Resource
| Id | DNase-seq/ENCSR690CVL |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR690CVL [biosample_summary="Homo sapiens with Alzheimer''s disease; posterior cingulate gyrus tissue female adult (90 or above years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (90 or above 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 {ENCFF002OZQ|/files/ENCFF002OZQ/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.37. 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_ENCSR690CVL | float |
DNase-seq_ENCSR690CVL |
DNase-seq ENCSR690CVL [biosample_summary="Homo sapiens with Alzheimer''s disease; posterior cingulate gyrus tissue female adult (90 or above years)"]
|
 |
[0.0303, 85.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 82720310 | 2.57% | 438409 |
| chr1 | 7800412 | 3.13% | 40995 |
| chr2 | 6778652 | 2.80% | 35803 |
| chr3 | 3907340 | 1.97% | 21055 |
| chr4 | 2312492 | 1.22% | 12757 |
| chr5 | 3745808 | 2.06% | 20205 |
| chr6 | 3322794 | 1.95% | 18103 |
| chr7 | 4461783 | 2.80% | 23831 |
| chr8 | 3460974 | 2.38% | 18424 |
| chr9 | 3485690 | 2.52% | 18590 |
| chr10 | 4888465 | 3.65% | 25840 |
| chr11 | 4684043 | 3.47% | 24305 |
| chr12 | 3878175 | 2.91% | 20792 |
| chr13 | 1484742 | 1.30% | 8204 |
| chr14 | 2885986 | 2.70% | 14957 |
| chr15 | 3072250 | 3.01% | 16294 |
| chr16 | 3878252 | 4.29% | 20345 |
| chr17 | 4911944 | 5.90% | 25544 |
| chr18 | 1509583 | 1.88% | 8244 |
| chr19 | 2762268 | 4.71% | 14398 |
| chr20 | 3395575 | 5.27% | 17816 |
| chr21 | 1342576 | 2.87% | 7017 |
| chr22 | 3059465 | 6.02% | 15528 |
| chrX | 1683506 | 1.08% | 9301 |
| chrY | 7535 | 0.01% | 61 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 438409 | 1 | 1060 | 188.68 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF030QSS.bed.gz | 4.16 MB | 811eff125172217574f318cb8c0a2c1f |
| ENCFF030QSS.tabix.bed.gz | 3.88 MB | 4ec1500283a4310713f4fab52ed7b7f8 |
| ENCFF030QSS.tabix.bed.gz.tbi | 466.55 KB | 175b70c7951e117c8d445c25167e64fb |
| genomic_resource.yaml | 2.25 KB | 897faa3f83a62219d3768e2bcf76a39d |
| statistics/ |