Resource
| Id | DNase-seq/ENCSR579RVI |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR579RVI [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 {ENCFF391NWO|/files/ENCFF391NWO/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.27. 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_ENCSR579RVI | float |
DNase-seq_ENCSR579RVI |
DNase-seq ENCSR579RVI [biosample_summary="Homo sapiens with Alzheimer''s disease; posterior cingulate gyrus tissue female adult (90 or above years)"]
|
 |
[0.0463, 10] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 18863344 | 0.59% | 100585 |
| chr1 | 1630892 | 0.66% | 8719 |
| chr2 | 1722764 | 0.71% | 9030 |
| chr3 | 895703 | 0.45% | 4824 |
| chr4 | 497236 | 0.26% | 2654 |
| chr5 | 896948 | 0.49% | 4786 |
| chr6 | 781771 | 0.46% | 4240 |
| chr7 | 1011432 | 0.63% | 5447 |
| chr8 | 837265 | 0.58% | 4482 |
| chr9 | 809850 | 0.59% | 4328 |
| chr10 | 1233234 | 0.92% | 6496 |
| chr11 | 1064101 | 0.79% | 5583 |
| chr12 | 741802 | 0.56% | 3994 |
| chr13 | 362778 | 0.32% | 1925 |
| chr14 | 659754 | 0.62% | 3453 |
| chr15 | 798999 | 0.78% | 4326 |
| chr16 | 683430 | 0.76% | 3707 |
| chr17 | 942241 | 1.13% | 5101 |
| chr18 | 423142 | 0.53% | 2279 |
| chr19 | 833774 | 1.42% | 4374 |
| chr20 | 622809 | 0.97% | 3356 |
| chr21 | 307026 | 0.66% | 1634 |
| chr22 | 713334 | 1.40% | 3735 |
| chrX | 392082 | 0.25% | 2104 |
| chrY | 977 | <0.01% | 8 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 100585 | 1 | 900 | 187.54 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF145VKP.bed.gz | 1021.05 KB | b5b9096f8d5559b7f6d2b674487c21d5 |
| ENCFF145VKP.tabix.bed.gz | 940.79 KB | 9e2b98637a9262b86df0cbd1f8a00764 |
| ENCFF145VKP.tabix.bed.gz.tbi | 253.8 KB | 8363fda491edea7be4aed5a63ec0f788 |
| genomic_resource.yaml | 2.25 KB | 49f3d0964e4c1f12c7458e8ba8646610 |
| statistics/ |