Resource
| Id | DNase-seq/ENCSR629TMA |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR629TMA [biosample_summary="Homo sapiens with mild cognitive impairment; head of caudate nucleus tissue female adult (83 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (83 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 {ENCFF614XTQ|/files/ENCFF614XTQ/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.39. 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_ENCSR629TMA | float |
DNase-seq_ENCSR629TMA |
DNase-seq ENCSR629TMA [biosample_summary="Homo sapiens with mild cognitive impairment; head of caudate nucleus tissue female adult (83 years)"]
|
 |
[0.0288, 24.7] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 28793892 | 0.89% | 141285 |
| chr1 | 2723569 | 1.09% | 13183 |
| chr2 | 2254047 | 0.93% | 11160 |
| chr3 | 1788817 | 0.90% | 8866 |
| chr4 | 1303604 | 0.69% | 6450 |
| chr5 | 1531280 | 0.84% | 7555 |
| chr6 | 1641343 | 0.96% | 8019 |
| chr7 | 1472755 | 0.92% | 7292 |
| chr8 | 1298654 | 0.89% | 6422 |
| chr9 | 1247763 | 0.90% | 6136 |
| chr10 | 1403436 | 1.05% | 6910 |
| chr11 | 1555901 | 1.15% | 7607 |
| chr12 | 1402146 | 1.05% | 6847 |
| chr13 | 721172 | 0.63% | 3574 |
| chr14 | 961204 | 0.90% | 4690 |
| chr15 | 918483 | 0.90% | 4513 |
| chr16 | 1052826 | 1.17% | 5177 |
| chr17 | 1290832 | 1.55% | 6237 |
| chr18 | 647918 | 0.81% | 3185 |
| chr19 | 1082779 | 1.85% | 5116 |
| chr20 | 827677 | 1.28% | 4076 |
| chr21 | 327367 | 0.70% | 1638 |
| chr22 | 590301 | 1.16% | 2850 |
| chrX | 749716 | 0.48% | 3780 |
| chrY | 302 | <0.01% | 2 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 141285 | 1 | 980 | 203.8 | 200 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF350RZI.bed.gz | 1.51 MB | 4da366e5ddb7577872a0a2ef57beb952 |
| ENCFF350RZI.tabix.bed.gz | 1.38 MB | 5ab14994cc91d5ab264fc0e12b420028 |
| ENCFF350RZI.tabix.bed.gz.tbi | 530.62 KB | 484d7edce07c664a1a6a5cf28c223296 |
| genomic_resource.yaml | 2.24 KB | 5c7f64cf69cda07304648d00effd0b29 |
| statistics/ |