Resource
| Id | DNase-seq/ENCSR098ISE |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR098ISE [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 {ENCFF189BYI|/files/ENCFF189BYI/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.39. 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_ENCSR098ISE | float |
DNase-seq_ENCSR098ISE |
DNase-seq ENCSR098ISE [biosample_summary="Homo sapiens with Alzheimer''s disease; posterior cingulate gyrus tissue female adult (90 or above years)"]
|
 |
[0.0317, 19.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 50510365 | 1.57% | 245677 |
| chr1 | 4643771 | 1.87% | 22418 |
| chr2 | 4052888 | 1.67% | 19612 |
| chr3 | 2356431 | 1.19% | 11596 |
| chr4 | 1449312 | 0.76% | 7004 |
| chr5 | 2045189 | 1.13% | 10074 |
| chr6 | 1775428 | 1.04% | 8746 |
| chr7 | 2717617 | 1.71% | 13214 |
| chr8 | 1929079 | 1.33% | 9349 |
| chr9 | 2265550 | 1.64% | 10964 |
| chr10 | 3057833 | 2.29% | 14864 |
| chr11 | 3121859 | 2.31% | 14727 |
| chr12 | 2105026 | 1.58% | 10483 |
| chr13 | 839543 | 0.73% | 4156 |
| chr14 | 1659870 | 1.55% | 8067 |
| chr15 | 1875778 | 1.84% | 9205 |
| chr16 | 2370248 | 2.62% | 11711 |
| chr17 | 3302282 | 3.97% | 16102 |
| chr18 | 870490 | 1.08% | 4290 |
| chr19 | 1901917 | 3.24% | 9291 |
| chr20 | 1990355 | 3.09% | 9739 |
| chr21 | 913641 | 1.96% | 4304 |
| chr22 | 2174123 | 4.28% | 10253 |
| chrX | 1088559 | 0.70% | 5479 |
| chrY | 3576 | 0.01% | 29 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 245677 | 1 | 1340 | 205.6 | 195 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF454AVH.bed.gz | 2.35 MB | c56bf12a3e2d53b8bff8d28f15edc656 |
| ENCFF454AVH.tabix.bed.gz | 2.21 MB | 5fd8234a2abb62b877da5344fbf33dc2 |
| ENCFF454AVH.tabix.bed.gz.tbi | 327.79 KB | 4cd38e27e9ef2870d0905799e932cf23 |
| genomic_resource.yaml | 2.25 KB | dea23106f8d71412f4f16e34c4935708 |
| statistics/ |