Resource
| Id | DNase-seq/ENCSR797FIM |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR797FIM [biosample_summary="Homo sapiens with Alzheimer''s disease; 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 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 {ENCFF351LGN|/files/ENCFF351LGN/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.27. 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_ENCSR797FIM | float |
DNase-seq_ENCSR797FIM |
DNase-seq ENCSR797FIM [biosample_summary="Homo sapiens with Alzheimer''s disease; head of caudate nucleus tissue female adult (90 or above years)"]
|
 |
[0.074, 13.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 8885953 | 0.28% | 48395 |
| chr1 | 854654 | 0.34% | 4674 |
| chr2 | 717055 | 0.30% | 3953 |
| chr3 | 435131 | 0.22% | 2364 |
| chr4 | 317393 | 0.17% | 1704 |
| chr5 | 405290 | 0.22% | 2233 |
| chr6 | 407717 | 0.24% | 2227 |
| chr7 | 424953 | 0.27% | 2320 |
| chr8 | 347487 | 0.24% | 1906 |
| chr9 | 438607 | 0.32% | 2411 |
| chr10 | 454255 | 0.34% | 2484 |
| chr11 | 539251 | 0.40% | 2933 |
| chr12 | 377318 | 0.28% | 2042 |
| chr13 | 163634 | 0.14% | 880 |
| chr14 | 283445 | 0.26% | 1502 |
| chr15 | 300003 | 0.29% | 1639 |
| chr16 | 331829 | 0.37% | 1804 |
| chr17 | 496214 | 0.60% | 2677 |
| chr18 | 146586 | 0.18% | 812 |
| chr19 | 522913 | 0.89% | 2768 |
| chr20 | 264047 | 0.41% | 1477 |
| chr21 | 127045 | 0.27% | 695 |
| chr22 | 331427 | 0.65% | 1839 |
| chrX | 198607 | 0.13% | 1041 |
| chrY | 1092 | <0.01% | 10 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 48395 | 1 | 1055 | 183.61 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF831KBP.bed.gz | 524.64 KB | 41055467ee653c3cc97cdf6d98c4206b |
| ENCFF831KBP.tabix.bed.gz | 477.47 KB | da2cce08fd09d568f0a4df188b1d1afa |
| ENCFF831KBP.tabix.bed.gz.tbi | 203.91 KB | 07cf319384b5df717d7778cb7ba0965c |
| genomic_resource.yaml | 2.25 KB | 334673e801cc4b00245ecaac7da38736 |
| statistics/ |