Resource
| Id | DNase-seq/ENCSR581LHW |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR581LHW [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 {ENCFF791PEK|/files/ENCFF791PEK/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.30. 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_ENCSR581LHW | float |
DNase-seq_ENCSR581LHW |
DNase-seq ENCSR581LHW [biosample_summary="Homo sapiens with Alzheimer''s disease; posterior cingulate gyrus tissue female adult (90 or above years)"]
|
 |
[0.0238, 11.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 59123150 | 1.84% | 284198 |
| chr1 | 5296323 | 2.13% | 25017 |
| chr2 | 5278986 | 2.18% | 25010 |
| chr3 | 2776490 | 1.40% | 13579 |
| chr4 | 1584215 | 0.83% | 7623 |
| chr5 | 2842094 | 1.57% | 13822 |
| chr6 | 2294187 | 1.34% | 11287 |
| chr7 | 3235406 | 2.03% | 15617 |
| chr8 | 2650070 | 1.83% | 12701 |
| chr9 | 2517684 | 1.82% | 12190 |
| chr10 | 3830007 | 2.86% | 18203 |
| chr11 | 3034404 | 2.25% | 14375 |
| chr12 | 2373368 | 1.78% | 11660 |
| chr13 | 1272208 | 1.11% | 6071 |
| chr14 | 2019773 | 1.89% | 9594 |
| chr15 | 2409415 | 2.36% | 11656 |
| chr16 | 2377847 | 2.63% | 11761 |
| chr17 | 3229707 | 3.88% | 15577 |
| chr18 | 1270825 | 1.58% | 6184 |
| chr19 | 2179039 | 3.72% | 10515 |
| chr20 | 2164171 | 3.36% | 10351 |
| chr21 | 1043700 | 2.23% | 4953 |
| chr22 | 1954891 | 3.85% | 9133 |
| chrX | 1484233 | 0.95% | 7287 |
| chrY | 4107 | 0.01% | 32 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 284198 | 1 | 1320 | 208.04 | 200 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF360YQN.bed.gz | 2.68 MB | 3cb70c6d3448029790a1eebf77d72cdc |
| ENCFF360YQN.tabix.bed.gz | 2.54 MB | a9850f4243cda5bb82667140cc4e6441 |
| ENCFF360YQN.tabix.bed.gz.tbi | 346.14 KB | d79af596a0495324ec4215cf124d9999 |
| genomic_resource.yaml | 2.25 KB | 5d6b5dcde2e6d6c3a3daf4aa0d400e00 |
| statistics/ |