Resource
| Id | DNase-seq/ENCSR555DLG |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR555DLG [biosample_summary="Homo sapiens with Alzheimer''s disease; posterior cingulate gyrus tissue male adult (90 or above years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male 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 {ENCFF960LMQ|/files/ENCFF960LMQ/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.35. 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_ENCSR555DLG | float |
DNase-seq_ENCSR555DLG |
DNase-seq ENCSR555DLG [biosample_summary="Homo sapiens with Alzheimer''s disease; posterior cingulate gyrus tissue male adult (90 or above years)"]
|
 |
[0.232, 13.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 3989949 | 0.12% | 21915 |
| chr1 | 406974 | 0.16% | 2256 |
| chr2 | 269021 | 0.11% | 1487 |
| chr3 | 223658 | 0.11% | 1226 |
| chr4 | 141498 | 0.07% | 777 |
| chr5 | 179052 | 0.10% | 1002 |
| chr6 | 199998 | 0.12% | 1131 |
| chr7 | 182413 | 0.11% | 999 |
| chr8 | 140054 | 0.10% | 796 |
| chr9 | 174077 | 0.13% | 961 |
| chr10 | 176369 | 0.13% | 988 |
| chr11 | 234124 | 0.17% | 1293 |
| chr12 | 202962 | 0.15% | 1114 |
| chr13 | 75708 | 0.07% | 402 |
| chr14 | 128737 | 0.12% | 709 |
| chr15 | 120042 | 0.12% | 669 |
| chr16 | 174861 | 0.19% | 941 |
| chr17 | 230360 | 0.28% | 1262 |
| chr18 | 57051 | 0.07% | 322 |
| chr19 | 314090 | 0.54% | 1594 |
| chr20 | 113598 | 0.18% | 636 |
| chr21 | 40552 | 0.09% | 232 |
| chr22 | 98922 | 0.19% | 549 |
| chrX | 102911 | 0.07% | 552 |
| chrY | 2917 | 0.01% | 17 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 21915 | 1 | 820 | 182.06 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF254AUY.bed.gz | 243.04 KB | cd38b40c6b201976e5f00a53f4177a52 |
| ENCFF254AUY.tabix.bed.gz | 218.48 KB | b604cb3a7acfb7db1d44e40468d08c8b |
| ENCFF254AUY.tabix.bed.gz.tbi | 140.92 KB | a5ac7c72fc979867a40b973b8b81faa0 |
| genomic_resource.yaml | 2.25 KB | 6dba7d4a3c491942d436b72c9e3e77b7 |
| statistics/ |