Resource
| Id | DNase-seq/ENCSR085XKS |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR085XKS [biosample_summary="Homo sapiens with Cognitive impairment, Alzheimer''s disease; head of caudate nucleus tissue male adult (80 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (80 years) with Cognitive impairment, Alzheimer's disease 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 {ENCFF226FYG|/files/ENCFF226FYG/} 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_ENCSR085XKS | float |
DNase-seq_ENCSR085XKS |
DNase-seq ENCSR085XKS [biosample_summary="Homo sapiens with Cognitive impairment, Alzheimer''s disease; head of caudate nucleus tissue male adult (80 years)"]
|
 |
[0.0469, 15.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 14702029 | 0.46% | 78480 |
| chr1 | 1391257 | 0.56% | 7324 |
| chr2 | 1131847 | 0.47% | 6130 |
| chr3 | 846058 | 0.43% | 4491 |
| chr4 | 539347 | 0.28% | 2877 |
| chr5 | 751685 | 0.41% | 4013 |
| chr6 | 757034 | 0.44% | 4041 |
| chr7 | 727211 | 0.46% | 3928 |
| chr8 | 608530 | 0.42% | 3284 |
| chr9 | 650100 | 0.47% | 3483 |
| chr10 | 793463 | 0.59% | 4308 |
| chr11 | 822020 | 0.61% | 4371 |
| chr12 | 669888 | 0.50% | 3529 |
| chr13 | 305777 | 0.27% | 1654 |
| chr14 | 493428 | 0.46% | 2612 |
| chr15 | 512314 | 0.50% | 2778 |
| chr16 | 553471 | 0.61% | 2942 |
| chr17 | 719133 | 0.86% | 3776 |
| chr18 | 290342 | 0.36% | 1603 |
| chr19 | 745409 | 1.27% | 3797 |
| chr20 | 471674 | 0.73% | 2557 |
| chr21 | 157538 | 0.34% | 847 |
| chr22 | 374023 | 0.74% | 2028 |
| chrX | 375158 | 0.24% | 2021 |
| chrY | 15322 | 0.03% | 86 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 78480 | 1 | 920 | 187.33 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF427TKQ.bed.gz | 862.13 KB | 43d4663926c902b12c09e9c91605acc8 |
| ENCFF427TKQ.tabix.bed.gz | 786.49 KB | 28dda26bba6fc9a11d23c443748ec915 |
| ENCFF427TKQ.tabix.bed.gz.tbi | 318.61 KB | 6e84b7b0f732f5aa4046d963bcb49fe7 |
| genomic_resource.yaml | 2.32 KB | 9909d8b8d86a0c9153054566542d78c4 |
| statistics/ |