Resource
| Id | DNase-seq/ENCSR524QPZ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR524QPZ [biosample_summary="Homo sapiens with mild cognitive impairment; head of caudate nucleus tissue female adult (78 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (78 years) with mild 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 {ENCFF719OSY|/files/ENCFF719OSY/} 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_ENCSR524QPZ | float |
DNase-seq_ENCSR524QPZ |
DNase-seq ENCSR524QPZ [biosample_summary="Homo sapiens with mild cognitive impairment; head of caudate nucleus tissue female adult (78 years)"]
|
 |
[0.107, 21.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 7867265 | 0.24% | 42966 |
| chr1 | 773574 | 0.31% | 4223 |
| chr2 | 551287 | 0.23% | 3048 |
| chr3 | 417080 | 0.21% | 2224 |
| chr4 | 286461 | 0.15% | 1578 |
| chr5 | 343917 | 0.19% | 1902 |
| chr6 | 373235 | 0.22% | 2022 |
| chr7 | 365613 | 0.23% | 2042 |
| chr8 | 313058 | 0.22% | 1734 |
| chr9 | 349884 | 0.25% | 1949 |
| chr10 | 363127 | 0.27% | 2002 |
| chr11 | 474499 | 0.35% | 2592 |
| chr12 | 368366 | 0.28% | 1998 |
| chr13 | 152242 | 0.13% | 831 |
| chr14 | 270506 | 0.25% | 1495 |
| chr15 | 250881 | 0.25% | 1366 |
| chr16 | 329295 | 0.36% | 1760 |
| chr17 | 490248 | 0.59% | 2649 |
| chr18 | 122561 | 0.15% | 685 |
| chr19 | 520846 | 0.89% | 2694 |
| chr20 | 230611 | 0.36% | 1290 |
| chr21 | 96069 | 0.21% | 536 |
| chr22 | 236248 | 0.46% | 1349 |
| chrX | 187235 | 0.12% | 993 |
| chrY | 422 | <0.01% | 4 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 42966 | 1 | 720 | 183.1 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF256HHR.bed.gz | 468.48 KB | cbcf038d570ec4dc65d7dc9e4e141121 |
| ENCFF256HHR.tabix.bed.gz | 428.77 KB | 8ae1bb7a6ca8f897048766ccb44a6429 |
| ENCFF256HHR.tabix.bed.gz.tbi | 216.01 KB | 031163e51c7afa9fa5003c420a646d8d |
| genomic_resource.yaml | 2.23 KB | 772386974bedc2271c854d2855d76b82 |
| statistics/ |