Resource
| Id | DNase-seq/ENCSR334MDJ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR334MDJ [biosample_summary="Homo sapiens with mild cognitive impairment; head of caudate nucleus tissue female adult (89 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female 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 {ENCFF591CAE|/files/ENCFF591CAE/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.30. 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_ENCSR334MDJ | float |
DNase-seq_ENCSR334MDJ |
DNase-seq ENCSR334MDJ [biosample_summary="Homo sapiens with mild cognitive impairment; head of caudate nucleus tissue female adult (89 years)"]
|
 |
[0.0519, 13.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 16100415 | 0.50% | 87101 |
| chr1 | 1475050 | 0.59% | 7954 |
| chr2 | 1267423 | 0.52% | 6942 |
| chr3 | 851343 | 0.43% | 4571 |
| chr4 | 591137 | 0.31% | 3209 |
| chr5 | 793348 | 0.44% | 4333 |
| chr6 | 822310 | 0.48% | 4456 |
| chr7 | 833443 | 0.52% | 4573 |
| chr8 | 680739 | 0.47% | 3713 |
| chr9 | 658333 | 0.48% | 3558 |
| chr10 | 870859 | 0.65% | 4755 |
| chr11 | 880843 | 0.65% | 4740 |
| chr12 | 715851 | 0.54% | 3834 |
| chr13 | 341670 | 0.30% | 1861 |
| chr14 | 519550 | 0.49% | 2812 |
| chr15 | 600609 | 0.59% | 3253 |
| chr16 | 651315 | 0.72% | 3545 |
| chr17 | 831401 | 1.00% | 4392 |
| chr18 | 305393 | 0.38% | 1709 |
| chr19 | 854831 | 1.46% | 4382 |
| chr20 | 511804 | 0.79% | 2809 |
| chr21 | 202702 | 0.43% | 1121 |
| chr22 | 460177 | 0.91% | 2510 |
| chrX | 378817 | 0.24% | 2056 |
| chrY | 1467 | <0.01% | 13 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 87101 | 1 | 1060 | 184.85 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF523RDN.bed.gz | 948.66 KB | 557c84a9dcec38f8d880fafb6e972490 |
| ENCFF523RDN.tabix.bed.gz | 865.2 KB | 1b229fce040128e5577345ed090e56fa |
| ENCFF523RDN.tabix.bed.gz.tbi | 330.65 KB | 5a135a57b0a1f85771a9d22439ff47f1 |
| genomic_resource.yaml | 2.24 KB | 9ad449ccebd9579d41ea3b4809989f3a |
| statistics/ |