Resource
| Id | DNase-seq/ENCSR306LNA |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR306LNA [biosample_summary="Homo sapiens with Alzheimer''s disease, Cognitive impairment; dorsolateral prefrontal cortex tissue male adult (73 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (73 years) with Alzheimer's disease, Cognitive impairment 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 {ENCFF147OGX|/files/ENCFF147OGX/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.26. 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_ENCSR306LNA | float |
DNase-seq_ENCSR306LNA |
DNase-seq ENCSR306LNA [biosample_summary="Homo sapiens with Alzheimer''s disease, Cognitive impairment; dorsolateral prefrontal cortex tissue male adult (73 years)"]
|
 |
[0.0373, 12.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 30044839 | 0.93% | 151153 |
| chr1 | 2686996 | 1.08% | 13260 |
| chr2 | 2819532 | 1.16% | 14077 |
| chr3 | 1704733 | 0.86% | 8612 |
| chr4 | 856241 | 0.45% | 4354 |
| chr5 | 1546669 | 0.85% | 7782 |
| chr6 | 1631036 | 0.95% | 8182 |
| chr7 | 1535076 | 0.96% | 7700 |
| chr8 | 1369159 | 0.94% | 6971 |
| chr9 | 1213957 | 0.88% | 6081 |
| chr10 | 2132143 | 1.59% | 10703 |
| chr11 | 1499152 | 1.11% | 7511 |
| chr12 | 1173390 | 0.88% | 5997 |
| chr13 | 704875 | 0.62% | 3598 |
| chr14 | 949371 | 0.89% | 4778 |
| chr15 | 1370811 | 1.34% | 6919 |
| chr16 | 995864 | 1.10% | 5042 |
| chr17 | 1397475 | 1.68% | 7089 |
| chr18 | 838302 | 1.04% | 4263 |
| chr19 | 1073808 | 1.83% | 5392 |
| chr20 | 938723 | 1.46% | 4808 |
| chr21 | 451403 | 0.97% | 2248 |
| chr22 | 718641 | 1.41% | 3578 |
| chrX | 424258 | 0.27% | 2143 |
| chrY | 13224 | 0.02% | 65 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 151153 | 1 | 1220 | 198.77 | 190 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF870ORN.bed.gz | 1.47 MB | 3f855e499a8693f45f2bb36c834ed2da |
| ENCFF870ORN.tabix.bed.gz | 1.38 MB | e69055d29507bb219840c25869d71e21 |
| ENCFF870ORN.tabix.bed.gz.tbi | 307.27 KB | b53a3e7449450977baca1e6fed23985f |
| genomic_resource.yaml | 2.33 KB | 7ff4b5442799a270f2ca985fe4c6c0e0 |
| statistics/ |