Resource
| Id | DNase-seq/ENCSR832XVZ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR832XVZ [biosample_summary="Homo sapiens with Alzheimer''s disease; dorsolateral prefrontal cortex 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 {ENCFF608CVY|/files/ENCFF608CVY/} processed by DNase-seq ENCODE4 v3.0.0 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_ENCSR832XVZ | float |
DNase-seq_ENCSR832XVZ |
DNase-seq ENCSR832XVZ [biosample_summary="Homo sapiens with Alzheimer''s disease; dorsolateral prefrontal cortex tissue female adult (86 years)"]
|
 |
[0.105, 11.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 7283149 | 0.23% | 40943 |
| chr1 | 720767 | 0.29% | 4038 |
| chr2 | 508671 | 0.21% | 2903 |
| chr3 | 417885 | 0.21% | 2367 |
| chr4 | 275871 | 0.15% | 1576 |
| chr5 | 359471 | 0.20% | 2063 |
| chr6 | 386570 | 0.23% | 2187 |
| chr7 | 343328 | 0.22% | 1959 |
| chr8 | 299133 | 0.21% | 1689 |
| chr9 | 313909 | 0.23% | 1769 |
| chr10 | 316121 | 0.24% | 1817 |
| chr11 | 410253 | 0.30% | 2332 |
| chr12 | 375315 | 0.28% | 2086 |
| chr13 | 144104 | 0.13% | 817 |
| chr14 | 237065 | 0.22% | 1348 |
| chr15 | 229752 | 0.23% | 1294 |
| chr16 | 295887 | 0.33% | 1618 |
| chr17 | 406880 | 0.49% | 2274 |
| chr18 | 119880 | 0.15% | 700 |
| chr19 | 473703 | 0.81% | 2432 |
| chr20 | 215316 | 0.33% | 1240 |
| chr21 | 75006 | 0.16% | 447 |
| chr22 | 181532 | 0.36% | 1014 |
| chrX | 176027 | 0.11% | 967 |
| chrY | 703 | <0.01% | 6 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 40943 | 4 | 825 | 177.89 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF951QLN.bed.gz | 452.25 KB | 355b645e374e6a8f7182b9d256d2658b |
| ENCFF951QLN.tabix.bed.gz | 407.35 KB | 0879cb4e785aaadcba236179e008e4e8 |
| ENCFF951QLN.tabix.bed.gz.tbi | 230.03 KB | 2458b1ed5c9146ce8a658feda545675b |
| genomic_resource.yaml | 2.23 KB | c956a0d613d657d056feccb10ec972f5 |
| statistics/ |