Resource
| Id | DNase-seq/ENCSR271QID |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR271QID [biosample_summary="Homo sapiens with mild cognitive impairment; 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 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 {ENCFF751SHB|/files/ENCFF751SHB/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.34. 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_ENCSR271QID | float |
DNase-seq_ENCSR271QID |
DNase-seq ENCSR271QID [biosample_summary="Homo sapiens with mild cognitive impairment; head of caudate nucleus tissue female adult (90 or above years)"]
|
 |
[0.0674, 13.7] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 11931349 | 0.37% | 62703 |
| chr1 | 1140562 | 0.46% | 6012 |
| chr2 | 894952 | 0.37% | 4764 |
| chr3 | 649385 | 0.33% | 3410 |
| chr4 | 460022 | 0.24% | 2431 |
| chr5 | 582791 | 0.32% | 3071 |
| chr6 | 609139 | 0.36% | 3157 |
| chr7 | 585043 | 0.37% | 3078 |
| chr8 | 523658 | 0.36% | 2789 |
| chr9 | 523911 | 0.38% | 2737 |
| chr10 | 608327 | 0.45% | 3225 |
| chr11 | 665814 | 0.49% | 3560 |
| chr12 | 568020 | 0.43% | 2900 |
| chr13 | 248618 | 0.22% | 1315 |
| chr14 | 412690 | 0.39% | 2192 |
| chr15 | 386809 | 0.38% | 2048 |
| chr16 | 484100 | 0.54% | 2562 |
| chr17 | 632763 | 0.76% | 3278 |
| chr18 | 220429 | 0.27% | 1177 |
| chr19 | 671507 | 1.15% | 3349 |
| chr20 | 353444 | 0.55% | 1905 |
| chr21 | 139502 | 0.30% | 733 |
| chr22 | 298898 | 0.59% | 1598 |
| chrX | 270315 | 0.17% | 1407 |
| chrY | 650 | <0.01% | 5 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 62703 | 1 | 900 | 190.28 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF651ZKO.bed.gz | 686.91 KB | 1e24e3b06352880a24fb7d60270978aa |
| ENCFF651ZKO.tabix.bed.gz | 625.85 KB | 30a05178b4f4fc2b4f65c53742414bd9 |
| ENCFF651ZKO.tabix.bed.gz.tbi | 273.76 KB | 89c1d5433118ee73f81fe4c182b48636 |
| genomic_resource.yaml | 2.28 KB | 86bd7d0e027843e5abb8c1985de23401 |
| statistics/ |