab5adcdbbc59bfff2d1ce8877cc06 |
| genomic_resource.yaml | 2.31 KB | 12dfb7743a8fc8b966cbd7b6e32f7495 |
| statistics/ |