Resource
| Id | DNase-seq/ENCSR373TLU |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR373TLU [biosample_summary="Homo sapiens with Alzheimer''s disease; head of caudate nucleus tissue female adult (86 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (86 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 {ENCFF328OIF|/files/ENCFF328OIF/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.38. 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_ENCSR373TLU | float |
DNase-seq_ENCSR373TLU |
DNase-seq ENCSR373TLU [biosample_summary="Homo sapiens with Alzheimer''s disease; head of caudate nucleus tissue female adult (86 years)"]
|
 |
[0.0125, 21.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 63890038 | 1.99% | 320913 |
| chr1 | 5797535 | 2.33% | 28658 |
| chr2 | 5812938 | 2.40% | 28826 |
| chr3 | 3370425 | 1.70% | 17064 |
| chr4 | 1846392 | 0.97% | 9354 |
| chr5 | 3200676 | 1.76% | 15894 |
| chr6 | 3070223 | 1.80% | 15701 |
| chr7 | 3526101 | 2.21% | 17895 |
| chr8 | 3058420 | 2.11% | 15494 |
| chr9 | 2702021 | 1.95% | 13649 |
| chr10 | 4307575 | 3.22% | 21390 |
| chr11 | 3131911 | 2.32% | 15828 |
| chr12 | 2419010 | 1.82% | 12239 |
| chr13 | 1472418 | 1.29% | 7457 |
| chr14 | 1963638 | 1.83% | 9803 |
| chr15 | 2540569 | 2.49% | 12855 |
| chr16 | 2355642 | 2.61% | 11981 |
| chr17 | 2815593 | 3.38% | 14226 |
| chr18 | 1809079 | 2.25% | 9087 |
| chr19 | 2161777 | 3.69% | 10789 |
| chr20 | 2220646 | 3.45% | 11058 |
| chr21 | 906030 | 1.94% | 4594 |
| chr22 | 1760001 | 3.46% | 8676 |
| chrX | 1636545 | 1.05% | 8355 |
| chrY | 4873 | 0.01% | 40 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 320913 | 1 | 1140 | 199.09 | 183 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF245WUR.bed.gz | 3.15 MB | 01cff26d6118c51146b0b917c7452f64 |
| ENCFF245WUR.tabix.bed.gz | 2.95 MB | 3b5dc4d4dace4f44045f156198f7d287 |
| ENCFF245WUR.tabix.bed.gz.tbi | 443.37 KB | 9951094fe1194337ab5918021f6055fb |
| genomic_resource.yaml | 2.21 KB | d9fe3662a66e0d5466f5702846fc9302 |
| statistics/ |