Resource
| Id | DNase-seq/ENCSR417LPB |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR417LPB [biosample_summary="Homo sapiens with Cognitive impairment; 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 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 {ENCFF251HNN|/files/ENCFF251HNN/} processed by DNase-seq ENCODE4 v3.0.0 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_ENCSR417LPB | float |
DNase-seq_ENCSR417LPB |
DNase-seq ENCSR417LPB [biosample_summary="Homo sapiens with Cognitive impairment; head of caudate nucleus tissue female adult (90 or above years)"]
|
 |
[0.0593, 16] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 19079856 | 0.59% | 104164 |
| chr1 | 1801192 | 0.72% | 9736 |
| chr2 | 1563632 | 0.65% | 8648 |
| chr3 | 1115892 | 0.56% | 6132 |
| chr4 | 757193 | 0.40% | 4157 |
| chr5 | 953034 | 0.52% | 5288 |
| chr6 | 1024378 | 0.60% | 5619 |
| chr7 | 939482 | 0.59% | 5205 |
| chr8 | 832880 | 0.57% | 4595 |
| chr9 | 812591 | 0.59% | 4448 |
| chr10 | 961928 | 0.72% | 5301 |
| chr11 | 1085003 | 0.80% | 5878 |
| chr12 | 909211 | 0.68% | 4894 |
| chr13 | 424682 | 0.37% | 2351 |
| chr14 | 636284 | 0.59% | 3461 |
| chr15 | 649174 | 0.64% | 3560 |
| chr16 | 723517 | 0.80% | 3925 |
| chr17 | 909547 | 1.09% | 4896 |
| chr18 | 380587 | 0.47% | 2149 |
| chr19 | 854345 | 1.46% | 4376 |
| chr20 | 608476 | 0.94% | 3287 |
| chr21 | 211349 | 0.45% | 1168 |
| chr22 | 472524 | 0.93% | 2578 |
| chrX | 452484 | 0.29% | 2508 |
| chrY | 471 | <0.01% | 4 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 104164 | 3 | 900 | 183.17 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF853FXM.bed.gz | 1.11 MB | bfc64f1a103156070f88a3dca9eaaba4 |
| ENCFF853FXM.tabix.bed.gz | 1.01 MB | c351ab02ecc95987c61b73834a7b3273 |
| ENCFF853FXM.tabix.bed.gz.tbi | 415.72 KB | e96984a79c1e09bdbbeb259d06aaa124 |
| genomic_resource.yaml | 2.25 KB | d8be02bb4e912ae5fabd77e0959f32b6 |
| statistics/ |