Resource
| Id | DNase-seq/ENCSR010SZN |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR010SZN [biosample_summary="Homo sapiens with Alzheimer''s disease; head of caudate nucleus 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 {ENCFF222PSK|/files/ENCFF222PSK/} 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_ENCSR010SZN | float |
DNase-seq_ENCSR010SZN |
DNase-seq ENCSR010SZN [biosample_summary="Homo sapiens with Alzheimer''s disease; head of caudate nucleus tissue female adult (90 or above years)"]
|
 |
[0.0353, 17.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 27998036 | 0.87% | 146772 |
| chr1 | 2527994 | 1.02% | 13275 |
| chr2 | 2544499 | 1.05% | 13295 |
| chr3 | 1532538 | 0.77% | 7993 |
| chr4 | 878000 | 0.46% | 4651 |
| chr5 | 1453328 | 0.80% | 7639 |
| chr6 | 1303960 | 0.76% | 6921 |
| chr7 | 1446842 | 0.91% | 7684 |
| chr8 | 1214210 | 0.84% | 6370 |
| chr9 | 1128498 | 0.82% | 5937 |
| chr10 | 1672019 | 1.25% | 8735 |
| chr11 | 1523081 | 1.13% | 7846 |
| chr12 | 1092275 | 0.82% | 5766 |
| chr13 | 593368 | 0.52% | 3140 |
| chr14 | 930543 | 0.87% | 4901 |
| chr15 | 1093080 | 1.07% | 5758 |
| chr16 | 1045531 | 1.16% | 5550 |
| chr17 | 1294293 | 1.55% | 6759 |
| chr18 | 655996 | 0.82% | 3446 |
| chr19 | 1141571 | 1.95% | 5824 |
| chr20 | 990971 | 1.54% | 5184 |
| chr21 | 411745 | 0.88% | 2096 |
| chr22 | 844216 | 1.66% | 4379 |
| chrX | 677406 | 0.43% | 3607 |
| chrY | 2072 | <0.01% | 16 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 146772 | 1 | 1105 | 190.76 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF361PSA.bed.gz | 1.51 MB | c05a04c0735809a4b5295b2917f30312 |
| ENCFF361PSA.tabix.bed.gz | 1.4 MB | 0f64964b0cc760c641f8fe560d56714c |
| ENCFF361PSA.tabix.bed.gz.tbi | 391.18 KB | 327c674ee85493727dcacd40ac98f63d |
| genomic_resource.yaml | 2.25 KB | 005df164c249dc42814edee2949628a1 |
| statistics/ |