Resource
| Id | DNase-seq/ENCSR677XGD |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR677XGD [biosample_summary="Homo sapiens with mild cognitive impairment; head of caudate nucleus tissue male adult (89 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (89 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 {ENCFF914GOI|/files/ENCFF914GOI/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 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_ENCSR677XGD | float |
DNase-seq_ENCSR677XGD |
DNase-seq ENCSR677XGD [biosample_summary="Homo sapiens with mild cognitive impairment; head of caudate nucleus tissue male adult (89 years)"]
|
 |
[0.0684, 15.7] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 11046232 | 0.34% | 60141 |
| chr1 | 1058004 | 0.42% | 5721 |
| chr2 | 872493 | 0.36% | 4775 |
| chr3 | 606997 | 0.31% | 3291 |
| chr4 | 451520 | 0.24% | 2448 |
| chr5 | 547377 | 0.30% | 2986 |
| chr6 | 554429 | 0.32% | 2992 |
| chr7 | 528900 | 0.33% | 2955 |
| chr8 | 494893 | 0.34% | 2739 |
| chr9 | 479934 | 0.35% | 2613 |
| chr10 | 612442 | 0.46% | 3295 |
| chr11 | 621265 | 0.46% | 3386 |
| chr12 | 502582 | 0.38% | 2716 |
| chr13 | 214281 | 0.19% | 1195 |
| chr14 | 365098 | 0.34% | 2002 |
| chr15 | 344559 | 0.34% | 1922 |
| chr16 | 414204 | 0.46% | 2255 |
| chr17 | 558672 | 0.67% | 3019 |
| chr18 | 219372 | 0.27% | 1247 |
| chr19 | 561454 | 0.96% | 2893 |
| chr20 | 315264 | 0.49% | 1728 |
| chr21 | 147588 | 0.32% | 825 |
| chr22 | 304852 | 0.60% | 1647 |
| chrX | 259879 | 0.17% | 1433 |
| chrY | 10173 | 0.02% | 58 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 60141 | 1 | 920 | 183.67 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF051EMZ.bed.gz | 658.78 KB | 31b3b49b7d37c5b8e4ece7d24e7e4950 |
| ENCFF051EMZ.tabix.bed.gz | 597.51 KB | a5533d25331146b3e47da00556f100fb |
| ENCFF051EMZ.tabix.bed.gz.tbi | 264.14 KB | f8423241d1ceb810f98dc4a4b502bc8f |
| genomic_resource.yaml | 2.23 KB | bebeeee93d1e8fa6ed0659cbfe21e459 |
| statistics/ |