Resource
| Id | DNase-seq/ENCSR419KXU |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR419KXU [biosample_summary="Homo sapiens with Alzheimer''s disease; dorsolateral prefrontal cortex 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 {ENCFF418AJG|/files/ENCFF418AJG/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 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_ENCSR419KXU | float |
DNase-seq_ENCSR419KXU |
DNase-seq ENCSR419KXU [biosample_summary="Homo sapiens with Alzheimer''s disease; dorsolateral prefrontal cortex tissue female adult (90 or above years)"]
|
 |
[0.0699, 10.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 11161705 | 0.35% | 56161 |
| chr1 | 985556 | 0.40% | 4955 |
| chr2 | 1046180 | 0.43% | 5248 |
| chr3 | 569317 | 0.29% | 2861 |
| chr4 | 404709 | 0.21% | 2002 |
| chr5 | 554472 | 0.31% | 2785 |
| chr6 | 438713 | 0.26% | 2245 |
| chr7 | 611619 | 0.38% | 3061 |
| chr8 | 535646 | 0.37% | 2614 |
| chr9 | 556452 | 0.40% | 2817 |
| chr10 | 661712 | 0.49% | 3338 |
| chr11 | 646821 | 0.48% | 3293 |
| chr12 | 378567 | 0.28% | 1931 |
| chr13 | 204597 | 0.18% | 1042 |
| chr14 | 373632 | 0.35% | 1832 |
| chr15 | 396461 | 0.39% | 2001 |
| chr16 | 411913 | 0.46% | 2107 |
| chr17 | 556909 | 0.67% | 2850 |
| chr18 | 223977 | 0.28% | 1101 |
| chr19 | 449838 | 0.77% | 2231 |
| chr20 | 355045 | 0.55% | 1806 |
| chr21 | 166480 | 0.36% | 858 |
| chr22 | 408368 | 0.80% | 2025 |
| chrX | 223965 | 0.14% | 1152 |
| chrY | 756 | <0.01% | 6 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 56161 | 1 | 1238 | 198.74 | 192 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF631LZV.bed.gz | 568.71 KB | e5b4cc83343678576d16078c00ccbfef |
| ENCFF631LZV.tabix.bed.gz | 531.1 KB | 1f56984b349569757f54cae1a0436bf7 |
| ENCFF631LZV.tabix.bed.gz.tbi | 176.8 KB | 74e6c9deeb2db07cc147381fb66b156f |
| genomic_resource.yaml | 2.28 KB | ab6f60b2cf9d71823422396e01103524 |
| statistics/ |